Starting phenix.real_space_refine on Wed Mar 20 04:27:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gad_8000/03_2024/5gad_8000_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gad_8000/03_2024/5gad_8000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gad_8000/03_2024/5gad_8000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gad_8000/03_2024/5gad_8000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gad_8000/03_2024/5gad_8000_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gad_8000/03_2024/5gad_8000_neut_updated.pdb" } resolution = 3.7 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3055 5.49 5 Mg 433 5.21 5 S 107 5.16 5 C 49354 2.51 5 N 18130 2.21 5 O 26926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "I ASP 124": "OD1" <-> "OD2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 44": "NH1" <-> "NH2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "N PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P ARG 25": "NH1" <-> "NH2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "Q PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 39": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "Q TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 101": "NH1" <-> "NH2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S ARG 21": "NH1" <-> "NH2" Residue "S GLU 23": "OE1" <-> "OE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 95": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "U GLU 5": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 54": "OE1" <-> "OE2" Residue "U GLU 56": "OE1" <-> "OE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V ARG 7": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "V PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 55": "OE1" <-> "OE2" Residue "W GLU 69": "OE1" <-> "OE2" Residue "W PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 85": "OE1" <-> "OE2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 74": "NH1" <-> "NH2" Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a GLU 37": "OE1" <-> "OE2" Residue "a ARG 45": "NH1" <-> "NH2" Residue "a PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ASP 31": "OD1" <-> "OD2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c GLU 32": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "i ASP 163": "OD1" <-> "OD2" Residue "i TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 185": "OD1" <-> "OD2" Residue "i GLU 204": "OE1" <-> "OE2" Residue "i GLU 277": "OE1" <-> "OE2" Residue "i GLU 392": "OE1" <-> "OE2" Residue "l PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 436": "OE1" <-> "OE2" Residue "l PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 98006 Number of models: 1 Model: "" Number of chains: 49 Chain: "1" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 926 Classifications: {'RNA': 43} Modifications used: {'rna3p_pur': 26, 'rna3p_pyr': 17} Link IDs: {'rna3p': 42} Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 61902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2883, 61902 Classifications: {'RNA': 2883} Modifications used: {'rna2p_pur': 280, 'rna2p_pyr': 149, 'rna3p_pur': 1386, 'rna3p_pyr': 1068} Link IDs: {'rna2p': 429, 'rna3p': 2453} Chain breaks: 4 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 946 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "K" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "M" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "N" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "O" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 993 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "R" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "S" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "T" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 756 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "V" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "W" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "X" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Z" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain breaks: 1 Chain: "a" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "i" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3337 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 436} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 71} Unresolved non-hydrogen planarities: 71 Chain: "k" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 137 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain: "l" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1492 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 192} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 412 Unusual residues: {' MG': 412} Classifications: {'undetermined': 412} Link IDs: {None: 411} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 92325 SG CYS f 11 74.500 81.470 178.879 1.00 60.00 S ATOM 92350 SG CYS f 14 77.644 82.923 177.829 1.00 60.00 S ATOM 92453 SG CYS f 27 77.955 79.762 179.788 1.00 60.00 S Time building chain proxies: 37.93, per 1000 atoms: 0.39 Number of scatterers: 98006 At special positions: 0 Unit cell: (268.69, 198.055, 239.605, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 107 16.00 P 3055 15.00 Mg 433 11.99 O 26926 8.00 N 18130 7.00 C 49354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.48 Conformation dependent library (CDL) restraints added in 4.8 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 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7610 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 50 sheets defined 32.5% alpha, 17.7% beta 1020 base pairs and 1574 stacking pairs defined. Time for finding SS restraints: 45.85 Creating SS restraints... Processing helix chain 'C' and resid 11 through 13 No H-bonds generated for 'chain 'C' and resid 11 through 13' Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 198 through 202 removed outlier: 4.212A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 263 through 266 Processing helix chain 'D' and resid 40 through 43 No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.714A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 101 Processing helix chain 'D' and resid 121 through 125 Processing helix chain 'E' and resid 16 through 19 No H-bonds generated for 'chain 'E' and resid 16 through 19' Processing helix chain 'E' and resid 25 through 38 Processing helix chain 'E' and resid 98 through 114 Processing helix chain 'E' and resid 131 through 141 Processing helix chain 'E' and resid 155 through 160 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 12 through 20 Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.727A pdb=" N ASP F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 143 through 145 No H-bonds generated for 'chain 'F' and resid 143 through 145' Processing helix chain 'F' and resid 163 through 173 Processing helix chain 'G' and resid 61 through 80 Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.661A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 28 Processing helix chain 'H' and resid 41 through 72 removed outlier: 5.673A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 96 through 104 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'I' and resid 5 through 21 Processing helix chain 'I' and resid 35 through 46 Processing helix chain 'I' and resid 57 through 66 removed outlier: 3.935A pdb=" N ARG I 62 " --> pdb=" O THR I 58 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY I 66 " --> pdb=" O ARG I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 72 No H-bonds generated for 'chain 'I' and resid 70 through 72' Processing helix chain 'I' and resid 93 through 103 removed outlier: 3.859A pdb=" N LYS I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 125 No H-bonds generated for 'chain 'I' and resid 123 through 125' Processing helix chain 'J' and resid 35 through 48 removed outlier: 5.607A pdb=" N SER J 48 " --> pdb=" O ALA J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 83 Processing helix chain 'J' and resid 103 through 116 Processing helix chain 'J' and resid 122 through 135 Processing helix chain 'K' and resid 25 through 37 removed outlier: 4.026A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 71 No H-bonds generated for 'chain 'K' and resid 68 through 71' Processing helix chain 'K' and resid 89 through 108 Proline residue: K 97 - end of helix removed outlier: 4.317A pdb=" N VAL K 100 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 121 removed outlier: 4.047A pdb=" N LYS K 121 " --> pdb=" O ALA K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 135 Processing helix chain 'L' and resid 105 through 107 No H-bonds generated for 'chain 'L' and resid 105 through 107' Processing helix chain 'L' and resid 113 through 117 Processing helix chain 'M' and resid 23 through 25 No H-bonds generated for 'chain 'M' and resid 23 through 25' Processing helix chain 'M' and resid 37 through 40 No H-bonds generated for 'chain 'M' and resid 37 through 40' Processing helix chain 'M' and resid 57 through 60 No H-bonds generated for 'chain 'M' and resid 57 through 60' Processing helix chain 'M' and resid 69 through 72 No H-bonds generated for 'chain 'M' and resid 69 through 72' Processing helix chain 'M' and resid 79 through 84 removed outlier: 4.206A pdb=" N ALA M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS M 84 " --> pdb=" O SER M 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 79 through 84' Processing helix chain 'M' and resid 92 through 97 Processing helix chain 'M' and resid 129 through 136 Processing helix chain 'N' and resid 43 through 56 Processing helix chain 'N' and resid 110 through 123 removed outlier: 4.354A pdb=" N LYS N 123 " --> pdb=" O LEU N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 31 Processing helix chain 'O' and resid 38 through 55 removed outlier: 3.715A pdb=" N ARG O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG O 46 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) Proline residue: O 50 - end of helix Processing helix chain 'O' and resid 60 through 70 Processing helix chain 'O' and resid 73 through 81 Processing helix chain 'O' and resid 83 through 86 No H-bonds generated for 'chain 'O' and resid 83 through 86' Processing helix chain 'O' and resid 118 through 123 Processing helix chain 'P' and resid 3 through 20 removed outlier: 4.861A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 61 removed outlier: 5.193A pdb=" N GLN P 61 " --> pdb=" O ALA P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 83 Processing helix chain 'P' and resid 101 through 112 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 54 through 56 No H-bonds generated for 'chain 'Q' and resid 54 through 56' Processing helix chain 'Q' and resid 98 through 101 Processing helix chain 'Q' and resid 105 through 107 No H-bonds generated for 'chain 'Q' and resid 105 through 