Starting phenix.real_space_refine on Wed Mar 20 07:15:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/03_2024/7bl5_12218_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/03_2024/7bl5_12218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/03_2024/7bl5_12218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/03_2024/7bl5_12218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/03_2024/7bl5_12218_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/03_2024/7bl5_12218_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.034 sd= 0.789 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 3033 5.49 5 Mg 2 5.21 5 S 116 5.16 5 C 50225 2.51 5 N 18357 2.21 5 O 27193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G ASP 46": "OD1" <-> "OD2" Residue "G TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ASP 91": "OD1" <-> "OD2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 120": "OE1" <-> "OE2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ASP 26": "OD1" <-> "OD2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 45": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ASP 55": "OD1" <-> "OD2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 2": "OE1" <-> "OE2" Residue "S ASP 77": "OD1" <-> "OD2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 4": "OE1" <-> "OE2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U GLU 59": "OE1" <-> "OE2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U GLU 87": "OE1" <-> "OE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 11": "OD1" <-> "OD2" Residue "W GLU 13": "OE1" <-> "OE2" Residue "W GLU 25": "OE1" <-> "OE2" Residue "W PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "X TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z GLU 36": "OE1" <-> "OE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z GLU 57": "OE1" <-> "OE2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ASP 39": "OD1" <-> "OD2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "I PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ASP 81": "OD1" <-> "OD2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "6 ASP 35": "OD1" <-> "OD2" Residue "6 GLU 70": "OE1" <-> "OE2" Residue "6 ARG 96": "NH1" <-> "NH2" Residue "6 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 4": "NH1" <-> "NH2" Residue "7 ARG 19": "NH1" <-> "NH2" Residue "7 ARG 33": "NH1" <-> "NH2" Residue "7 GLU 57": "OE1" <-> "OE2" Residue "7 ARG 76": "NH1" <-> "NH2" Residue "7 GLU 78": "OE1" <-> "OE2" Residue "7 ASP 92": "OD1" <-> "OD2" Residue "7 ASP 101": "OD1" <-> "OD2" Residue "7 ARG 131": "NH1" <-> "NH2" Residue "7 ARG 157": "NH1" <-> "NH2" Residue "7 GLU 160": "OE1" <-> "OE2" Residue "7 GLU 166": "OE1" <-> "OE2" Residue "7 GLU 172": "OE1" <-> "OE2" Residue "7 ARG 196": "NH1" <-> "NH2" Residue "7 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 272": "NH1" <-> "NH2" Residue "7 ARG 276": "NH1" <-> "NH2" Residue "7 GLU 294": "OE1" <-> "OE2" Residue "7 GLU 307": "OE1" <-> "OE2" Residue "7 ASP 315": "OD1" <-> "OD2" Residue "8 ARG 90": "NH1" <-> "NH2" Residue "8 ASP 93": "OD1" <-> "OD2" Residue "8 PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 119": "OE1" <-> "OE2" Residue "8 ASP 144": "OD1" <-> "OD2" Residue "8 GLU 158": "OE1" <-> "OE2" Residue "8 ARG 169": "NH1" <-> "NH2" Residue "8 GLU 182": "OE1" <-> "OE2" Residue "9 GLU 6": "OE1" <-> "OE2" Residue "9 ARG 25": "NH1" <-> "NH2" Residue "9 GLU 48": "OE1" <-> "OE2" Residue "9 GLU 51": "OE1" <-> "OE2" Residue "9 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 129": "NH1" <-> "NH2" Residue "9 ARG 136": "NH1" <-> "NH2" Residue "9 GLU 151": "OE1" <-> "OE2" Residue "9 ARG 177": "NH1" <-> "NH2" Residue "9 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 206": "OE1" <-> "OE2" Residue "9 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 230": "NH1" <-> "NH2" Residue "9 ARG 239": "NH1" <-> "NH2" Residue "9 GLU 307": "OE1" <-> "OE2" Residue "9 TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 35": "OD1" <-> "OD2" Residue "b PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 98927 Number of models: 1 Model: "" Number of chains: 46 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: {'PTRANS': 6, '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: "G" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1281 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "J" 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: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "Q" 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: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" 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: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" 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: "V" 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: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" 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: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" 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: "0" 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: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" 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: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2548 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "P" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "6" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "7" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2533 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 23, 'TRANS': 293} Chain breaks: 1 Chain: "8" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1281 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "9" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2582 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain: "M" 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: "A" Number of atoms: 62534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2913, 62534 Classifications: {'RNA': 2913} Modifications used: {'rna2p_pur': 274, 'rna2p_pyr': 156, 'rna3p_pur': 1406, 'rna3p_pyr': 1077} Link IDs: {'rna2p': 430, 'rna3p': 2482} Chain breaks: 1 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: "e" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} 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: "b" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 364 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "9" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" 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: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 98635 SG CYS b 16 79.008 16.543 86.917 1.00241.22 S ATOM 98647 SG CYS b 18 81.272 13.966 87.816 1.00237.97 S ATOM 98789 SG CYS b 37 78.821 16.632 90.288 1.00237.10 S ATOM 98810 SG CYS b 40 79.991 14.096 90.093 1.00239.59 S Time building chain proxies: 38.78, per 1000 atoms: 0.39 Number of scatterers: 98927 At special positions: 0 Unit cell: (230.64, 225.68, 261.64, 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 116 16.00 P 3033 15.00 Mg 2 11.99 O 27193 8.00 N 18357 7.00 C 50225 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 43.50 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 100 " pdb="ZN ZN b 100 " - pdb=" SG CYS b 37 " pdb="ZN ZN b 100 " - pdb=" SG CYS b 40 " pdb="ZN ZN b 100 " - pdb=" SG CYS b 18 " pdb="ZN ZN b 100 " - pdb=" SG CYS b 16 " Number of angles added : 6 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 51 sheets defined 25.9% alpha, 15.3% beta 978 base pairs and 1556 stacking pairs defined. Time for finding SS restraints: 47.05 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 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.585A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.623A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 102 Processing helix chain 'D' and resid 121 through 124 No H-bonds generated for 'chain 'D' and resid 121 through 124' Processing helix chain 'E' and resid 25 through 39 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 161 Processing helix chain 'E' and resid 179 through 182 No H-bonds generated for 'chain 'E' and resid 179 through 182' Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'G' and resid 2 through 5 No H-bonds generated for 'chain 'G' and resid 2 through 5' Processing helix chain 'G' and resid 60 through 75 removed outlier: 3.523A pdb=" N GLN G 63 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY G 65 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG G 68 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL G 75 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.714A pdb=" N GLN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 37 Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 89 through 106 removed outlier: 3.531A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Proline residue: J 97 - end of helix removed outlier: 4.462A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.946A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'L' and resid 3 through 5 No H-bonds generated for 'chain 'L' and resid 3 through 5' Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 129 through 138 removed outlier: 3.591A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 46 removed outlier: 4.239A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 56 removed outlier: 3.759A pdb=" N ILE N 52 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR N 53 " --> pdb=" O GLU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 68 Processing helix chain 'N' and resid 73 through 78 Processing helix chain 'N' and resid 83 through 86 No H-bonds generated for 'chain 'N' and resid 83 through 86' Processing helix chain 'O' and resid 3 through 21 removed outlier: 4.110A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR O 12 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 83 removed outlier: 4.172A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 113 removed outlier: 3.710A pdb=" N LEU O 106 " --> pdb=" O ARG O 102 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 19 Processing helix chain 'Q' and resid 25 through 28 Processing helix chain 'Q' and resid 31 through 71 removed outlier: 4.291A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE Q 61 " --> pdb=" O ARG Q 57 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA Q 62 " --> pdb=" O GLN Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 84 Processing helix chain 'Q' and resid 91 through 100 Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.518A pdb=" N GLU Q 110 " --> pdb=" O THR Q 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 23 removed outlier: 3.553A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 37 Processing helix chain 'S' and resid 42 through 60 Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 4 through 9 removed outlier: 3.881A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 25 removed outlier: 4.418A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 50 removed outlier: 3.843A pdb=" N VAL T 47 " --> pdb=" O ILE T 43 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'V' and resid 14 through 23 removed outlier: 3.791A pdb=" N ALA V 22 " --> pdb=" O ARG V 18 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 52 removed outlier: 3.821A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 57 removed outlier: 4.001A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 54 through 57' Processing helix chain 'X' and resid 52 through 61 Processing helix chain 'X' and resid 63 through 73 Processing helix chain 'Y' and resid 5 through 7 No H-bonds generated for 'chain 'Y' and resid 5 through 7' Processing helix chain 'Y' and resid 10 through 23 removed outlier: 3.539A pdb=" N LEU Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 27 through 33 removed outlier: 3.770A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA Y 32 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 27 through 33' Processing helix chain 'Y' and resid 41 through 54 removed outlier: 4.092A pdb=" N ARG Y 48 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 41 through 50 removed outlier: 3.721A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 9 through 15 removed outlier: 3.564A pdb=" N ARG 0 15 " --> pdb=" O LYS 0 11 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 19 No H-bonds generated for 'chain '0' and resid 17 through 19' Processing helix chain '2' and resid 9 through 16 removed outlier: 3.532A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 21 No H-bonds generated for 'chain '2' and resid 18 through 21' Processing helix chain '2' and resid 25 through 37 Processing helix chain 'I' and resid 35 through 38 removed outlier: 4.074A pdb=" N CYS I 38 " --> pdb=" O MET I 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 45 through 48 No H-bonds generated for 'chain 'I' and resid 45 through 48' Processing helix chain 'I' and resid 77 through 80 removed outlier: 3.887A pdb=" N LYS I 80 " --> pdb=" O VAL I 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 77 through 80' Processing helix chain 'I' and resid 108 through 111 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 129 through 131 No H-bonds generated for 'chain 'I' and resid 129 through 131' Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 117 Processing helix chain 'P' and resid 5 through 11 removed outlier: 4.054A pdb=" N GLN P 9 " --> pdb=" O LYS P 5 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 5 through 11' Processing helix chain 'P' and resid 53 through 55 No H-bonds generated for 'chain 'P' and resid 53 through 55' Processing helix chain 'P' and resid 97 through 100 removed outlier: 3.600A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 100' Processing helix chain '6' and resid 3 through 17 removed outlier: 3.850A pdb=" N ASP 6 12 " --> pdb=" O ASP 6 8 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS 6 13 " --> pdb=" O PHE 6 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU 6 17 " --> pdb=" O LYS 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 61 removed outlier: 3.631A pdb=" N ALA 6 61 " --> pdb=" O GLN 6 57 " (cutoff:3.500A) Processing helix chain '6' and resid 92 through 97 removed outlier: 4.070A pdb=" N ARG 6 96 " --> pdb=" O GLU 6 92 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU 6 97 " --> pdb=" O GLU 6 93 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 92 through 97' Processing helix chain '7' and resid 20 through 27 removed outlier: 3.594A pdb=" N LEU 7 24 " --> pdb=" O LEU 7 20 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA 7 25 " --> pdb=" O ASP 7 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU 7 26 " --> pdb=" O GLN 7 22 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET 7 27 " --> pdb=" O ALA 7 23 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 20 through 27' Processing helix chain '7' and resid 33 through 41 removed outlier: 3.915A pdb=" N TRP 7 39 " --> pdb=" O ARG 7 35 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 122 Processing helix chain '7' and resid 124 through 128 removed outlier: 3.959A pdb=" N ALA 7 127 " --> pdb=" O PRO 7 124 " (cutoff:3.500A) Processing helix chain '7' and resid 130 through 133 Processing helix chain '7' and resid 152 through 164 Processing helix chain '7' and resid 235 through 241 Processing helix chain '7' and resid 265 through 273 Processing helix chain '7' and resid 303 through 319 Processing helix chain '8' and resid 29 through 47 Processing helix chain '8' and resid 51 through 56 removed outlier: 3.832A pdb=" N ASP 8 55 " --> pdb=" O LYS 8 51 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS 8 56 " --> pdb=" O ASN 8 52 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 51 through 56' Processing helix chain '8' and resid 61 through 72 removed outlier: 3.688A pdb=" N LEU 8 69 " --> pdb=" O ALA 8 65 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN 8 71 " --> pdb=" O ILE 8 67 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG 8 72 " --> pdb=" O GLU 8 68 " (cutoff:3.500A) Processing helix chain '8' and resid 75 through 90 removed outlier: 3.502A pdb=" N MET 8 88 " --> pdb=" O LEU 8 84 " (cutoff:3.500A) Processing helix chain '8' and resid 95 through 104 Processing helix chain '8' and resid 109 through 126 removed outlier: 3.720A pdb=" N ARG 8 122 " --> pdb=" O LEU 8 118 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP 8 123 " --> pdb=" O GLU 8 119 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG 8 124 " --> pdb=" O ASN 8 120 " (cutoff:3.500A) Processing helix chain '8' and resid 133 through 139 Processing helix chain '8' and resid 145 through 160 removed outlier: 4.031A pdb=" N THR 8 150 " --> pdb=" O GLN 8 146 " (cutoff:3.500A) Processing helix chain '8' and resid 168 through 180 removed outlier: 3.662A pdb=" N PHE 8 172 " --> pdb=" O ALA 8 168 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU 8 180 " --> pdb=" O ARG 8 176 " (cutoff:3.500A) Processing helix chain '9' and resid 57 through 61 Processing helix chain '9' and resid 128 through 130 No H-bonds generated for 'chain '9' and resid 128 through 130' Processing helix chain '9' and resid 172 through 176 Processing helix chain '9' and resid 229 through 234 removed outlier: 5.018A pdb=" N HIS 9 234 " --> pdb=" O ARG 9 230 " (cutoff:3.500A) Processing helix chain '9' and resid 258 through 267 removed outlier: 4.273A pdb=" N ILE 9 263 " --> pdb=" O ALA 9 259 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU 9 266 " --> pdb=" O ILE 9 262 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU 9 267 " --> pdb=" O ILE 9 263 " (cutoff:3.500A) Processing helix chain '9' and resid 272 through 275 Processing helix chain '9' and resid 292 through 303 removed outlier: 4.013A pdb=" N LYS 9 296 " --> pdb=" O GLU 9 292 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA 9 297 " --> pdb=" O ALA 9 293 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA 9 301 " --> pdb=" O ALA 9 297 " (cutoff:3.500A) Processing helix chain '9' and resid 321 through 334 Processing helix chain 'M' and resid 43 through 56 removed outlier: 4.086A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.688A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 26 No H-bonds generated for 'chain 'H' and resid 23 through 26' Processing helix chain 'H' and resid 43 through 58 removed outlier: 3.593A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 74 removed outlier: 3.520A pdb=" N ALA H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (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 106 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'e' and resid 5 through 20 removed outlier: 3.725A pdb=" N ALA e 19 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS e 20 " --> pdb=" O SER e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 34 through 40 removed outlier: 3.569A pdb=" N THR e 39 " --> pdb=" O VAL e 35 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 Processing helix chain 'e' and resid 64 through 66 No H-bonds generated for 'chain 'e' and resid 64 through 66' Processing helix chain 'e' and resid 72 through 78 removed outlier: 4.222A pdb=" N PHE e 76 " --> pdb=" O LYS e 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL e 77 " --> pdb=" O ASP e 74 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY e 78 " --> pdb=" O ALA e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 94 through 101 removed outlier: 4.034A pdb=" N PHE e 99 " --> pdb=" O PHE e 96 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 113 No H-bonds generated for 'chain 'e' and resid 111 through 113' Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 11 through 19 removed outlier: 3.577A pdb=" N MET F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 59 Processing helix chain 'F' and resid 94 through 104 removed outlier: 3.719A pdb=" N ARG F 101 " --> pdb=" O GLU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 109 No H-bonds generated for 'chain 'F' and resid 107 through 109' Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.629A pdb=" N ARG F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'C' and resid 100 through 104 removed outlier: 5.762A pdb=" N LEU C 94 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL C 77 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= D, first strand: chain 'C' and resid 180 through 184 removed outlier: 4.089A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.563A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 78 through 83 removed outlier: 3.929A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 167 through 171 removed outlier: 7.166A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS E 185 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE E 149 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL E 187 " --> pdb=" O ILE E 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'G' and resid 17 through 19 removed outlier: 4.373A pdb=" N VAL G 22 " --> pdb=" O ASN G 19 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 160 through 163 removed outlier: 3.643A pdb=" N PHE G 82 " --> pdb=" O GLY G 134 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 86 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE G 130 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= K, first strand: chain 'J' and resid 138 through 140 removed outlier: 4.616A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= M, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.493A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= O, first strand: chain 'O' and resid 25 through 27 Processing sheet with id= P, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.531A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.132A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.303A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.141A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'S' and resid 81 through 87 removed outlier: 3.992A pdb=" N MET S 82 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS S 98 " --> pdb=" O MET S 82 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.398A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU T 61 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'U' and resid 21 through 23 Processing sheet with id= W, first strand: chain 'U' and resid 40 through 45 removed outlier: 3.774A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY U 56 " --> pdb=" O GLN U 45 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'U' and resid 82 through 86 Processing sheet with id= Y, first strand: chain 'U' and resid 24 through 27 removed outlier: 7.001A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'V' and resid 3 through 5 removed outlier: 6.973A pdb=" N THR V 62 " --> pdb=" O ILE V 4 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE V 29 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE V 91 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR V 31 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU V 41 " --> pdb=" O GLU V 7 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU V 7 " --> pdb=" O GLU V 41 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'W' and