107' Processing helix chain 'R' and resid 7 through 20 Processing helix chain 'R' and resid 26 through 30 Processing helix chain 'R' and resid 32 through 71 removed outlier: 3.639A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 3.769A 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: 3.925A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 85 Processing helix chain 'R' and resid 92 through 101 Processing helix chain 'R' and resid 103 through 117 Processing helix chain 'T' and resid 14 through 24 removed outlier: 3.554A pdb=" N LEU T 19 " --> pdb=" O GLN T 15 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.723A 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) Processing helix chain 'T' and resid 29 through 38 Processing helix chain 'T' and resid 43 through 62 Processing helix chain 'T' and resid 66 through 68 No H-bonds generated for 'chain 'T' and resid 66 through 68' Processing helix chain 'T' and resid 89 through 91 No H-bonds generated for 'chain 'T' and resid 89 through 91' Processing helix chain 'U' and resid 4 through 9 removed outlier: 3.925A pdb=" N LYS U 9 " --> pdb=" O GLU U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 26 Processing helix chain 'U' and resid 40 through 50 Processing helix chain 'V' and resid 67 through 69 No H-bonds generated for 'chain 'V' and resid 67 through 69' Processing helix chain 'W' and resid 13 through 22 Processing helix chain 'W' and resid 44 through 50 Processing helix chain 'W' and resid 55 through 58 No H-bonds generated for 'chain 'W' and resid 55 through 58' Processing helix chain 'Y' and resid 53 through 62 Processing helix chain 'Y' and resid 64 through 74 Processing helix chain 'Z' and resid 6 through 8 No H-bonds generated for 'chain 'Z' and resid 6 through 8' Processing helix chain 'Z' and resid 11 through 34 removed outlier: 3.581A pdb=" N LEU Z 19 " --> pdb=" O ASN Z 15 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 62 removed outlier: 3.938A 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 18 through 27 Processing helix chain 'a' and resid 42 through 50 Processing helix chain 'b' and resid 10 through 19 removed outlier: 3.581A pdb=" N ARG b 17 " --> pdb=" O ARG b 13 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 18 through 22 Processing helix chain 'd' and resid 25 through 37 Processing helix chain 'e' and resid 8 through 13 removed outlier: 3.687A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 8 through 13' Processing helix chain 'e' and resid 38 through 45 Processing helix chain 'e' and resid 55 through 61 Processing helix chain 'f' and resid 31 through 33 No H-bonds generated for 'chain 'f' and resid 31 through 33' Processing helix chain 'i' and resid 5 through 18 Processing helix chain 'i' and resid 24 through 40 Processing helix chain 'i' and resid 45 through 58 Processing helix chain 'i' and resid 70 through 85 Processing helix chain 'i' and resid 113 through 128 Processing helix chain 'i' and resid 144 through 154 Processing helix chain 'i' and resid 168 through 182 Processing helix chain 'i' and resid 199 through 212 Processing helix chain 'i' and resid 227 through 238 removed outlier: 3.890A pdb=" N ALA i 230 " --> pdb=" O GLN i 227 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA i 233 " --> pdb=" O ALA i 230 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS i 234 " --> pdb=" O ASN i 231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE i 236 " --> pdb=" O ALA i 233 " (cutoff:3.500A) Processing helix chain 'i' and resid 258 through 265 Processing helix chain 'i' and resid 279 through 281 No H-bonds generated for 'chain 'i' and resid 279 through 281' Processing helix chain 'i' and resid 287 through 295 Processing helix chain 'i' and resid 300 through 326 removed outlier: 5.357A pdb=" N UNK i 315 " --> pdb=" O UNK i 311 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N UNK i 316 " --> pdb=" O UNK i 312 " (cutoff:3.500A) Processing helix chain 'i' and resid 331 through 343 Processing helix chain 'i' and resid 348 through 353 removed outlier: 3.853A pdb=" N UNK i 353 " --> pdb=" O UNK i 349 " (cutoff:3.500A) Processing helix chain 'i' and resid 355 through 358 No H-bonds generated for 'chain 'i' and resid 355 through 358' Processing helix chain 'i' and resid 369 through 380 removed outlier: 3.775A pdb=" N VAL i 374 " --> pdb=" O ASP i 370 " (cutoff:3.500A) Processing helix chain 'i' and resid 385 through 389 Processing helix chain 'i' and resid 391 through 393 No H-bonds generated for 'chain 'i' and resid 391 through 393' Processing helix chain 'i' and resid 396 through 405 Processing helix chain 'i' and resid 410 through 432 Processing helix chain 'i' and resid 435 through 440 Processing helix chain 'k' and resid 28 through 43 removed outlier: 3.685A pdb=" N LEU k 36 " --> pdb=" O LEU k 32 " (cutoff:3.500A) Proline residue: k 43 - end of helix Processing helix chain 'l' and resid 306 through 319 Processing helix chain 'l' and resid 336 through 347 removed outlier: 4.152A pdb=" N LEU l 340 " --> pdb=" O ALA l 336 " (cutoff:3.500A) Processing helix chain 'l' and resid 360 through 373 Processing helix chain 'l' and resid 393 through 407 Processing helix chain 'l' and resid 425 through 438 removed outlier: 3.943A pdb=" N SER l 429 " --> pdb=" O GLN l 425 " (cutoff:3.500A) Processing helix chain 'l' and resid 455 through 464 removed outlier: 3.686A pdb=" N ALA l 461 " --> pdb=" O PHE l 458 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP l 462 " --> pdb=" O SER l 459 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE l 464 " --> pdb=" O ALA l 461 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.525A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL C 78 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= D, first strand: chain 'C' and resid 181 through 185 removed outlier: 6.540A pdb=" N ARG C 175 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.534A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 80 through 83 removed outlier: 6.549A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 2 through 4 Processing sheet with id= H, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.374A pdb=" N VAL E 186 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL E 121 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET E 188 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 128 through 132 removed outlier: 6.844A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N CYS F 87 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU F 66 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 16 through 20 Processing sheet with id= K, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= L, first strand: chain 'G' and resid 161 through 164 Processing sheet with id= M, first strand: chain 'G' and resid 95 through 99 Processing sheet with id= N, first strand: chain 'H' and resid 18 through 20 Processing sheet with id= O, first strand: chain 'H' and resid 78 through 82 removed outlier: 3.719A pdb=" N VAL H 147 " --> pdb=" O ILE H 80 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 116 through 118 removed outlier: 3.624A pdb=" N ALA I 110 " --> pdb=" O VAL I 27 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA I 25 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER I 24 " --> pdb=" O VAL I 85 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 9 through 14 Processing sheet with id= R, first strand: chain 'K' and resid 15 through 19 removed outlier: 6.640A pdb=" N TYR K 53 " --> pdb=" O TYR K 16 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL K 18 " --> pdb=" O TYR K 53 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE K 55 " --> pdb=" O VAL K 18 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 73 through 77 Processing sheet with id= T, first strand: chain 'L' and resid 19 through 24 removed outlier: 6.690A pdb=" N LYS L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL L 24 " --> pdb=" O ILE L 38 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE L 38 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 74 through 77 removed outlier: 6.282A pdb=" N PHE M 107 " --> pdb=" O ALA M 75 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE M 77 " --> pdb=" O PHE M 107 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS M 109 " --> pdb=" O ILE M 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'M' and resid 121 through 123 removed outlier: 6.686A pdb=" N LYS M 141 " --> pdb=" O VAL M 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'N' and resid 128 through 132 removed outlier: 3.721A pdb=" N TYR N 103 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA N 35 " --> pdb=" O VAL N 101 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL N 101 " --> pdb=" O ALA N 35 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 39 through 42 removed outlier: 3.514A pdb=" N ASN N 88 " --> pdb=" O GLU N 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE N 73 " --> pdb=" O GLU N 90 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TRP N 92 " --> pdb=" O LYS N 71 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS N 71 " --> pdb=" O TRP N 92 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 33 through 37 removed outlier: 3.698A pdb=" N ALA O 108 " --> pdb=" O ARG O 103 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY O 101 " --> pdb=" O MET O 110 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR O 112 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LYS O 99 " --> pdb=" O TYR O 112 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLU O 114 " --> pdb=" O ILE O 97 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE O 97 " --> pdb=" O GLU O 114 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 91 through 93 removed outlier: 3.552A pdb=" N VAL P 49 " --> pdb=" O VAL P 39 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Q' and resid 83 through 88 removed outlier: 6.882A pdb=" N THR Q 25 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N GLU Q 44 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE Q 64 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR Q 60 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE Q 50 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA Q 58 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 10 through 14 removed outlier: 6.963A pdb=" N GLN S 6 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL S 38 " --> pdb=" O GLN S 6 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'S' and resid 19 through 23 Processing sheet with id= AD, first strand: chain 'S' and resid 32 through 35 removed outlier: 6.483A pdb=" N GLU S 62 " --> pdb=" O ILE S 98 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE S 98 " --> pdb=" O GLU S 62 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'S' and resid 72 through 78 removed outlier: 4.209A pdb=" N TYR S 83 