resid 47 through 49 Processing sheet with id= AB, first strand: chain 'W' and resid 62 through 68 Processing sheet with id= AC, first strand: chain 'X' and resid 12 through 15 Processing sheet with id= AD, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.718A pdb=" N VAL X 39 " --> pdb=" O ARG X 44 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id= AF, first strand: chain '1' and resid 6 through 11 Processing sheet with id= AG, first strand: chain '1' and resid 35 through 39 removed outlier: 3.528A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 98 through 101 Processing sheet with id= AI, first strand: chain 'K' and resid 6 through 9 removed outlier: 6.739A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'P' and resid 82 through 87 removed outlier: 3.781A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY P 44 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain '6' and resid 23 through 26 removed outlier: 3.656A pdb=" N ILE 6 23 " --> pdb=" O ILE 6 39 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL 6 89 " --> pdb=" O ILE 6 78 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE 6 78 " --> pdb=" O VAL 6 89 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '7' and resid 4 through 10 removed outlier: 4.401A pdb=" N ALA 7 69 " --> pdb=" O VAL 7 5 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 144 through 149 removed outlier: 6.250A pdb=" N ASN 7 97 " --> pdb=" O ILE 7 86 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE 7 86 " --> pdb=" O ASN 7 97 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 169 through 176 removed outlier: 4.292A pdb=" N ARG 7 169 " --> pdb=" O LEU 7 228 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 283 through 287 removed outlier: 3.568A pdb=" N TRP 7 297 " --> pdb=" O LEU 7 284 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 7 286 " --> pdb=" O MET 7 295 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '9' and resid 64 through 66 removed outlier: 8.773A pdb=" N PHE 9 65 " --> pdb=" O SER 9 8 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU 9 10 " --> pdb=" O PHE 9 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA 9 7 " --> pdb=" O LEU 9 154 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG 9 150 " --> pdb=" O VAL 9 11 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '9' and resid 86 through 91 removed outlier: 3.639A pdb=" N ALA 9 118 " --> pdb=" O VAL 9 45 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET 9 47 " --> pdb=" O LEU 9 116 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU 9 116 " --> pdb=" O MET 9 47 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA 9 49 " --> pdb=" O ARG 9 114 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ARG 9 114 " --> pdb=" O ALA 9 49 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '9' and resid 162 through 166 removed outlier: 5.855A pdb=" N VAL 9 240 " --> pdb=" O GLY 9 163 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU 9 165 " --> pdb=" O VAL 9 240 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU 9 242 " --> pdb=" O LEU 9 165 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain '9' and resid 199 through 201 Processing sheet with id= AT, first strand: chain 'M' and resid 128 through 132 removed outlier: 3.606A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'M' and resid 39 through 42 removed outlier: 3.621A pdb=" N GLY M 39 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU M 90 " --> pdb=" O ILE M 73 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TRP M 92 " --> pdb=" O LYS M 71 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LYS M 71 " --> pdb=" O TRP M 92 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.544A pdb=" N ILE H 4 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 78 through 82 removed outlier: 4.049A pdb=" N ILE H 80 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL H 147 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'F' and resid 152 through 155 removed outlier: 7.103A pdb=" N THR F 67 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N CYS F 86 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU F 65 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'b' and resid 21 through 24 removed outlier: 3.756A pdb=" N ILE b 24 " --> pdb=" O ILE b 12 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE b 12 " --> pdb=" O ILE b 24 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU b 32 " --> pdb=" O SER b 15 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2474 hydrogen bonds 3866 hydrogen bond angles 0 basepair planarities 978 basepair parallelities 1556 stacking parallelities Total time for adding SS restraints: 146.00 Time building geometry restraints manager: 46.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17762 1.33 - 1.46: 42727 1.46 - 1.58: 40420 1.58 - 1.70: 6063 1.70 - 1.82: 210 Bond restraints: 107182 Sorted by residual: bond pdb=" C2 C A 106 " pdb=" O2 C A 106 " ideal model delta sigma weight residual 1.240 1.216 0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" CA VAL 6 27 " pdb=" C VAL 6 27 " ideal model delta sigma weight residual 1.520 1.534 -0.014 1.23e-02 6.61e+03 1.33e+00 bond pdb=" C3' G A 271 " pdb=" O3' G A 271 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.25e+00 bond pdb=" C PRO I 21 " pdb=" N PRO I 22 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.16e+00 bond pdb=" C3' U A2249 " pdb=" O3' U A2249 " ideal model delta sigma weight residual 1.427 1.443 -0.016 1.50e-02 4.44e+03 1.16e+00 ... (remaining 107177 not shown) Histogram of bond angle deviations from ideal: 98.87 - 106.34: 18100 106.34 - 113.81: 66496 113.81 - 121.28: 47690 121.28 - 128.75: 24383 128.75 - 136.23: 3109 Bond angle restraints: 159778 Sorted by residual: angle pdb=" C PRO V 81 " pdb=" N TYR V 82 " pdb=" CA TYR V 82 " ideal model delta sigma weight residual 121.54 114.09 7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C SER L 68 " pdb=" N ARG L 69 " pdb=" CA ARG L 69 " ideal model delta sigma weight residual 121.54 128.79 -7.25 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C3' U A2249 " pdb=" O3' U A2249 " pdb=" P G A2250 " ideal model delta sigma weight residual 120.20 125.08 -4.88 1.50e+00 4.44e-01 1.06e+01 angle pdb=" C3' G A 271 " pdb=" O3' G A 271 " pdb=" P A A 272 " ideal model delta sigma weight residual 120.20 125.07 -4.87 1.50e+00 4.44e-01 1.05e+01 angle pdb=" CB MET 6 49 " pdb=" CG MET 6 49 " pdb=" SD MET 6 49 " ideal model delta sigma weight residual 112.70 121.77 -9.07 3.00e+00 1.11e-01 9.14e+00 ... (remaining 159773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 60219 35.68 - 71.36: 7339 71.36 - 107.03: 853 107.03 - 142.71: 13 142.71 - 178.39: 9 Dihedral angle restraints: 68433 sinusoidal: 56094 harmonic: 12339 Sorted by residual: dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 62.30 137.70 1 1.50e+01 4.44e-03 7.42e+01 dihedral pdb=" O4' C A1914 " pdb=" C1' C A1914 " pdb=" N1 C A1914 " pdb=" C2 C A1914 " ideal model delta sinusoidal sigma weight residual -128.00 50.39 -178.39 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A1915 " pdb=" C1' U A1915 " pdb=" N1 U A1915 " pdb=" C2 U A1915 " ideal model delta sinusoidal sigma weight residual -128.00 50.32 -178.32 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 68430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 18121 0.039 - 0.078: 1616 0.078 - 0.117: 555 0.117 - 0.155: 50 0.155 - 0.194: 6 Chirality restraints: 20348 Sorted by residual: chirality pdb=" C3' G A 271 " pdb=" C4' G A 271 " pdb=" O3' G A 271 " pdb=" C2' G A 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" C3' U A2249 " pdb=" C4' U A2249 " pdb=" O3' U A2249 " pdb=" C2' U A2249 