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'T' and resid 2 through 7 removed outlier: 6.839A pdb=" N SER T 108 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL T 71 " --> pdb=" O SER T 108 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 82 through 87 Processing sheet with id= AH, first strand: chain 'U' and resid 11 through 14 removed outlier: 6.843A pdb=" N LYS U 33 " --> pdb=" O ARG U 12 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL U 31 " --> pdb=" O PRO U 14 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS U 81 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL U 57 " --> pdb=" O THR U 86 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'U' and resid 67 through 70 Processing sheet with id= AJ, first strand: chain 'V' and resid 22 through 24 Processing sheet with id= AK, first strand: chain 'V' and resid 41 through 45 Processing sheet with id= AL, first strand: chain 'V' and resid 83 through 88 Processing sheet with id= AM, first strand: chain 'V' and resid 25 through 28 removed outlier: 7.135A pdb=" N ILE V 35 " --> pdb=" O LYS V 26 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'W' and resid 3 through 6 removed outlier: 6.567A pdb=" N THR W 62 " --> pdb=" O ILE W 4 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA W 6 " --> pdb=" O THR W 62 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL W 64 " --> pdb=" O ALA W 6 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP W 90 " --> pdb=" O GLN W 75 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL W 77 " --> pdb=" O HIS W 88 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N HIS W 88 " --> pdb=" O VAL W 77 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE W 89 " --> pdb=" O PRO W 27 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'X' and resid 45 through 47 removed outlier: 7.252A pdb=" N LYS X 78 " --> pdb=" O HIS X 46 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'X' and resid 51 through 53 Processing sheet with id= AQ, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id= AR, first strand: chain 'Y' and resid 33 through 40 Processing sheet with id= AS, first strand: chain 'a' and resid 35 through 38 Processing sheet with id= AT, first strand: chain 'c' and resid 20 through 25 Processing sheet with id= AU, first strand: chain 'f' and resid 2 through 4 Processing sheet with id= AV, first strand: chain 'f' and resid 14 through 19 Processing sheet with id= AW, first strand: chain 'i' and resid 282 through 284 removed outlier: 7.865A pdb=" N VAL i 245 " --> pdb=" O LYS i 271 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU i 273 " --> pdb=" O VAL i 245 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU i 247 " --> pdb=" O LEU i 273 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ASP i 158 " --> pdb=" O VAL i 134 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N SER i 136 " --> pdb=" O ASP i 158 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N PHE i 160 " --> pdb=" O SER i 136 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'l' and resid 480 through 482 removed outlier: 7.488A pdb=" N ILE l 443 " --> pdb=" O ARG l 469 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE l 471 " --> pdb=" O ILE l 443 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU l 445 " --> pdb=" O ILE l 471 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU l 414 " --> pdb=" O VAL l 295 " (cutoff:3.500A) 1186 hydrogen bonds defined for protein. 3357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2566 hydrogen bonds 4034 hydrogen bond angles 0 basepair planarities 1020 basepair parallelities 1574 stacking parallelities Total time for adding SS restraints: 189.01 Time building geometry restraints manager: 45.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.54: 98607 1.54 - 1.88: 7230 1.88 - 2.22: 0 2.22 - 2.56: 0 2.56 - 2.90: 1 Bond restraints: 105838 Sorted by residual: bond pdb=" C SER Z 40 " pdb=" N HIS Z 41 " ideal model delta sigma weight residual 1.335 2.898 -1.563 1.33e-02 5.65e+03 1.38e+04 bond pdb=" N GLU U 89 " pdb=" CA GLU U 89 " ideal model delta sigma weight residual 1.457 1.596 -0.138 1.29e-02 6.01e+03 1.15e+02 bond pdb=" CA LYS U 88 " pdb=" C LYS U 88 " ideal model delta sigma weight residual 1.524 1.657 -0.134 1.33e-02 5.65e+03 1.01e+02 bond pdb=" C LYS U 88 " pdb=" N GLU U 89 " ideal model delta sigma weight residual 1.332 1.471 -0.139 1.40e-02 5.10e+03 9.81e+01 bond pdb=" N3B GNP i1400 " pdb=" PG GNP i1400 " ideal model delta sigma weight residual 1.801 1.680 0.121 2.00e-02 2.50e+03 3.64e+01 ... (remaining 105833 not shown) Histogram of bond angle deviations from ideal: 93.15 - 103.42: 7596 103.42 - 113.69: 74450 113.69 - 123.96: 61653 123.96 - 134.23: 14297 134.23 - 144.50: 11 Bond angle restraints: 158007 Sorted by residual: angle pdb=" O SER Z 40 " pdb=" C SER Z 40 " pdb=" N HIS Z 41 " ideal model delta sigma weight residual 122.33 93.15 29.18 1.34e+00 5.57e-01 4.74e+02 angle pdb=" NH1 ARG l 476 " pdb=" CZ ARG l 476 " pdb=" NH2 ARG l 476 " ideal model delta sigma weight residual 119.30 144.50 -25.20 1.30e+00 5.92e-01 3.76e+02 angle pdb=" CA SER Z 40 " pdb=" C SER Z 40 " pdb=" N HIS Z 41 " ideal model delta sigma weight residual 117.82 95.19 22.63 1.42e+00 4.96e-01 2.54e+02 angle pdb=" NE ARG l 476 " pdb=" CZ ARG l 476 " pdb=" NH1 ARG l 476 " ideal model delta sigma weight residual 121.50 107.78 13.72 1.00e+00 1.00e+00 1.88e+02 angle pdb=" NE ARG l 476 " pdb=" CZ ARG l 476 " pdb=" NH2 ARG l 476 " ideal model delta sigma weight residual 119.20 107.72 11.48 9.00e-01 1.23e+00 1.63e+02 ... (remaining 158002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 59170 35.39 - 70.77: 7663 70.77 - 106.16: 846 106.16 - 141.55: 16 141.55 - 176.93: 10 Dihedral angle restraints: 67705 sinusoidal: 55907 harmonic: 11798 Sorted by residual: dihedral pdb=" CA LEU i 240 " pdb=" C LEU i 240 " pdb=" N PRO i 241 " pdb=" CA PRO i 241 " ideal model delta harmonic sigma weight residual -180.00 -119.87 -60.13 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" C4' U A1344 " pdb=" C3' U A1344 " pdb=" C2' U A1344 " pdb=" C1' U A1344 " ideal model delta sinusoidal sigma weight residual -35.00 31.98 -66.98 1 8.00e+00 1.56e-02 9.13e+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 30.67 -65.67 1 8.00e+00 1.56e-02 8.82e+01 ... (remaining 67702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 19747 0.118 - 0.236: 441 0.236 - 0.354: 13 0.354 - 0.473: 2 0.473 - 0.591: 4 Chirality restraints: 20207 Sorted by residual: chirality pdb=" C2' GNP i1400 " pdb=" C1' GNP i1400 " pdb=" C3' GNP i1400 " pdb=" O2' GNP i1400 " both_signs ideal model delta sigma weight residual False -2.55 -1.96 -0.59 2.00e-01 2.50e+01 8.72e+00 chirality pdb=" C1' GNP l1400 " pdb=" C2' GNP l1400 " pdb=" N9 GNP l1400 " pdb=" O4' GNP l1400 " both_signs ideal model delta sigma weight residual False 2.36 1.79 0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" C2' GNP l1400 " pdb=" C1' GNP l1400 " pdb=" C3' GNP l1400 " pdb=" O2' GNP l1400 " both_signs ideal model delta sigma weight residual False -2.55 -2.06 -0.49 2.00e-01 2.50e+01 6.08e+00 ... (remaining 20204 not shown) Planarity restraints: 8670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER Z 40 " 0.173 2.00e-02 2.50e+03 2.63e-01 6.91e+02 pdb=" C SER Z 40 " -0.437 2.00e-02 2.50e+03 pdb=" O SER Z 40 " 0.234 2.00e-02 2.50e+03 pdb=" N HIS Z 41 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 25 " -0.059 5.00e-02 4.00e+02 9.00e-02 1.30e+01 pdb=" N PRO J 26 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO J 26 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO J 26 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' GNP i1400 " -0.037 2.00e-02 2.50e+03 1.83e-02 1.01e+01 pdb=" C2 GNP i1400 " 0.014 2.00e-02 2.50e+03 pdb=" C4 GNP i1400 " 0.001 2.00e-02 2.50e+03 pdb=" C5 GNP i1400 " 0.009 2.00e-02 2.50e+03 pdb=" C6 GNP i1400 " -0.016 2.00e-02 2.50e+03 pdb=" C8 GNP i1400 " -0.005 2.00e-02 2.50e+03 pdb=" N1 GNP i1400 " 0.011 2.00e-02 2.50e+03 pdb=" N2 GNP i1400 " -0.013 2.00e-02 2.50e+03 pdb=" N3 GNP i1400 " 0.018 2.00e-02 2.50e+03 pdb=" N7 GNP i1400 " 0.020 2.00e-02 2.50e+03 pdb=" N9 GNP i1400 " 0.022 2.00e-02 2.50e+03 pdb=" O6 GNP i1400 " -0.024 2.00e-02 2.50e+03 ... (remaining 8667 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 311 2.37 - 3.00: 48645 3.00 - 3.63: 169910 3.63 - 4.27: 295003 4.27 - 4.90: 392067 Nonbonded interactions: 905936 Sorted by model distance: nonbonded pdb=" OP1 A A 751 " pdb="MG MG A3020 " model vdw 1.737 2.170 nonbonded pdb=" OP1 U A 827 " pdb="MG MG A3027 " model vdw 1.758 2.170 nonbonded pdb=" OP2 U A 963 " pdb="MG MG A3030 " model vdw 1.770 2.170 nonbonded pdb=" OP1 A A1780 " pdb="MG MG A3086 " model vdw 1.817 2.170 nonbonded pdb=" O4 U A1263 " pdb="MG MG A3180 " model vdw 1.821 2.170 ... (remaining 905931 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 11.040 Check model and map are aligned: 1.050 Set scattering table: 0.660 Process input model: 396.610 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 416.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 0.009 1.563 105838 Z= 0.592 Angle : 1.109 29.179 158007 Z= 0.635 Chirality : 0.048 0.591 20207 Planarity : 0.006 0.263 8670 Dihedral : 23.562 176.933 60095 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.46 % Rotamer: Outliers : 10.34 % Allowed : 12.19 % Favored : 77.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.10), residues: 4013 helix: -3.25 (0.10), residues: 1309 sheet: -1.30 (0.16), residues: 770 loop : -1.47 (0.11), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 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 0.013 0.001 ARG i 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1704 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1363 time to evaluate : 4.453 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: C 24 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8409 (tp) REVERT: C 121 ASP cc_start: 0.7284 (p0) cc_final: 0.7036 (p0) REVERT: C 180 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6832 (pt0) REVERT: D 43 ASP cc_start: 0.6920 (m-30) cc_final: 0.6295 (m-30) REVERT: D 139 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8784 (p) REVERT: D 174 SER cc_start: 0.9023 (m) cc_final: 0.8820 (p) REVERT: E 62 GLN cc_start: 0.8684 (tp40) cc_final: 0.7662 (tp40) REVERT: E 148 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8233 (mm) REVERT: F 7 TYR cc_start: 0.7771 (t80) cc_final: 0.7298 (t80) REVERT: F 144 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7143 (m-30) REVERT: G 11 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8129 (p) REVERT: G 115 HIS cc_start: 0.6862 (t70) cc_final: 0.6285 (t70) REVERT: H 90 LEU cc_start: 0.6583 (mp) cc_final: 0.5699 (mt) REVERT: K 32 LEU cc_start: 0.9193 (mt) cc_final: 0.8889 (mt) REVERT: K 40 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8219 (p90) REVERT: K 81 ILE cc_start: 0.9362 (tp) cc_final: 0.8932 (tp) REVERT: K 103 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8269 (mm) REVERT: K 131 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7768 (p0) REVERT: K 136 GLN cc_start: 0.8218 (mt0) cc_final: 0.8002 (mt0) REVERT: L 8 LEU cc_start: 0.9022 (mp) cc_final: 0.7300 (mt) REVERT: L 20 MET cc_start: 0.7553 (ttp) cc_final: 0.6981 (ttp) REVERT: L 22 ILE cc_start: 0.9081 (pt) cc_final: 0.8729 (pt) REVERT: L 58 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8758 (pp) REVERT: M 1 MET cc_start: 0.6569 (ttp) cc_final: 0.6356 (ttp) REVERT: M 30 THR cc_start: 0.8660 (p) cc_final: 0.8448 (p) REVERT: N 1 MET cc_start: 0.7853 (ttp) cc_final: 0.7335 (mtp) REVERT: N 17 ASN cc_start: 0.8676 (t0) cc_final: 0.8425 (t0) REVERT: N 106 ASP cc_start: 0.6922 (p0) cc_final: 0.6637 (p0) REVERT: N 119 LEU cc_start: 0.8439 (mt) cc_final: 0.7589 (mt) REVERT: O 78 LYS cc_start: 0.8965 (tttt) cc_final: 0.8622 (tttt) REVERT: O 99 LYS cc_start: 0.8278 (mtmm) cc_final: 0.7952 (mtmm) REVERT: P 36 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: P 48 LEU cc_start: 0.8896 (mt) cc_final: 0.8600 (mt) REVERT: Q 32 VAL cc_start: 0.7694 (m) cc_final: 0.7403 (t) REVERT: Q 99 TYR cc_start: 0.8647 (p90) cc_final: 0.8362 (p90) REVERT: R 32 TYR cc_start: 0.9176 (t80) cc_final: 0.8931 (t80) REVERT: R 51 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8189 (mpt90) REVERT: R 97 ASP cc_start: 0.7418 (t0) cc_final: 0.6732 (t0) REVERT: R 107 THR cc_start: 0.8650 (m) cc_final: 0.7885 (m) REVERT: S 29 THR cc_start: 0.8246 (m) cc_final: 0.7547 (m) REVERT: S 41 ILE cc_start: 0.8637 (mt) cc_final: 0.8404 (mm) REVERT: S 99 THR cc_start: 0.8797 (p) cc_final: 0.7836 (p) REVERT: T 13 SER cc_start: 0.8691 (p) cc_final: 0.8396 (t) REVERT: T 19 LEU cc_start: 0.9054 (mt) cc_final: 0.8138 (mt) REVERT: T 36 LEU cc_start: 0.9228 (mt) cc_final: 0.8939 (mt) REVERT: T 39 THR cc_start: 0.8884 (m) cc_final: 0.8642 (p) REVERT: T 52 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7193 (mt-10) REVERT: T 75 PHE cc_start: 0.8792 (p90) cc_final: 0.8384 (p90) REVERT: T 81 SER cc_start: 0.9018 (m) cc_final: 0.8757 (p) REVERT: T 100 THR cc_start: 0.8815 (p) cc_final: 0.8323 (p) REVERT: T 104 THR cc_start: 0.9162 (m) cc_final: 0.8580 (p) REVERT: U 15 HIS cc_start: 0.8485 (t70) cc_final: 0.8222 (t70) REVERT: U 43 ILE cc_start: 0.9401 (mt) cc_final: 0.9194 (mt) REVERT: U 84 TYR cc_start: 0.8443 (m-80) cc_final: 0.8040 (m-10) REVERT: U 86 THR cc_start: 0.8278 (m) cc_final: 0.7770 (p) REVERT: V 17 LYS cc_start: 0.8798 (pttt) cc_final: 0.8482 (ptpt) REVERT: V 39 ILE cc_start: 0.8857 (mm) cc_final: 0.8286 (mm) REVERT: V 41 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7890 (mm) REVERT: W 8 VAL cc_start: 0.8878 (m) cc_final: 0.8659 (t) REVERT: W 62 THR cc_start: 0.8461 (p) cc_final: 0.7633 (p) REVERT: X 56 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8372 (p0) REVERT: X 85 GLU cc_start: 0.4208 (OUTLIER) cc_final: 0.3887 (pt0) REVERT: Y 56 MET cc_start: 0.8212 (mtt) cc_final: 0.8007 (mtt) REVERT: Z 20 ASN cc_start: 0.7580 (m-40) cc_final: 0.6838 (m110) REVERT: Z 48 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8446 (mtt-85) REVERT: a 30 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8062 (tpp80) REVERT: b 28 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7276 (mm) REVERT: b 34 SER cc_start: 0.9000 (p) cc_final: 0.8785 (p) REVERT: b 40 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8197 (tpt170) REVERT: b 44 THR cc_start: 0.8820 (p) cc_final: 0.8558 (p) REVERT: c 8 LYS cc_start: 0.8444 (mtpt) cc_final: 0.7914 (mtpt) REVERT: d 11 LYS cc_start: 0.8992 (mttt) cc_final: 0.8641 (mtpp) REVERT: d 43 THR cc_start: 0.9085 (p) cc_final: 0.8818 (p) REVERT: d 44 VAL cc_start: 0.8946 (m) cc_final: 0.8693 (p) REVERT: e 7 VAL cc_start: 0.9409 (t) cc_final: 0.9193 (m) REVERT: e 34 THR cc_start: 0.8916 (m) cc_final: 0.8655 (m) REVERT: f 20 ASP cc_start: 0.7518 (t0) cc_final: 0.7028 (t0) REVERT: i 86 MET cc_start: 0.1010 (mmm) cc_final: 0.0302 (mmm) REVERT: i 279 THR cc_start: 0.4240 (p) cc_final: 0.3949 (p) REVERT: l 394 MET cc_start: 0.2323 (OUTLIER) cc_final: 0.2077 (mpp) outliers start: 341 outliers final: 54 residues processed: 1561 average time/residue: 1.0156 time to fit residues: 2606.7102 Evaluate side-chains 948 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 874 time to evaluate : 4.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain Q residue 115 ASN Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 83 TYR Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 98 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 85 GLU Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain a residue 30 ARG Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 52 ARG Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain i residue 261 SER Chi-restraints excluded: chain l residue 394 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 594 optimal weight: 5.9990 chunk 533 optimal weight: 3.9990 chunk 296 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 285 optimal weight: 10.0000 chunk 551 optimal weight: 9.9990 chunk 213 optimal weight: 40.0000 chunk 335 optimal weight: 5.9990 chunk 410 optimal weight: 20.0000 chunk 639 optimal weight: 8.9990 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 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS C 153 GLN D 140 HIS D 167 ASN E 41 GLN E 94 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN G 115 HIS H 11 ASN H 33 GLN J 105 GLN L 3 GLN L 82 ASN M 35 HIS ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 HIS O 23 ASN Q 41 GLN Q 66 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN R 72 ASN T 9 HIS U 48 GLN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 46 HIS Y 23 ASN Z 15 ASN Z 31 GLN ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN c 19 HIS i 26 ASN i 62 HIS i 196 HIS ** i 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 409 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 105838 Z= 0.307 Angle : 0.676 10.590 158007 Z= 0.350 Chirality : 0.038 0.318 20207 Planarity : 0.005 0.095 8670 Dihedral : 23.427 179.658 52345 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.61 % Rotamer: Outliers : 5.94 % Allowed : 20.75 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.12), residues: 4015 helix: -0.81 (0.13), residues: 1295 sheet: -0.80 (0.16), residues: 822 loop : -0.70 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 125 HIS 0.018 0.001 HIS Z 41 PHE 0.033 0.002 PHE l 365 TYR 0.021 0.002 TYR M 58 ARG 0.015 0.001 ARG S 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 955 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7182 (mt-10) REVERT: C 121 ASP cc_start: 0.7126 (p0) cc_final: 0.6754 (p0) REVERT: C 180 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6678 (pt0) REVERT: D 2 ILE cc_start: 0.8396 (pt) cc_final: 0.7764 (pt) REVERT: D 165 MET cc_start: 0.7985 (ttp) cc_final: 0.7744 (ttm) REVERT: E 46 GLN cc_start: 0.8872 (mp10) cc_final: 0.8187 (mp10) REVERT: E 97 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7627 (m110) REVERT: E 171 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6942 (p0) REVERT: F 50 LEU cc_start: 0.8563 (tp) cc_final: 0.8237 (tp) REVERT: F 144 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: G 76 VAL cc_start: 0.9437 (OUTLIER) cc_final: 0.9235 (p) REVERT: H 7 ASP cc_start: 0.7583 (p0) cc_final: 0.7344 (p0) REVERT: L 58 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8790 (pp) REVERT: L 112 PHE cc_start: 0.8485 (m-10) cc_final: 0.8278 (m-10) REVERT: L 121 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7520 (tm-30) REVERT: M 67 THR cc_start: 0.9126 (m) cc_final: 0.8603 (t) REVERT: N 1 MET cc_start: 0.8101 (ttp) cc_final: 0.7834 (ttp) REVERT: N 17 ASN cc_start: 0.8723 (t0) cc_final: 0.8367 (t0) REVERT: O 1 MET cc_start: 0.7805 (mtp) cc_final: 0.7557 (mtp) REVERT: O 2 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6945 (ttp-110) REVERT: O 43 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7659 (tp30) REVERT: P 36 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: Q 11 GLU cc_start: 0.8153 (pp20) cc_final: 0.7816 (pp20) REVERT: R 32 TYR cc_start: 0.8939 (t80) cc_final: 0.8604 (t80) REVERT: R 97 ASP cc_start: 0.7161 (t0) cc_final: 0.5805 (t0) REVERT: S 51 VAL cc_start: 0.9298 (OUTLIER) cc_final: 0.8992 (m) REVERT: T 65 ASP cc_start: 0.6747 (t0) cc_final: 0.5642 (t0) REVERT: W 58 SER cc_start: 0.8047 (p) cc_final: 0.6833 (p) REVERT: Z 4 LYS cc_start: 0.8044 (pttm) cc_final: 0.7670 (pttm) REVERT: Z 40 SER cc_start: 0.9080 (p) cc_final: 0.8796 (p) REVERT: a 6 LYS cc_start: 0.8236 (mmtt) cc_final: 0.6357 (mmtt) REVERT: c 8 LYS cc_start: 0.8240 (mtpt) cc_final: 0.8010 (mtpt) REVERT: d 15 SER cc_start: 0.9061 (m) cc_final: 0.8736 (p) REVERT: f 20 ASP cc_start: 0.7394 (t0) cc_final: 0.6932 (t0) REVERT: f 23 ILE cc_start: 0.9140 (mm) cc_final: 0.8773 (mm) REVERT: i 86 MET cc_start: 0.0938 (mmm) cc_final: 0.0225 (mmm) REVERT: l 394 MET cc_start: 0.2559 (OUTLIER) cc_final: 0.2326 (mpp) outliers start: 196 outliers final: 100 residues processed: 1063 average time/residue: 0.9384 time to fit residues: 1703.0567 Evaluate side-chains 886 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 776 time to evaluate : 4.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 106 GLU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 25 ASP Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 2 ARG Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 59 GLN Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 69 THR Chi-restraints excluded: chain i residue 336 GLU Chi-restraints excluded: chain l residue 376 ILE Chi-restraints excluded: chain l residue 394 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 355 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 532 optimal weight: 9.9990 chunk 435 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 640 optimal weight: 10.0000 chunk 691 optimal weight: 40.0000 chunk 570 optimal weight: 10.0000 chunk 635 optimal weight: 9.9990 chunk 218 optimal weight: 30.0000 chunk 513 optimal weight: 5.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS E 41 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 HIS ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN ** I 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN M 35 HIS ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN O 23 ASN P 43 ASN ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 HIS T 7 HIS T 9 HIS ** V 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 23 ASN Z 15 ASN ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 GLN e 43 HIS f 35 GLN i 209 HIS i 381 ASN l 413 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 105838 Z= 0.432 Angle : 0.734 13.349 158007 Z= 0.375 Chirality : 0.040 0.319 20207 Planarity : 0.006 0.104 8670 Dihedral : 23.398 179.317 52254 Min Nonbonded Distance : 0.705 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 7.95 % Allowed : 21.26 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.81 (0.12), residues: 4015 helix: -0.29 (0.14), residues: 1303 sheet: -0.49 (0.18), residues: 765 loop : -0.60 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 64 HIS 0.009 0.002 HIS P 100 PHE 0.027 0.002 PHE l 365 TYR 0.018 0.002 TYR P 36 ARG 0.014 0.001 ARG d 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 808 time to evaluate : 4.