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" C1' U A1313 " pdb=" O4' U A1313 " pdb=" C2' U A1313 " pdb=" N1 U A1313 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 20345 not shown) Planarity restraints: 9003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 106 " 0.005 2.00e-02 2.50e+03 2.75e-02 1.70e+01 pdb=" N1 C A 106 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C A 106 " -0.068 2.00e-02 2.50e+03 pdb=" O2 C A 106 " 0.043 2.00e-02 2.50e+03 pdb=" N3 C A 106 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C A 106 " -0.008 2.00e-02 2.50e+03 pdb=" N4 C A 106 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C A 106 " 0.012 2.00e-02 2.50e+03 pdb=" C6 C A 106 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY e 78 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO e 79 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO e 79 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO e 79 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A 81 " -0.005 2.00e-02 2.50e+03 1.30e-02 5.08e+00 pdb=" N9 G A 81 " 0.001 2.00e-02 2.50e+03 pdb=" C8 G A 81 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A 81 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G A 81 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A 81 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 81 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G A 81 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 81 " 0.035 2.00e-02 2.50e+03 pdb=" N2 G A 81 " -0.026 2.00e-02 2.50e+03 pdb=" N3 G A 81 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G A 81 " -0.001 2.00e-02 2.50e+03 ... (remaining 9000 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 2101 2.60 - 3.18: 78741 3.18 - 3.75: 197015 3.75 - 4.33: 256457 4.33 - 4.90: 349208 Nonbonded interactions: 883522 Sorted by model distance: nonbonded pdb=" O SER F 117 " pdb=" OH TYR F 127 " model vdw 2.029 2.440 nonbonded pdb=" N2 G A2294 " pdb=" O2 C A2338 " model vdw 2.076 2.496 nonbonded pdb=" O2B GDP 91001 " pdb="MG MG 91002 " model vdw 2.099 2.170 nonbonded pdb=" OG SER 7 34 " pdb=" OP2 U A1923 " model vdw 2.107 2.440 nonbonded pdb=" N2 G A1948 " pdb=" O6 G A1959 " model vdw 2.125 2.520 ... (remaining 883517 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.810 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: 0.130 Extract box with map and model: 8.530 Check model and map are aligned: 1.120 Set scattering table: 0.740 Process input model: 359.970 Find NCS groups from input model: 1.850 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 375.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 : 0.002 0.031 107182 Z= 0.109 Angle : 0.451 9.806 159778 Z= 0.242 Chirality : 0.027 0.194 20348 Planarity : 0.003 0.067 9003 Dihedral : 22.798 178.388 60485 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.11 % Allowed : 0.28 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 4280 helix: -0.33 (0.16), residues: 1057 sheet: 0.26 (0.20), residues: 744 loop : -1.17 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 9 326 HIS 0.011 0.001 HIS G 110 PHE 0.021 0.001 PHE V 56 TYR 0.022 0.001 TYR K 32 ARG 0.015 0.001 ARG R 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 991 time to evaluate : 4.528 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: E 43 THR cc_start: 0.8352 (p) cc_final: 0.8047 (p) REVERT: G 74 MET cc_start: 0.7905 (ptt) cc_final: 0.7559 (ptp) REVERT: G 146 ASP cc_start: 0.8269 (m-30) cc_final: 0.7929 (m-30) REVERT: G 166 GLU cc_start: 0.7297 (pp20) cc_final: 0.6940 (pp20) REVERT: J 57 LEU cc_start: 0.9315 (mt) cc_final: 0.9091 (mt) REVERT: L 93 ASN cc_start: 0.8377 (m110) cc_final: 0.8126 (m-40) REVERT: N 75 ILE cc_start: 0.8766 (mm) cc_final: 0.8409 (mm) REVERT: N 100 CYS cc_start: 0.8036 (p) cc_final: 0.7776 (p) REVERT: O 117 PHE cc_start: 0.6440 (p90) cc_final: 0.5445 (p90) REVERT: R 41 ILE cc_start: 0.9309 (mp) cc_final: 0.8951 (mp) REVERT: R 68 ARG cc_start: 0.8342 (mtp-110) cc_final: 0.8136 (mtp-110) REVERT: T 3 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7777 (mtm110) REVERT: T 39 THR cc_start: 0.8054 (p) cc_final: 0.7826 (p) REVERT: V 91 PHE cc_start: 0.5618 (m-80) cc_final: 0.5400 (m-80) REVERT: W 39 THR cc_start: 0.8459 (p) cc_final: 0.8221 (p) REVERT: W 52 ASP cc_start: 0.8603 (p0) cc_final: 0.8337 (p0) REVERT: X 69 GLU cc_start: 0.8767 (tp30) cc_final: 0.8556 (tp30) REVERT: Y 47 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8398 (ttp80) REVERT: Y 48 ARG cc_start: 0.8820 (mmt-90) cc_final: 0.8601 (mmt-90) REVERT: Y 49 ASP cc_start: 0.7950 (m-30) cc_final: 0.7331 (m-30) REVERT: 1 24 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8526 (pttt) REVERT: 1 25 ASN cc_start: 0.8813 (t0) cc_final: 0.7997 (t0) REVERT: I 35 MET cc_start: 0.6021 (ttm) cc_final: 0.5301 (ppp) REVERT: 7 15 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6802 (mp10) REVERT: 7 188 PRO cc_start: 0.7560 (Cg_exo) cc_final: 0.7288 (Cg_endo) REVERT: 7 307 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6756 (tm-30) REVERT: 8 95 GLU cc_start: 0.8426 (tp30) cc_final: 0.7872 (tp30) REVERT: 8 104 LEU cc_start: 0.9105 (tt) cc_final: 0.8378 (mt) REVERT: 9 50 ASP cc_start: 0.8373 (t70) cc_final: 0.7814 (t0) REVERT: 9 71 GLN cc_start: 0.7724 (mm110) cc_final: 0.7470 (mm110) REVERT: 9 331 PHE cc_start: 0.7746 (t80) cc_final: 0.7491 (t80) REVERT: M 12 MET cc_start: 0.4811 (tpp) cc_final: 0.3868 (ttm) REVERT: F 100 GLU cc_start: 0.7936 (mm-30) cc_final: 0.6633 (tm-30) REVERT: b 1 MET cc_start: 0.4482 (tmm) cc_final: 0.4077 (mtm) outliers start: 4 outliers final: 1 residues processed: 992 average time/residue: 0.9055 time to fit residues: 1562.4921 Evaluate side-chains 830 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 828 time to evaluate : 4.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 9 residue 143 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 610 optimal weight: 20.0000 chunk 548 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 369 optimal weight: 30.0000 chunk 292 optimal weight: 30.0000 chunk 566 optimal weight: 10.0000 chunk 219 optimal weight: 0.6980 chunk 344 optimal weight: 20.0000 chunk 421 optimal weight: 20.0000 chunk 656 optimal weight: 10.0000 overall best weight: 7.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN O 38 GLN O 104 GLN Q 51 GLN Q 55 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN Y 20 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN 0 41 HIS 2 16 HIS 2 29 GLN P 11 GLN 6 20 GLN 6 47 HIS ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 91 GLN 8 154 ASN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 HIS H 43 ASN b 41 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 107182 Z= 0.363 Angle : 0.691 12.363 159778 Z= 0.348 Chirality : 0.037 0.291 20348 Planarity : 0.005 0.074 9003 Dihedral : 23.340 179.975 52051 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.53 % Allowed : 14.47 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.12), residues: 4280 helix: -0.49 (0.15), residues: 1126 sheet: -0.28 (0.19), residues: 760 loop : -1.33 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP C 212 HIS 0.012 0.002 HIS 8 108 PHE 0.032 0.003 PHE C 29 TYR 0.039 0.003 TYR O 99 ARG 0.011 0.001 ARG S 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 917 time to evaluate : 4.