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: C 180 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6788 (pt0) REVERT: C 181 MET cc_start: 0.8589 (mmm) cc_final: 0.8042 (mmt) REVERT: C 264 ASP cc_start: 0.7345 (m-30) cc_final: 0.6877 (m-30) REVERT: D 139 SER cc_start: 0.8746 (m) cc_final: 0.8175 (p) REVERT: D 165 MET cc_start: 0.7986 (ttp) cc_final: 0.7697 (ttm) REVERT: E 46 GLN cc_start: 0.8854 (mp10) cc_final: 0.8638 (mm-40) REVERT: E 199 MET cc_start: 0.7671 (ppp) cc_final: 0.7213 (ppp) REVERT: F 38 MET cc_start: 0.7009 (tpt) cc_final: 0.6721 (tpt) REVERT: F 50 LEU cc_start: 0.8513 (tp) cc_final: 0.8304 (tp) REVERT: G 149 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7680 (tpt-90) REVERT: H 42 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.6609 (tptp) REVERT: H 97 ARG cc_start: 0.6038 (mpt-90) cc_final: 0.5271 (mpt180) REVERT: I 113 PHE cc_start: 0.1780 (OUTLIER) cc_final: 0.1343 (t80) REVERT: K 14 ASP cc_start: 0.7342 (t0) cc_final: 0.6887 (t0) REVERT: K 98 GLU cc_start: 0.7825 (mp0) cc_final: 0.7546 (mm-30) REVERT: L 54 LYS cc_start: 0.9013 (tttt) cc_final: 0.8722 (tttm) REVERT: L 80 ASP cc_start: 0.7933 (m-30) cc_final: 0.7729 (m-30) REVERT: L 112 PHE cc_start: 0.8643 (m-10) cc_final: 0.8429 (m-10) REVERT: L 121 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7415 (tm-30) REVERT: N 1 MET cc_start: 0.8064 (ttp) cc_final: 0.7856 (ttp) REVERT: R 97 ASP cc_start: 0.7640 (t0) cc_final: 0.7410 (t0) REVERT: S 51 VAL cc_start: 0.9347 (OUTLIER) cc_final: 0.9099 (m) REVERT: T 7 HIS cc_start: 0.8886 (OUTLIER) cc_final: 0.8675 (t-170) REVERT: T 15 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8213 (tm-30) REVERT: T 33 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8457 (mt) REVERT: V 46 GLN cc_start: 0.6592 (tm-30) cc_final: 0.6241 (tm-30) REVERT: Y 65 ASP cc_start: 0.8104 (p0) cc_final: 0.7762 (p0) REVERT: Y 67 VAL cc_start: 0.9380 (p) cc_final: 0.8730 (p) REVERT: Z 56 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8829 (mm) REVERT: a 37 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7168 (mt-10) REVERT: c 7 GLU cc_start: 0.7541 (pm20) cc_final: 0.5432 (pm20) REVERT: d 15 SER cc_start: 0.9088 (m) cc_final: 0.8714 (p) REVERT: d 22 MET cc_start: 0.8494 (tpp) cc_final: 0.8178 (tpp) REVERT: e 26 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8301 (m-70) REVERT: e 61 CYS cc_start: 0.8216 (m) cc_final: 0.7959 (m) REVERT: f 20 ASP cc_start: 0.7240 (t0) cc_final: 0.6769 (t0) REVERT: f 23 ILE cc_start: 0.9134 (mm) cc_final: 0.8796 (mm) REVERT: i 86 MET cc_start: 0.0993 (mmm) cc_final: 0.0212 (mmm) outliers start: 262 outliers final: 161 residues processed: 961 average time/residue: 0.9137 time to fit residues: 1508.3660 Evaluate side-chains 889 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 718 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 113 PHE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 106 GLU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain N residue 25 ASP Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain O residue 2 ARG Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 86 ARG Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 60 GLU Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 59 GLN Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 27 ILE Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 59 ILE Chi-restraints excluded: chain T residue 7 HIS Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 78 SER Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 72 VAL Chi-restraints excluded: chain W residue 83 LYS Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 20 ASP Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 7 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 26 HIS Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 69 THR Chi-restraints excluded: chain i residue 253 ASP Chi-restraints excluded: chain i residue 385 MET Chi-restraints excluded: chain l residue 376 ILE Chi-restraints excluded: chain l residue 419 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 632 optimal weight: 7.9990 chunk 481 optimal weight: 0.3980 chunk 332 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 430 optimal weight: 6.9990 chunk 642 optimal weight: 20.0000 chunk 680 optimal weight: 5.9990 chunk 335 optimal weight: 0.9990 chunk 609 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS H 145 ASN K 136 GLN ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 HIS T 40 ASN V 53 ASN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 ASN Z 20 ASN i 26 ASN ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 105838 Z= 0.208 Angle : 0.572 13.114 158007 Z= 0.299 Chirality : 0.034 0.314 20207 Planarity : 0.005 0.080 8670 Dihedral : 23.311 178.145 52237 Min Nonbonded Distance : 1.037 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.69 % Favored : 97.21 % Rotamer: Outliers : 5.31 % Allowed : 24.36 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.38 (0.13), residues: 4015 helix: 0.16 (0.14), residues: 1304 sheet: -0.35 (0.17), residues: 799 loop : -0.36 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 80 HIS 0.017 0.001 HIS T 7 PHE 0.026 0.002 PHE N 31 TYR 0.020 0.001 TYR T 38 ARG 0.010 0.001 ARG i 415 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 808 time to evaluate : 4.466 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: C 72 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7280 (m-30) REVERT: C 181 MET cc_start: 0.8516 (mmm) cc_final: 0.8061 (mmt) REVERT: C 264 ASP cc_start: 0.7120 (m-30) cc_final: 0.6670 (m-30) REVERT: D 1 MET cc_start: 0.7092 (tmm) cc_final: 0.6809 (tmm) REVERT: D 139 SER cc_start: 0.8735 (m) cc_final: 0.8206 (p) REVERT: D 165 MET cc_start: 0.7937 (ttp) cc_final: 0.7416 (ttm) REVERT: E 199 MET cc_start: 0.7565 (ppp) cc_final: 0.7305 (ppp) REVERT: F 52 ASN cc_start: 0.7599 (p0) cc_final: 0.6741 (p0) REVERT: H 42 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7292 (tptp) REVERT: I 69 PHE cc_start: 0.6178 (m-80) cc_final: 0.5917 (m-10) REVERT: I 113 PHE cc_start: 0.2313 (OUTLIER) cc_final: 0.1700 (t80) REVERT: L 51 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7672 (pttm) REVERT: L 112 PHE cc_start: 0.8639 (m-10) cc_final: 0.8354 (m-10) REVERT: L 121 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7642 (tm-30) REVERT: N 1 MET cc_start: 0.8018 (ttp) cc_final: 0.7794 (ttp) REVERT: N 119 LEU cc_start: 0.8413 (mp) cc_final: 0.8121 (mp) REVERT: R 79 PHE cc_start: 0.9096 (t80) cc_final: 0.8874 (t80) REVERT: S 1 MET cc_start: 0.7790 (tmm) cc_final: 0.7341 (tpp) REVERT: S 51 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9026 (m) REVERT: S 76 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8896 (mtmm) REVERT: T 15 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8187 (tm-30) REVERT: T 92 ARG cc_start: 0.7258 (ptp90) cc_final: 0.7006 (ptp90) REVERT: V 46 GLN cc_start: 0.6512 (tm-30) cc_final: 0.6149 (tm-30) REVERT: X 70 GLU cc_start: 0.7705 (pm20) cc_final: 0.7013 (pm20) REVERT: X 72 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8298 (mtmm) REVERT: Y 22 LEU cc_start: 0.9118 (mm) cc_final: 0.8916 (mm) REVERT: Y 65 ASP cc_start: 0.8234 (p0) cc_final: 0.7960 (p0) REVERT: Y 67 VAL cc_start: 0.9273 (p) cc_final: 0.8745 (t) REVERT: Z 40 SER cc_start: 0.8966 (p) cc_final: 0.8676 (p) REVERT: b 7 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8751 (ttmt) REVERT: d 14 ARG cc_start: 0.9125 (ttm170) cc_final: 0.8725 (tpp80) REVERT: d 15 SER cc_start: 0.9163 (m) cc_final: 0.8636 (p) REVERT: d 22 MET cc_start: 0.8677 (tpp) cc_final: 0.8283 (tpp) REVERT: e 30 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8561 (mmt90) REVERT: e 61 CYS cc_start: 0.8129 (m) cc_final: 0.7911 (m) REVERT: f 20 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6842 (t0) REVERT: f 23 ILE cc_start: 0.9147 (mm) cc_final: 0.8851 (mm) REVERT: i 86 MET cc_start: 0.0676 (mmm) cc_final: -0.0004 (mmm) REVERT: k 27 MET cc_start: 0.5314 (mmp) cc_final: 0.4760 (tpt) outliers start: 175 outliers final: 99 residues processed: 913 average time/residue: 0.9249 time to fit residues: 1455.2171 Evaluate side-chains 832 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 727 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 113 PHE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 2 ARG Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 79 LYS Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 77 LYS Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 55 THR Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 30 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 7 VAL Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 20 ASP Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 69 THR Chi-restraints excluded: chain i residue 409 GLN Chi-restraints excluded: chain k residue 37 LEU Chi-restraints excluded: chain l residue 376 ILE Chi-restraints excluded: chain l residue 419 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 566 optimal weight: 0.6980 chunk 386 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 506 optimal weight: 10.0000 chunk 280 optimal weight: 10.0000 chunk 580 optimal weight: 7.9990 chunk 470 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 347 optimal weight: 9.9990 chunk 610 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN J 31 GLN K 136 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 HIS ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN d 6 GLN ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 105838 Z= 0.297 Angle : 0.617 12.754 158007 Z= 0.319 Chirality : 0.036 0.318 20207 Planarity : 0.005 0.080 8670 Dihedral : 23.240 178.346 52228 Min Nonbonded Distance : 1.004 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.99 % Favored : 96.89 % Rotamer: Outliers : 6.46 % Allowed : 24.17 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.13), residues: 4015 helix: 0.21 (0.14), residues: 1303 sheet: -0.30 (0.18), residues: 794 loop : -0.38 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 78 HIS 0.008 0.001 HIS l 392 PHE 0.036 0.002 PHE l 365 TYR 0.026 0.002 TYR T 38 ARG 0.008 0.001 ARG U 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 758 time to evaluate : 5.949 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: C 72 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7208 (m-30) REVERT: C 181 MET cc_start: 0.8513 (mmm) cc_final: 0.7931 (mmm) REVERT: C 264 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6781 (m-30) REVERT: D 1 MET cc_start: 0.7479 (tmm) cc_final: 0.6660 (tmm) REVERT: D 30 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7512 (tm-30) REVERT: D 108 ASP cc_start: 0.7518 (m-30) cc_final: 0.7188 (p0) REVERT: D 139 SER cc_start: 0.8697 (m) cc_final: 0.8141 (p) REVERT: D 165 MET cc_start: 0.7956 (ttp) cc_final: 0.7430 (ttm) REVERT: E 199 MET cc_start: 0.7580 (ppp) cc_final: 0.7092 (ppp) REVERT: G 149 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7620 (tpt-90) REVERT: I 113 PHE cc_start: 0.2303 (OUTLIER) cc_final: 0.1738 (t80) REVERT: L 51 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7760 (pttm) REVERT: L 112 PHE cc_start: 0.8730 (m-10) cc_final: 0.8385 (m-10) REVERT: L 121 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7706 (tm-30) REVERT: N 136 MET cc_start: 0.5526 (OUTLIER) cc_final: 0.5275 (tpt) REVERT: O 2 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7524 (ttp-110) REVERT: P 69 ASP cc_start: 0.8379 (p0) cc_final: 0.8125 (p0) REVERT: R 89 GLU cc_start: 0.7026 (tp30) cc_final: 0.6766 (tp30) REVERT: S 51 VAL cc_start: 0.9345 (OUTLIER) cc_final: 0.9057 (m) REVERT: S 76 LYS cc_start: 0.9086 (mtpp) cc_final: 0.8765 (mtmm) REVERT: T 1 MET cc_start: 0.7647 (ppp) cc_final: 0.7396 (ppp) REVERT: T 15 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8215 (tm-30) REVERT: U 24 MET cc_start: 0.7785 (tpp) cc_final: 0.7565 (tpt) REVERT: W 42 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8456 (mt) REVERT: X 29 GLU cc_start: 0.6718 (pt0) cc_final: 0.6479 (pt0) REVERT: X 70 GLU cc_start: 0.7815 (pm20) cc_final: 0.7216 (pm20) REVERT: X 72 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8165 (mtmm) REVERT: Y 65 ASP cc_start: 0.8288 (p0) cc_final: 0.8011 (p0) REVERT: Z 25 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8099 (tm-30) REVERT: Z 40 SER cc_start: 0.8936 (p) cc_final: 0.8698 (p) REVERT: c 7 GLU cc_start: 0.7356 (pm20) cc_final: 0.6516 (pm20) REVERT: c 36 LEU cc_start: 0.8808 (mm) cc_final: 0.8495 (mp) REVERT: d 14 ARG cc_start: 0.9135 (ttm170) cc_final: 0.8727 (tpp80) REVERT: d 15 SER cc_start: 0.9169 (m) cc_final: 0.8621 (p) REVERT: d 22 MET cc_start: 0.8642 (tpp) cc_final: 0.8210 (tpp) REVERT: e 30 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8505 (mmt90) REVERT: e 61 CYS cc_start: 0.8139 (m) cc_final: 0.7930 (m) REVERT: f 20 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6884 (t0) REVERT: f 23 ILE cc_start: 0.9113 (mm) cc_final: 0.8814 (mm) REVERT: i 86 MET cc_start: 0.0699 (mmm) cc_final: 0.0016 (mmm) REVERT: i 202 MET cc_start: 0.5616 (mmm) cc_final: 0.5112 (mmt) REVERT: i 278 LYS cc_start: 0.5343 (tptp) cc_final: 0.5053 (tppt) REVERT: k 27 MET cc_start: 0.5315 (mmp) cc_final: 0.4809 (tpt) REVERT: l 449 ASP cc_start: -0.1931 (OUTLIER) cc_final: -0.4632 (t70) outliers start: 213 outliers final: 162 residues processed: 878 average time/residue: 0.9967 time to fit residues: 1523.1810 Evaluate side-chains 878 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 705 time to evaluate : 4.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 113 PHE Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 96 ARG Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 106 GLU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain N residue 25 ASP Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 2 ARG Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 110 MET Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 88 LYS Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 56 GLN Chi-restraints excluded: chain R residue 59 GLN Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 59 ILE Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 79 LYS Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 72 VAL Chi-restraints excluded: chain W residue 83 LYS Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 77 LYS Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 55 THR Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 20 ASP Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 30 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 7 VAL Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 20 ASP Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 69 THR Chi-restraints excluded: chain i residue 335 LEU Chi-restraints excluded: chain i residue 381 ASN Chi-restraints excluded: chain i residue 409 GLN Chi-restraints excluded: chain k residue 37 LEU Chi-restraints excluded: chain l residue 376 ILE Chi-restraints excluded: chain l residue 419 ILE Chi-restraints excluded: chain l residue 449 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 228 optimal weight: 10.0000 chunk 612 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 399 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 681 optimal weight: 7.9990 chunk 565 optimal weight: 4.9990 chunk 315 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 357 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 ASN T 7 HIS Y 23 ASN ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 105838 Z= 0.348 Angle : 0.644 12.400 158007 Z= 0.333 Chirality : 0.037 0.316 20207 Planarity : 0.005 0.077 8670 Dihedral : 23.249 177.846 52223 Min Nonbonded Distance : 1.003 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.36 % Favored : 96.54 % Rotamer: Outliers : 7.22 % Allowed : 24.33 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.42 (0.13), residues: 4015 helix: 0.22 (0.14), residues: 1294 sheet: -0.36 (0.18), residues: 811 loop : -0.45 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 78 HIS 0.006 0.001 HIS c 46 PHE 0.027 0.002 PHE l 365 TYR 0.022 0.002 TYR T 38 ARG 0.013 0.001 ARG J 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 750 time to evaluate : 4.400 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: C 82 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6790 (mt-10) REVERT: C 181 MET cc_start: 0.8434 (mmm) cc_final: 0.7941 (mmm) REVERT: C 264 ASP cc_start: 0.7298 (m-30) cc_final: 0.6831 (m-30) REVERT: D 1 MET cc_start: 0.7679 (tmm) cc_final: 0.6936 (tmm) REVERT: D 139 SER cc_start: 0.8658 (m) cc_final: 0.8178 (p) REVERT: D 165 MET cc_start: 0.7867 (ttp) cc_final: 0.7362 (ttm) REVERT: E 46 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8222 (mm-40) REVERT: E 199 MET cc_start: 0.7638 (ppp) cc_final: 0.7220 (ppp) REVERT: G 69 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7548 (tmm-80) REVERT: G 149 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7630 (tpt-90) REVERT: H 97 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.5809 (mpt180) REVERT: I 113 PHE cc_start: 0.1927 (OUTLIER) cc_final: 0.1358 (t80) REVERT: J 36 MET cc_start: 0.5563 (mmp) cc_final: 0.5355 (mmp) REVERT: L 51 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7802 (pttm) REVERT: L 93 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7696 (mm-40) REVERT: L 112 PHE cc_start: 0.8710 (m-10) cc_final: 0.8353 (m-10) REVERT: L 121 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7719 (tm-30) REVERT: O 56 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8966 (mtmm) REVERT: O 112 TYR cc_start: 0.9051 (m-10) cc_final: 0.8651 (m-10) REVERT: P 69 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8155 (p0) REVERT: Q 11 GLU cc_start: 0.8501 (pp20) cc_final: 0.8263 (pp20) REVERT: R 89 GLU cc_start: 0.7225 (tp30) cc_final: 0.6853 (tp30) REVERT: S 51 VAL cc_start: 0.9359 (OUTLIER) cc_final: 0.9084 (m) REVERT: S 76 LYS cc_start: 0.9109 (mtpp) cc_final: 0.8821 (mtmm) REVERT: T 15 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8276 (tm-30) REVERT: U 24 MET cc_start: 0.7821 (tpp) cc_final: 0.7371 (tpt) REVERT: W 42 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8471 (mt) REVERT: X 72 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8143 (mtpp) REVERT: Y 65 ASP cc_start: 0.8385 (p0) cc_final: 0.8117 (p0) REVERT: Z 25 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8195 (tm-30) REVERT: Z 40 SER cc_start: 0.8975 (p) cc_final: 0.8692 (p) REVERT: a 6 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8381 (mmmt) REVERT: c 36 LEU cc_start: 0.8750 (mm) cc_final: 0.8391 (mp) REVERT: d 15 SER cc_start: 0.9175 (m) cc_final: 0.8686 (p) REVERT: d 22 MET cc_start: 0.8647 (tpp) cc_final: 0.8014 (tpp) REVERT: e 30 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8561 (mmt90) REVERT: f 20 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6780 (t0) REVERT: f 23 ILE cc_start: 0.9111 (mm) cc_final: 0.8870 (mm) REVERT: i 86 MET cc_start: 0.0687 (mmm) cc_final: 0.0022 (mmm) REVERT: i 278 LYS cc_start: 0.5718 (tptp) cc_final: 0.5453 (tppt) REVERT: k 27 MET cc_start: 0.5244 (mmp) cc_final: 0.4756 (tpt) REVERT: l 449 ASP cc_start: -0.2141 (OUTLIER) cc_final: -0.4623 (t70) outliers start: 238 outliers final: 169 residues processed: 889 average time/residue: 0.9151 time to fit residues: 1405.1196 Evaluate side-chains 890 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 709 time to evaluate : 4.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 113 PHE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 106 GLU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain N residue 25 ASP Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 2 ARG Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 110 MET Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 88 LYS Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 56 GLN Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 79 LYS Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 72 VAL Chi-restraints excluded: chain W residue 83 LYS Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Y residue 77 LYS Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 29 ARG Chi-restraints excluded: chain Z residue 55 THR Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 20 ASP Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 30 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 7 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 20 ASP Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 69 THR Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain i residue 380 ILE Chi-restraints excluded: chain i residue 409 GLN Chi-restraints excluded: chain l residue 376 ILE Chi-restraints excluded: chain l residue 403 VAL Chi-restraints excluded: chain l residue 419 ILE Chi-restraints excluded: chain l residue 449 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 656 optimal weight: 50.0000 chunk 76 optimal weight: 10.0000 chunk 388 optimal weight: 0.7980 chunk 497 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 chunk 573 optimal weight: 5.9990 chunk 380 optimal weight: 1.9990 chunk 678 optimal weight: 20.0000 chunk 424 optimal weight: 8.9990 chunk 413 optimal weight: 1.9990 chunk 313 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN H 145 ASN R 20 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 ASN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 ASN Y 23 ASN Z 15 ASN ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 26 ASN ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 105838 Z= 0.205 Angle : 0.572 13.342 158007 Z= 0.297 Chirality : 0.034 0.315 20207 Planarity : 0.004 0.081 8670 Dihedral : 23.222 179.128 52222 Min Nonbonded Distance : 1.076 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.81 % Rotamer: Outliers : 5.61 % Allowed : 26.69 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.19 (0.13), residues: 4015 helix: 0.40 (0.14), residues: 1293 sheet: -0.27 (0.18), residues: 801 loop : -0.30 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 78 HIS 0.004 0.001 HIS N 13 PHE 0.029 0.001 PHE l 365 TYR 0.018 0.001 TYR T 38 ARG 0.008 0.000 ARG b 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 789 time to evaluate : 4.422 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: C 82 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6964 (mt-10) REVERT: C 103 TYR cc_start: 0.8703 (m-10) cc_final: 0.8387 (m-10) REVERT: C 181 MET cc_start: 0.8401 (mmm) cc_final: 0.8038 (mmm) REVERT: D 1 MET cc_start: 0.7714 (tmm) cc_final: 0.7229 (tmm) REVERT: D 139 SER cc_start: 0.8499 (m) cc_final: 0.7942 (p) REVERT: D 165 MET cc_start: 0.7757 (ttp) cc_final: 0.7278 (ttm) REVERT: E 46 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8128 (mm-40) REVERT: G 69 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7417 (tmm-80) REVERT: G 149 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7560 (tpt-90) REVERT: H 97 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.5534 (mpt180) REVERT: I 69 PHE cc_start: 0.6208 (m-10) cc_final: 0.5940 (m-10) REVERT: I 113 PHE cc_start: 0.2151 (OUTLIER) cc_final: 0.1675 (t80) REVERT: J 36 MET cc_start: 0.5544 (mmp) cc_final: 0.5340 (mmp) REVERT: L 51 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7703 (pttm) REVERT: L 93 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7787 (mm-40) REVERT: L 112 PHE cc_start: 0.8644 (m-10) cc_final: 0.8305 (m-10) REVERT: L 121 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7774 (tm-30) REVERT: Q 26 VAL cc_start: 0.9139 (t) cc_final: 0.8861 (p) REVERT: Q 44 GLU cc_start: 0.7421 (tp30) cc_final: 0.7074 (tp30) REVERT: R 89 GLU cc_start: 0.7133 (tp30) cc_final: 0.6728 (tp30) REVERT: S 51 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9079 (m) REVERT: S 76 LYS cc_start: 0.9073 (mtpp) cc_final: 0.8855 (mtmm) REVERT: T 1 MET cc_start: 0.7588 (ppp) cc_final: 0.7221 (ppp) REVERT: T 15 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8222 (tm-30) REVERT: U 24 MET cc_start: 0.7902 (tpp) cc_final: 0.7556 (tpt) REVERT: W 47 VAL cc_start: 0.9350 (m) cc_final: 0.9073 (t) REVERT: W 85 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8421 (mttp) REVERT: X 70 GLU cc_start: 0.7804 (pm20) cc_final: 0.7185 (pm20) REVERT: X 72 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8287 (mtmm) REVERT: Y 65 ASP cc_start: 0.8353 (p0) cc_final: 0.8120 (p0) REVERT: Z 25 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8120 (tm-30) REVERT: Z 40 SER cc_start: 0.8864 (p) cc_final: 0.8637 (p) REVERT: c 36 LEU cc_start: 0.8675 (mm) cc_final: 0.8373 (mp) REVERT: f 20 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6848 (t0) REVERT: f 23 ILE cc_start: 0.9089 (mm) cc_final: 0.8871 (mm) REVERT: i 86 MET cc_start: 0.0569 (mmm) cc_final: -0.0097 (mmm) REVERT: i 278 LYS cc_start: 0.5744 (tptp) cc_final: 0.5193 (tptm) REVERT: l 449 ASP cc_start: -0.2046 (OUTLIER) cc_final: -0.4447 (t0) outliers start: 185 outliers final: 133 residues processed: 893 average time/residue: 0.9200 time to fit residues: 1409.9461 Evaluate side-chains 870 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 728 time to evaluate : 5.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 113 PHE Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain N residue 25 ASP Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 2 ARG Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 110 MET Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 88 LYS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 79 LYS Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 83 LYS Chi-restraints excluded: chain W residue 85 LYS Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Y residue 77 LYS Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 55 THR Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 20 ASP Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 30 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 7 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 20 ASP Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 69 THR Chi-restraints excluded: chain i residue 105 MET Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain i residue 380 ILE Chi-restraints excluded: chain i residue 409 GLN Chi-restraints excluded: chain k residue 38 LEU Chi-restraints excluded: chain l residue 419 ILE Chi-restraints excluded: chain l residue 449 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 419 optimal weight: 0.0020 chunk 270 optimal weight: 10.0000 chunk 405 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 431 optimal weight: 0.0980 chunk 462 optimal weight: 0.9990 chunk 335 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 533 optimal weight: 1.9990 overall best weight: 1.2194 ------------------------------------------------------------------------------- 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** E 41 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN R 20 GLN R 56 GLN R 72 ASN S 82 HIS ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 4 GLN c 19 HIS d 6 GLN ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 105838 Z= 0.138 Angle : 0.546 15.169 158007 Z= 0.281 Chirality : 0.031 0.414 20207 Planarity : 0.004 0.119 8670 Dihedral : 23.142 178.459 52221 Min Nonbonded Distance : 1.167 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.91 % Favored : 96.99 % Rotamer: Outliers : 3.67 % Allowed : 28.94 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.06 (0.13), residues: 4015 helix: 0.58 (0.15), residues: 1285 sheet: -0.23 (0.18), residues: 813 loop : -0.25 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 78 HIS 0.005 0.001 HIS H 128 PHE 0.028 0.001 PHE l 365 TYR 0.020 0.001 TYR O 94 ARG 0.014 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 814 time to evaluate : 4.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6646 (mt-10) REVERT: C 103 TYR cc_start: 0.8548 (m-10) cc_final: 0.8166 (m-10) REVERT: C 146 MET cc_start: 0.8298 (mtm) cc_final: 0.7908 (mtp) REVERT: D 1 MET cc_start: 0.7748 (tmm) cc_final: 0.6764 (tmm) REVERT: D 139 SER cc_start: 0.8403 (m) cc_final: 0.7877 (p) REVERT: D 149 ASN cc_start: 0.8415 (t0) cc_final: 0.8028 (t0) REVERT: D 165 MET cc_start: 0.7696 (ttp) cc_final: 0.7130 (ttm) REVERT: E 46 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8051 (mm-40) REVERT: G 149 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7441 (tpt-90) REVERT: H 97 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5592 (mpt180) REVERT: K 131 ASN cc_start: 0.7581 (p0) cc_final: 0.7339 (p0) REVERT: L 51 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7688 (pttm) REVERT: L 93 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7631 (mm-40) REVERT: L 112 PHE cc_start: 0.8569 (m-10) cc_final: 0.8246 (m-10) REVERT: M 81 ASP cc_start: 0.6787 (m-30) cc_final: 0.6520 (m-30) REVERT: N 110 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7188 (tm-30) REVERT: O 2 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8054 (ttp80) REVERT: Q 11 GLU cc_start: 0.8514 (pp20) cc_final: 0.8282 (pp20) REVERT: Q 26 VAL cc_start: 0.9206 (t) cc_final: 0.8853 (p) REVERT: Q 44 GLU cc_start: 0.7442 (tp30) cc_final: 0.6999 (tp30) REVERT: T 1 MET cc_start: 0.7515 (ppp) cc_final: 0.7154 (ppp) REVERT: T 15 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8055 (tm-30) REVERT: U 6 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8306 (tpp80) REVERT: U 29 THR cc_start: 0.9131 (m) cc_final: 0.8908 (p) REVERT: W 47 VAL cc_start: 0.9333 (m) cc_final: 0.9082 (t) REVERT: W 69 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7305 (tm-30) REVERT: X 70 GLU cc_start: 0.7568 (pm20) cc_final: 0.6823 (pm20) REVERT: Z 25 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8165 (tm-30) REVERT: Z 40 SER cc_start: 0.8619 (p) cc_final: 0.8411 (p) REVERT: c 25 LYS cc_start: 0.7510 (tttp) cc_final: 0.7226 (tttp) REVERT: c 36 LEU cc_start: 0.8599 (mm) cc_final: 0.8289 (mp) REVERT: e 30 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8310 (mmt90) REVERT: f 3 VAL cc_start: 0.9151 (t) cc_final: 0.8720 (m) REVERT: f 20 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6785 (t0) REVERT: i 86 MET cc_start: 0.0560 (mmm) cc_final: 0.0008 (mmm) REVERT: l 394 MET cc_start: 0.3661 (mmm) cc_final: 0.2519 (mtm) REVERT: l 449 ASP cc_start: -0.2214 (OUTLIER) cc_final: -0.4425 (t0) outliers start: 121 outliers final: 91 residues processed: 889 average time/residue: 0.9221 time to fit residues: 1408.4178 Evaluate side-chains 850 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 752 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 2 ARG Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 110 MET Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 88 LYS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain S residue 37 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 79 LYS Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 77 LYS Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 20 ASP Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 30 LYS Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 20 ASP Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 69 THR Chi-restraints excluded: chain i residue 105 MET Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain i residue 224 MET Chi-restraints excluded: chain i residue 380 ILE Chi-restraints excluded: chain i residue 409 GLN Chi-restraints excluded: chain l residue 376 ILE Chi-restraints excluded: chain l residue 403 VAL Chi-restraints excluded: chain l residue 419 ILE Chi-restraints excluded: chain l residue 449 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 617 optimal weight: 8.9990 chunk 650 optimal weight: 50.0000 chunk 593 optimal weight: 9.9990 chunk 632 optimal weight: 7.9990 chunk 649 optimal weight: 6.9990 chunk 380 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 496 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 571 optimal weight: 6.9990 chunk 598 optimal weight: 0.0980 overall best weight: 5.8188 ------------------------------------------------------------------------------- 