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 156 SER cc_start: 0.8916 (t) cc_final: 0.8699 (t) REVERT: C 247 TRP cc_start: 0.8376 (m100) cc_final: 0.7975 (m100) REVERT: D 79 LEU cc_start: 0.8587 (tp) cc_final: 0.8371 (tp) REVERT: E 78 TRP cc_start: 0.7616 (m-10) cc_final: 0.7362 (m-10) REVERT: G 74 MET cc_start: 0.7823 (ptt) cc_final: 0.7346 (ptp) REVERT: G 166 GLU cc_start: 0.7400 (pp20) cc_final: 0.7050 (pp20) REVERT: J 102 GLU cc_start: 0.8438 (mp0) cc_final: 0.8053 (mp0) REVERT: L 93 ASN cc_start: 0.8508 (m110) cc_final: 0.8206 (m-40) REVERT: N 73 ASN cc_start: 0.7772 (t0) cc_final: 0.7549 (t0) REVERT: N 100 CYS cc_start: 0.8482 (p) cc_final: 0.8179 (p) REVERT: O 30 ARG cc_start: 0.6684 (mtm110) cc_final: 0.6399 (mtm-85) REVERT: Q 55 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8203 (mm-40) REVERT: Q 70 GLN cc_start: 0.8633 (tp-100) cc_final: 0.7943 (tp-100) REVERT: Q 101 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7457 (p0) REVERT: R 85 LYS cc_start: 0.8654 (ptmt) cc_final: 0.8301 (mtpt) REVERT: S 8 ARG cc_start: 0.8093 (mtt90) cc_final: 0.7697 (mtt90) REVERT: S 34 ASP cc_start: 0.8415 (m-30) cc_final: 0.8214 (m-30) REVERT: T 1 MET cc_start: 0.4579 (mmp) cc_final: 0.3967 (mmt) REVERT: T 3 ARG cc_start: 0.8021 (mtp85) cc_final: 0.7776 (mtm180) REVERT: T 28 ASN cc_start: 0.8811 (t0) cc_final: 0.8456 (t0) REVERT: V 5 ASN cc_start: 0.7337 (p0) cc_final: 0.6940 (m-40) REVERT: V 81 PRO cc_start: 0.7392 (Cg_exo) cc_final: 0.7039 (Cg_endo) REVERT: V 91 PHE cc_start: 0.6695 (m-80) cc_final: 0.6386 (m-80) REVERT: W 39 THR cc_start: 0.8471 (p) cc_final: 0.8217 (p) REVERT: W 52 ASP cc_start: 0.8720 (p0) cc_final: 0.8464 (p0) REVERT: W 64 LYS cc_start: 0.8474 (pttt) cc_final: 0.8271 (pttp) REVERT: X 55 MET cc_start: 0.8632 (mtp) cc_final: 0.8153 (mtp) REVERT: Y 17 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8330 (tm-30) REVERT: Y 19 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8569 (mm) REVERT: Y 44 LYS cc_start: 0.8948 (tptp) cc_final: 0.8590 (tptt) REVERT: Y 49 ASP cc_start: 0.8048 (m-30) cc_final: 0.7535 (m-30) REVERT: 1 25 ASN cc_start: 0.8712 (t0) cc_final: 0.7908 (t0) REVERT: 2 18 PHE cc_start: 0.8062 (t80) cc_final: 0.7675 (t80) REVERT: 2 22 MET cc_start: 0.8307 (mpp) cc_final: 0.7728 (mpp) REVERT: I 35 MET cc_start: 0.6133 (ttm) cc_final: 0.5234 (ppp) REVERT: K 3 GLN cc_start: 0.8110 (pt0) cc_final: 0.7903 (pt0) REVERT: P 26 GLU cc_start: 0.8021 (tp30) cc_final: 0.7712 (tp30) REVERT: 6 90 MET cc_start: 0.7740 (tpp) cc_final: 0.7221 (mmp) REVERT: 7 15 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: 7 179 MET cc_start: 0.7711 (mmp) cc_final: 0.7163 (mmp) REVERT: 7 204 MET cc_start: 0.5938 (ttt) cc_final: 0.5551 (ttm) REVERT: 7 288 HIS cc_start: 0.2917 (OUTLIER) cc_final: 0.2058 (m-70) REVERT: 8 88 MET cc_start: 0.8120 (pmm) cc_final: 0.7635 (pmm) REVERT: 8 93 ASP cc_start: 0.8410 (p0) cc_final: 0.8185 (p0) REVERT: 8 111 GLN cc_start: 0.8444 (tp40) cc_final: 0.8119 (tp-100) REVERT: 9 26 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6258 (tt0) REVERT: 9 50 ASP cc_start: 0.8145 (t70) cc_final: 0.7919 (t0) REVERT: 9 105 MET cc_start: 0.8007 (mmm) cc_final: 0.7645 (mtt) REVERT: 9 116 LEU cc_start: 0.8422 (tp) cc_final: 0.8134 (tt) REVERT: 9 331 PHE cc_start: 0.8039 (t80) cc_final: 0.7812 (t80) REVERT: M 1 MET cc_start: 0.6773 (OUTLIER) cc_final: 0.6402 (ppp) REVERT: M 53 MET cc_start: 0.7236 (mtm) cc_final: 0.5674 (tmm) REVERT: M 100 LYS cc_start: 0.5015 (pttm) cc_final: 0.4575 (mtmm) REVERT: M 105 MET cc_start: 0.7747 (tpp) cc_final: 0.7332 (tmm) REVERT: F 25 MET cc_start: 0.7854 (tmm) cc_final: 0.7389 (tmm) REVERT: F 50 ASP cc_start: 0.7738 (m-30) cc_final: 0.7513 (m-30) REVERT: F 78 ILE cc_start: 0.6185 (mm) cc_final: 0.5699 (tp) REVERT: F 137 PHE cc_start: 0.7729 (m-80) cc_final: 0.7075 (m-80) outliers start: 125 outliers final: 88 residues processed: 974 average time/residue: 0.9207 time to fit residues: 1541.5920 Evaluate side-chains 907 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 812 time to evaluate : 4.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 36 CYS Chi-restraints excluded: chain 6 residue 78 ILE Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 115 VAL Chi-restraints excluded: chain 7 residue 209 VAL Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 252 VAL Chi-restraints excluded: chain 7 residue 288 HIS Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 123 ASP Chi-restraints excluded: chain 8 residue 154 ASN Chi-restraints excluded: chain 9 residue 8 SER Chi-restraints excluded: chain 9 residue 26 GLU Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 62 GLU Chi-restraints excluded: chain 9 residue 111 HIS Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 205 ASN Chi-restraints excluded: chain 9 residue 217 LEU Chi-restraints excluded: chain 9 residue 291 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain F residue 141 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 364 optimal weight: 9.9990 chunk 203 optimal weight: 8.9990 chunk 546 optimal weight: 10.0000 chunk 447 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 657 optimal weight: 10.0000 chunk 710 optimal weight: 5.9990 chunk 585 optimal weight: 10.0000 chunk 652 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 527 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 HIS ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN Q 55 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN S 7 HIS T 91 GLN X 22 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN 0 18 HIS 2 16 HIS 2 29 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN 6 47 HIS ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 117 ASN ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 108 HIS ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 107182 Z= 0.357 Angle : 0.673 12.590 159778 Z= 0.343 Chirality : 0.038 0.285 20348 Planarity : 0.005 0.098 9003 Dihedral : 23.467 179.297 52049 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.31 % Allowed : 18.93 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -1.60 (0.12), residues: 4280 helix: -0.53 (0.15), residues: 1129 sheet: -0.49 (0.18), residues: 758 loop : -1.53 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP 7 39 HIS 0.043 0.002 HIS 2 16 PHE 0.055 0.003 PHE R 53 TYR 0.035 0.003 TYR O 99 ARG 0.022 0.001 ARG H 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 890 time to evaluate : 4.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 212 TRP cc_start: 0.7924 (p90) cc_final: 0.7616 (p90) REVERT: C 247 TRP cc_start: 0.8388 (m100) cc_final: 0.7849 (m100) REVERT: D 90 PHE cc_start: 0.8320 (m-80) cc_final: 0.7838 (m-10) REVERT: E 25 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7637 (tm-30) REVERT: E 199 MET cc_start: 0.9095 (ptm) cc_final: 0.8764 (ppp) REVERT: G 74 MET cc_start: 0.7943 (ptt) cc_final: 0.7502 (ptp) REVERT: G 124 CYS cc_start: 0.7957 (p) cc_final: 0.7628 (p) REVERT: G 166 GLU cc_start: 0.7349 (pp20) cc_final: 0.6824 (pp20) REVERT: J 98 GLU cc_start: 0.8154 (pm20) cc_final: 0.7912 (pm20) REVERT: J 102 GLU cc_start: 0.8479 (mp0) cc_final: 0.8005 (mp0) REVERT: L 93 ASN cc_start: 0.8724 (m110) cc_final: 0.8417 (m-40) REVERT: N 75 ILE cc_start: 0.9102 (mm) cc_final: 0.8826 (mm) REVERT: Q 70 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8068 (tp-100) REVERT: Q 101 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7324 (p0) REVERT: R 85 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8144 (ptmt) REVERT: S 1 MET cc_start: 0.5888 (ppp) cc_final: 0.5507 (ptm) REVERT: S 18 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8336 (mtm-85) REVERT: S 34 ASP cc_start: 0.8294 (m-30) cc_final: 0.7991 (m-30) REVERT: S 95 ARG cc_start: 0.7273 (mmm160) cc_final: 0.6820 (tpp80) REVERT: T 1 MET cc_start: 0.4895 (mmp) cc_final: 0.4570 (mmt) REVERT: T 28 ASN cc_start: 0.8892 (t0) cc_final: 0.8490 (t0) REVERT: T 91 GLN cc_start: 0.7884 (mt0) cc_final: 0.7640 (mt0) REVERT: U 100 GLU cc_start: 0.7558 (mp0) cc_final: 0.7320 (mp0) REVERT: V 1 MET cc_start: 0.4338 (ppp) cc_final: 0.3743 (ppp) REVERT: V 11 GLU cc_start: 0.8614 (pp20) cc_final: 0.8209 (pp20) REVERT: V 81 PRO cc_start: 0.7598 (Cg_exo) cc_final: 0.7236 (Cg_endo) REVERT: W 52 ASP cc_start: 0.8756 (p0) cc_final: 0.8459 (p0) REVERT: W 64 LYS cc_start: 0.8538 (pttt) cc_final: 0.8321 (pttp) REVERT: W 68 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7835 (mmmt) REVERT: X 22 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8341 (m110) REVERT: Y 19 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8448 (mm) REVERT: Y 47 ARG cc_start: 0.9068 (ttp80) cc_final: 0.8827 (ttp80) REVERT: Y 49 ASP cc_start: 0.8165 (m-30) cc_final: 0.7839 (m-30) REVERT: 1 25 ASN cc_start: 0.8732 (t0) cc_final: 0.8345 (t0) REVERT: 1 39 ASP cc_start: 0.8417 (t0) cc_final: 0.8023 (t0) REVERT: 2 25 LYS cc_start: 0.8745 (pptt) cc_final: 0.8487 (pptt) REVERT: P 26 GLU cc_start: 0.7750 (tp30) cc_final: 0.7482 (tp30) REVERT: 6 6 LEU cc_start: 0.8513 (tt) cc_final: 0.8224 (mt) REVERT: 6 79 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8796 (p) REVERT: 7 15 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7819 (mp10) REVERT: 7 67 ILE cc_start: 0.6296 (mp) cc_final: 0.6085 (tt) REVERT: 7 232 ARG cc_start: 0.5633 (mtt180) cc_final: 0.5245 (mtt180) REVERT: 7 288 HIS cc_start: 0.3932 (OUTLIER) cc_final: 0.3338 (m-70) REVERT: 7 307 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6751 (tm-30) REVERT: 9 331 PHE cc_start: 0.8296 (t80) cc_final: 0.7993 (t80) REVERT: M 1 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.6122 (ppp) REVERT: M 53 MET cc_start: 0.6484 (mtm) cc_final: 0.5063 (tmm) REVERT: M 64 TRP cc_start: 0.5466 (m-90) cc_final: 0.4634 (m-90) REVERT: M 100 LYS cc_start: 0.4677 (pttm) cc_final: 0.3820 (mtmm) REVERT: M 105 MET cc_start: 0.7805 (tpp) cc_final: 0.7352 (tmm) REVERT: F 50 ASP cc_start: 0.7836 (m-30) cc_final: 0.7550 (m-30) REVERT: F 137 PHE cc_start: 0.7850 (m-80) cc_final: 0.7304 (m-80) REVERT: F 153 ILE cc_start: 0.8389 (pt) cc_final: 0.8108 (mt) REVERT: b 1 MET cc_start: 0.3712 (tmm) cc_final: 0.2908 (mtm) outliers start: 188 outliers final: 134 residues processed: 981 average time/residue: 0.9086 time to fit residues: 1539.0706 Evaluate side-chains 971 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 829 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 15 LYS Chi-restraints excluded: chain W residue 20 LYS Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain 6 residue 27 VAL Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 36 CYS Chi-restraints excluded: chain 6 residue 54 HIS Chi-restraints excluded: chain 6 residue 78 ILE Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 7 residue 5 VAL Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 30 ASP Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 209 VAL Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 252 VAL Chi-restraints excluded: chain 7 residue 288 HIS Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 123 ASP Chi-restraints excluded: chain 9 residue 8 SER Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 88 ILE Chi-restraints excluded: chain 9 residue 111 HIS Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 205 ASN Chi-restraints excluded: chain 9 residue 291 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 154 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 649 optimal weight: 20.0000 chunk 494 optimal weight: 30.0000 chunk 341 optimal weight: 30.0000 chunk 72 optimal weight: 0.0050 chunk 313 optimal weight: 0.8980 chunk 441 optimal weight: 10.0000 chunk 660 optimal weight: 10.0000 chunk 698 optimal weight: 30.0000 chunk 344 optimal weight: 9.9990 chunk 625 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 overall best weight: 5.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN D 148 GLN E 90 GLN G 142 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS T 70 HIS ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN 1 18 HIS K 3 GLN K 88 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 47 HIS 7 15 GLN ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 120 ASN ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 154 ASN ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 107182 Z= 0.246 Angle : 0.587 11.931 159778 Z= 0.300 Chirality : 0.035 0.310 20348 Planarity : 0.004 0.073 9003 Dihedral : 23.440 178.632 52049 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 5.40 % Allowed : 21.33 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -1.53 (0.12), residues: 4280 helix: -0.35 (0.15), residues: 1140 sheet: -0.63 (0.18), residues: 762 loop : -1.49 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 9 122 HIS 0.011 0.001 HIS J 80 PHE 0.024 0.002 PHE L 64 TYR 0.023 0.002 TYR K 32 ARG 0.009 0.001 ARG 9 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 896 time to evaluate : 4.751 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: C 212 TRP cc_start: 0.7892 (p90) cc_final: 0.7640 (p90) REVERT: C 247 TRP cc_start: 0.8444 (m100) cc_final: 0.7996 (m100) REVERT: E 25 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7604 (tm-30) REVERT: E 154 ASP cc_start: 0.7820 (t0) cc_final: 0.7559 (t70) REVERT: E 199 MET cc_start: 0.9109 (ptm) cc_final: 0.8748 (ppp) REVERT: G 74 MET cc_start: 0.8041 (ptt) cc_final: 0.7561 (ptp) REVERT: G 124 CYS cc_start: 0.7873 (p) cc_final: 0.7474 (p) REVERT: G 166 GLU cc_start: 0.7461 (pp20) cc_final: 0.7034 (pp20) REVERT: J 98 GLU cc_start: 0.8081 (pm20) cc_final: 0.7725 (pm20) REVERT: L 93 ASN cc_start: 0.8630 (m110) cc_final: 0.8337 (m-40) REVERT: L 111 ILE cc_start: 0.8597 (pt) cc_final: 0.8395 (pt) REVERT: N 20 MET cc_start: 0.8259 (tpp) cc_final: 0.8018 (tpp) REVERT: Q 65 ASN cc_start: 0.8861 (t0) cc_final: 0.8645 (t0) REVERT: Q 70 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8376 (tp-100) REVERT: Q 101 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7343 (p0) REVERT: R 62 GLU cc_start: 0.7326 (tp30) cc_final: 0.6830 (tt0) REVERT: S 1 MET cc_start: 0.5866 (ppp) cc_final: 0.5553 (ptm) REVERT: S 18 ARG cc_start: 0.8499 (mtm-85) cc_final: 0.8222 (mtm-85) REVERT: S 34 ASP cc_start: 0.8274 (m-30) cc_final: 0.7899 (m-30) REVERT: S 95 ARG cc_start: 0.7068 (mmm160) cc_final: 0.6576 (tpp80) REVERT: T 28 ASN cc_start: 0.8895 (t0) cc_final: 0.8480 (t0) REVERT: V 1 MET cc_start: 0.4380 (ppp) cc_final: 0.3889 (ppp) REVERT: V 5 ASN cc_start: 0.7286 (p0) cc_final: 0.6922 (m-40) REVERT: V 11 GLU cc_start: 0.8370 (pp20) cc_final: 0.8083 (pp20) REVERT: V 81 PRO cc_start: 0.7539 (Cg_exo) cc_final: 0.7182 (Cg_endo) REVERT: W 52 ASP cc_start: 0.8742 (p0) cc_final: 0.8450 (p0) REVERT: W 64 LYS cc_start: 0.8527 (pttt) cc_final: 0.8307 (pttp) REVERT: Y 17 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8533 (tm-30) REVERT: Y 19 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8403 (mm) REVERT: Y 22 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7114 (tt) REVERT: Y 45 GLN cc_start: 0.7995 (pp30) cc_final: 0.7785 (pp30) REVERT: Y 49 ASP cc_start: 0.8078 (m-30) cc_final: 0.7689 (m-30) REVERT: 1 25 ASN cc_start: 0.8558 (t0) cc_final: 0.8200 (t0) REVERT: P 26 GLU cc_start: 0.7747 (tp30) cc_final: 0.7514 (tp30) REVERT: 6 79 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8761 (p) REVERT: 7 67 ILE cc_start: 0.6420 (mp) cc_final: 0.6138 (tt) REVERT: 7 137 ARG cc_start: 0.6709 (mmt180) cc_final: 0.6447 (mmt180) REVERT: 7 179 MET cc_start: 0.7602 (mmp) cc_final: 0.7200 (mmt) REVERT: 7 204 MET cc_start: 0.6877 (tmm) cc_final: 0.5716 (mmm) REVERT: 7 232 ARG cc_start: 0.5517 (mtt180) cc_final: 0.4761 (mmp-170) REVERT: 7 288 HIS cc_start: 0.3654 (OUTLIER) cc_final: 0.3011 (m-70) REVERT: 9 26 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6212 (tt0) REVERT: 9 140 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7543 (mm-40) REVERT: 9 331 PHE cc_start: 0.8284 (t80) cc_final: 0.7979 (t80) REVERT: M 11 LYS cc_start: 0.7052 (tmtt) cc_final: 0.6672 (ptpt) REVERT: M 53 MET cc_start: 0.6479 (mtm) cc_final: 0.5069 (tmm) REVERT: M 100 LYS cc_start: 0.4774 (pttm) cc_final: 0.4150 (mtmm) REVERT: M 105 MET cc_start: 0.7713 (tpp) cc_final: 0.7110 (tmm) REVERT: F 50 ASP cc_start: 0.7784 (m-30) cc_final: 0.7480 (m-30) REVERT: F 93 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7186 (mm-30) REVERT: F 99 PHE cc_start: 0.8537 (t80) cc_final: 0.7813 (t80) REVERT: F 137 PHE cc_start: 0.7703 (m-80) cc_final: 0.7191 (m-80) REVERT: F 153 ILE cc_start: 0.8405 (pt) cc_final: 0.8103 (mt) REVERT: F 166 ARG cc_start: 0.8303 (tpp-160) cc_final: 0.7450 (mmt90) REVERT: b 1 MET cc_start: 0.3450 (tmm) cc_final: 0.2735 (mtm) outliers start: 191 outliers final: 140 residues processed: 990 average time/residue: 0.9739 time to fit residues: 1685.7848 Evaluate side-chains 991 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 845 time to evaluate : 4.