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** D 167 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN R 44 GLN R 56 GLN ** T 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 HIS c 45 GLN i 154 GLN ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 105838 Z= 0.280 Angle : 0.609 14.513 158007 Z= 0.313 Chirality : 0.034 0.331 20207 Planarity : 0.005 0.081 8670 Dihedral : 23.080 178.576 52220 Min Nonbonded Distance : 0.998 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 4.25 % Allowed : 28.45 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.16 (0.13), residues: 4015 helix: 0.47 (0.14), residues: 1294 sheet: -0.28 (0.18), residues: 831 loop : -0.30 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 78 HIS 0.007 0.001 HIS S 82 PHE 0.027 0.002 PHE l 365 TYR 0.016 0.002 TYR b 48 ARG 0.009 0.001 ARG J 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 747 time to evaluate : 4.474 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: C 82 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6778 (mt-10) REVERT: C 103 TYR cc_start: 0.8678 (m-10) cc_final: 0.8290 (m-10) REVERT: C 181 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7962 (mmt) REVERT: D 1 MET cc_start: 0.7904 (tmm) cc_final: 0.7602 (tmm) REVERT: D 94 GLN cc_start: 0.8342 (tt0) cc_final: 0.8142 (pt0) REVERT: D 139 SER cc_start: 0.8494 (m) cc_final: 0.7980 (p) REVERT: D 165 MET cc_start: 0.7736 (ttp) cc_final: 0.7179 (ttm) REVERT: E 46 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8077 (mm-40) REVERT: G 69 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8030 (tmm-80) REVERT: G 149 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7509 (tpt-90) REVERT: H 7 ASP cc_start: 0.8352 (p0) cc_final: 0.8076 (p0) REVERT: H 97 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.4750 (mpt-90) REVERT: K 131 ASN cc_start: 0.7705 (p0) cc_final: 0.7462 (p0) REVERT: L 51 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7733 (pttt) REVERT: L 93 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7776 (mm-40) REVERT: L 112 PHE cc_start: 0.8670 (m-10) cc_final: 0.8351 (m-10) REVERT: Q 26 VAL cc_start: 0.9194 (t) cc_final: 0.8905 (p) REVERT: Q 44 GLU cc_start: 0.7302 (tp30) cc_final: 0.6905 (tp30) REVERT: S 1 MET cc_start: 0.8197 (tmm) cc_final: 0.7721 (tpt) REVERT: T 1 MET cc_start: 0.7548 (ppp) cc_final: 0.7216 (ppp) REVERT: T 15 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8199 (tm-30) REVERT: T 92 ARG cc_start: 0.7604 (ptt-90) cc_final: 0.7397 (ptt-90) REVERT: U 6 ARG cc_start: 0.8641 (mmm-85) cc_final: 0.8332 (tpp80) REVERT: W 1 MET cc_start: 0.7699 (tpp) cc_final: 0.7393 (tpt) REVERT: W 47 VAL cc_start: 0.9353 (m) cc_final: 0.9113 (t) REVERT: X 72 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7967 (mtmm) REVERT: Z 25 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8192 (tm-30) REVERT: Z 40 SER cc_start: 0.8862 (p) cc_final: 0.8643 (p) REVERT: a 58 GLU cc_start: 0.7303 (pm20) cc_final: 0.6882 (pm20) REVERT: c 7 GLU cc_start: 0.7218 (pm20) cc_final: 0.6614 (pm20) REVERT: c 36 LEU cc_start: 0.8739 (mm) cc_final: 0.8438 (mp) REVERT: d 15 SER cc_start: 0.9238 (m) cc_final: 0.8612 (p) REVERT: i 86 MET cc_start: 0.0593 (mmm) cc_final: -0.0073 (mmm) outliers start: 140 outliers final: 119 residues processed: 828 average time/residue: 0.9164 time to fit residues: 1309.9422 Evaluate side-chains 843 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 719 time to evaluate : 4.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 2 ARG Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 110 MET Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 88 LYS Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 78 SER Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 79 LYS Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 83 LYS Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 77 LYS Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 55 THR Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 20 ASP Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 30 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 7 VAL Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 69 THR Chi-restraints excluded: chain i residue 105 MET Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain i residue 224 MET Chi-restraints excluded: chain i residue 380 ILE Chi-restraints excluded: chain i residue 409 GLN Chi-restraints excluded: chain l residue 376 ILE Chi-restraints excluded: chain l residue 403 VAL Chi-restraints excluded: chain l residue 419 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 630 optimal weight: 7.9990 chunk 415 optimal weight: 9.9990 chunk 668 optimal weight: 50.0000 chunk 408 optimal weight: 6.9990 chunk 317 optimal weight: 2.9990 chunk 464 optimal weight: 0.8980 chunk 701 optimal weight: 30.0000 chunk 645 optimal weight: 8.9990 chunk 558 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 431 optimal weight: 50.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 GLN k 29 GLN ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 105838 Z= 0.274 Angle : 0.616 15.342 158007 Z= 0.317 Chirality : 0.034 0.326 20207 Planarity : 0.005 0.080 8670 Dihedral : 23.138 177.799 52220 Min Nonbonded Distance : 1.017 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 3.91 % Allowed : 29.21 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.18 (0.13), residues: 4015 helix: 0.46 (0.15), residues: 1296 sheet: -0.28 (0.18), residues: 825 loop : -0.32 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 78 HIS 0.007 0.001 HIS S 82 PHE 0.029 0.002 PHE l 365 TYR 0.019 0.002 TYR K 75 ARG 0.013 0.001 ARG b 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 737 time to evaluate : 4.469 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: C 72 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7433 (m-30) REVERT: C 82 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6839 (mt-10) REVERT: C 103 TYR cc_start: 0.8710 (m-10) cc_final: 0.8349 (m-10) REVERT: C 132 MET cc_start: 0.7406 (mtm) cc_final: 0.7013 (mtp) REVERT: C 181 MET cc_start: 0.8196 (mmm) cc_final: 0.7911 (mmt) REVERT: C 188 CYS cc_start: 0.7320 (p) cc_final: 0.6177 (p) REVERT: D 1 MET cc_start: 0.7890 (tmm) cc_final: 0.7666 (tmm) REVERT: D 139 SER cc_start: 0.8658 (m) cc_final: 0.8243 (p) REVERT: D 165 MET cc_start: 0.7672 (ttp) cc_final: 0.7128 (ttm) REVERT: E 46 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8158 (mm-40) REVERT: G 69 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8039 (tmm-80) REVERT: G 149 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7561 (tpt-90) REVERT: H 7 ASP cc_start: 0.8378 (p0) cc_final: 0.8096 (p0) REVERT: H 83 LYS cc_start: 0.6776 (tptp) cc_final: 0.6502 (mtmt) REVERT: H 97 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.5731 (mpt180) REVERT: K 131 ASN cc_start: 0.7661 (p0) cc_final: 0.7441 (p0) REVERT: L 51 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7731 (pttm) REVERT: L 93 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7734 (mm-40) REVERT: L 112 PHE cc_start: 0.8671 (m-10) cc_final: 0.8302 (m-10) REVERT: Q 26 VAL cc_start: 0.9134 (t) cc_final: 0.8932 (p) REVERT: Q 44 GLU cc_start: 0.7303 (tp30) cc_final: 0.6962 (tp30) REVERT: S 1 MET cc_start: 0.8202 (tmm) cc_final: 0.7783 (tpt) REVERT: T 1 MET cc_start: 0.7534 (ppp) cc_final: 0.7211 (ppp) REVERT: T 15 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8203 (tm-30) REVERT: U 6 ARG cc_start: 0.8652 (mmm-85) cc_final: 0.8390 (tpp80) REVERT: W 1 MET cc_start: 0.7556 (tpp) cc_final: 0.7253 (tpt) REVERT: W 47 VAL cc_start: 0.9355 (m) cc_final: 0.9125 (t) REVERT: Z 25 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8158 (tm-30) REVERT: Z 40 SER cc_start: 0.8907 (p) cc_final: 0.8670 (p) REVERT: c 36 LEU cc_start: 0.8739 (mm) cc_final: 0.8430 (mp) REVERT: d 15 SER cc_start: 0.9236 (m) cc_final: 0.8600 (p) REVERT: f 23 ILE cc_start: 0.9058 (mm) cc_final: 0.8778 (mm) REVERT: i 86 MET cc_start: 0.0536 (mmm) cc_final: -0.0103 (mmm) REVERT: l 376 ILE cc_start: -0.0842 (OUTLIER) cc_final: -0.1147 (tp) outliers start: 129 outliers final: 114 residues processed: 813 average time/residue: 0.9208 time to fit residues: 1297.1629 Evaluate side-chains 839 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 719 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 25 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 110 MET Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 2 ASP Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 88 LYS Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 78 SER Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 79 LYS Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 ASN Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 70 GLU Chi-restraints excluded: chain Y residue 77 LYS Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 55 THR Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 30 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 69 THR Chi-restraints excluded: chain i residue 105 MET Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain i residue 224 MET Chi-restraints excluded: chain i residue 380 ILE Chi-restraints excluded: chain i residue 409 GLN Chi-restraints excluded: chain l residue 376 ILE Chi-restraints excluded: chain l residue 403 VAL Chi-restraints excluded: chain l residue 419 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 342 optimal weight: 10.0000 chunk 443 optimal weight: 7.9990 chunk 594 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 514 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 559 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 574 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- 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** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.055654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.041178 restraints weight = 529918.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.042269 restraints weight = 181722.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.042836 restraints weight = 99639.096| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 105838 Z= 0.326 Angle : 0.652 15.293 158007 Z= 0.334 Chirality : 0.036 0.332 20207 Planarity : 0.005 0.080 8670 Dihedral : 23.154 177.594 52220 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 4.16 % Allowed : 29.21 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.26 (0.13), residues: 4015 helix: 0.41 (0.14), residues: 1290 sheet: -0.38 (0.18), residues: 815 loop : -0.35 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 78 HIS 0.008 0.001 HIS S 82 PHE 0.029 0.002 PHE l 365 TYR 0.017 0.002 TYR L 32 ARG 0.009 0.001 ARG U 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22549.73 seconds wall clock time: 399 minutes 37.68 seconds (23977.68 seconds total)