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 15 LYS Chi-restraints excluded: chain W residue 20 LYS Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 24 LYS Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain 6 residue 22 ILE Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 54 HIS Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 76 ASP Chi-restraints excluded: chain 6 residue 78 ILE Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 7 residue 30 ASP Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 209 VAL Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 252 VAL Chi-restraints excluded: chain 7 residue 284 LEU Chi-restraints excluded: chain 7 residue 288 HIS Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 133 ILE Chi-restraints excluded: chain 9 residue 8 SER Chi-restraints excluded: chain 9 residue 12 VAL Chi-restraints excluded: chain 9 residue 26 GLU Chi-restraints excluded: chain 9 residue 28 TYR Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 78 CYS Chi-restraints excluded: chain 9 residue 88 ILE Chi-restraints excluded: chain 9 residue 114 ARG Chi-restraints excluded: chain 9 residue 167 MET Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 180 SER Chi-restraints excluded: chain 9 residue 205 ASN Chi-restraints excluded: chain 9 residue 217 LEU Chi-restraints excluded: chain 9 residue 291 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain b residue 5 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 582 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 520 optimal weight: 10.0000 chunk 288 optimal weight: 30.0000 chunk 596 optimal weight: 50.0000 chunk 483 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 356 optimal weight: 7.9990 chunk 627 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 overall best weight: 8.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 47 HIS ** 7 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN F 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 107182 Z= 0.374 Angle : 0.711 12.752 159778 Z= 0.361 Chirality : 0.039 0.349 20348 Planarity : 0.005 0.069 9003 Dihedral : 23.571 179.923 52046 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 7.09 % Allowed : 21.93 % Favored : 70.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.12), residues: 4280 helix: -0.59 (0.15), residues: 1137 sheet: -0.97 (0.18), residues: 748 loop : -1.64 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP 9 46 HIS 0.013 0.002 HIS J 80 PHE 0.031 0.002 PHE Q 78 TYR 0.037 0.003 TYR 9 310 ARG 0.013 0.001 ARG 9 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 860 time to evaluate : 5.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7685 (mm110) REVERT: C 247 TRP cc_start: 0.8510 (m100) cc_final: 0.7970 (m100) REVERT: D 79 LEU cc_start: 0.8527 (tp) cc_final: 0.8307 (tp) REVERT: E 25 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7477 (tm-30) REVERT: E 154 ASP cc_start: 0.7873 (t0) cc_final: 0.7655 (t70) REVERT: E 199 MET cc_start: 0.9109 (ptm) cc_final: 0.8787 (ppp) REVERT: G 74 MET cc_start: 0.8104 (ptt) cc_final: 0.7680 (ptp) REVERT: G 124 CYS cc_start: 0.8307 (p) cc_final: 0.7925 (p) REVERT: G 151 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.6057 (mpt180) REVERT: G 166 GLU cc_start: 0.7195 (pp20) cc_final: 0.6578 (pp20) REVERT: J 98 GLU cc_start: 0.8248 (pm20) cc_final: 0.8022 (pm20) REVERT: J 102 GLU cc_start: 0.8135 (mp0) cc_final: 0.7918 (mp0) REVERT: L 111 ILE cc_start: 0.8595 (pt) cc_final: 0.8370 (pt) REVERT: N 99 LYS cc_start: 0.9056 (mtmt) cc_final: 0.8799 (mtmt) REVERT: N 107 ASN cc_start: 0.8813 (t0) cc_final: 0.8581 (t0) REVERT: Q 51 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7654 (tm-30) REVERT: Q 70 GLN cc_start: 0.8681 (tp-100) cc_final: 0.7952 (tp-100) REVERT: Q 101 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7343 (p0) REVERT: Q 110 GLU cc_start: 0.8760 (tt0) cc_final: 0.8202 (pt0) REVERT: R 85 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8171 (ptmt) REVERT: S 18 ARG cc_start: 0.8547 (mtm-85) cc_final: 0.8268 (mtm-85) REVERT: S 59 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7180 (mt-10) REVERT: S 95 ARG cc_start: 0.7268 (mmm160) cc_final: 0.6865 (mmm160) REVERT: T 28 ASN cc_start: 0.8984 (t0) cc_final: 0.8591 (t0) REVERT: V 5 ASN cc_start: 0.7451 (p0) cc_final: 0.6905 (m-40) REVERT: W 22 PHE cc_start: 0.8000 (m-80) cc_final: 0.7746 (m-80) REVERT: W 52 ASP cc_start: 0.8726 (p0) cc_final: 0.8463 (p0) REVERT: W 64 LYS cc_start: 0.8521 (pttt) cc_final: 0.8288 (pttp) REVERT: X 22 ASN cc_start: 0.8522 (m110) cc_final: 0.7881 (m-40) REVERT: Y 19 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8436 (mm) REVERT: Y 45 GLN cc_start: 0.8340 (pp30) cc_final: 0.7806 (pp30) REVERT: Y 49 ASP cc_start: 0.8168 (m-30) cc_final: 0.7843 (m-30) REVERT: 1 18 HIS cc_start: 0.7663 (t-170) cc_final: 0.7450 (t-170) REVERT: 2 25 LYS cc_start: 0.8667 (pptt) cc_final: 0.8394 (pptt) REVERT: I 135 MET cc_start: 0.5570 (ptm) cc_final: 0.5281 (ptt) REVERT: K 110 GLU cc_start: 0.8727 (tm-30) cc_final: 0.7882 (tm-30) REVERT: P 26 GLU cc_start: 0.7989 (tp30) cc_final: 0.7775 (tp30) REVERT: 6 79 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8513 (p) REVERT: 7 137 ARG cc_start: 0.6739 (mmt180) cc_final: 0.6360 (mmt180) REVERT: 7 179 MET cc_start: 0.7820 (mmp) cc_final: 0.7344 (mmt) REVERT: 7 232 ARG cc_start: 0.5698 (mtt180) cc_final: 0.5314 (mmp-170) REVERT: 7 288 HIS cc_start: 0.4011 (OUTLIER) cc_final: 0.3372 (m-70) REVERT: 7 307 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6684 (tm-30) REVERT: 8 107 ARG cc_start: 0.8129 (mmp80) cc_final: 0.7603 (mmt180) REVERT: 9 26 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6063 (tt0) REVERT: 9 41 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: 9 113 GLN cc_start: 0.7701 (mt0) cc_final: 0.7304 (mt0) REVERT: 9 331 PHE cc_start: 0.8358 (t80) cc_final: 0.8060 (t80) REVERT: M 40 ARG cc_start: 0.4153 (mtt-85) cc_final: 0.3901 (mtt90) REVERT: M 53 MET cc_start: 0.6411 (mtm) cc_final: 0.5141 (tmm) REVERT: M 105 MET cc_start: 0.7850 (tpp) cc_final: 0.7106 (tmm) REVERT: H 7 ASP cc_start: 0.8520 (t0) cc_final: 0.8291 (t0) REVERT: F 16 MET cc_start: 0.7381 (ttm) cc_final: 0.7175 (tpp) REVERT: F 50 ASP cc_start: 0.7835 (m-30) cc_final: 0.7586 (m-30) REVERT: F 76 PHE cc_start: 0.6548 (m-80) cc_final: 0.5775 (t80) REVERT: F 82 TYR cc_start: 0.6675 (t80) cc_final: 0.6452 (t80) REVERT: F 137 PHE cc_start: 0.7865 (m-80) cc_final: 0.7387 (m-80) REVERT: F 153 ILE cc_start: 0.8542 (pt) cc_final: 0.8305 (mt) REVERT: F 166 ARG cc_start: 0.8392 (tpp-160) cc_final: 0.7525 (mmt90) REVERT: b 1 MET cc_start: 0.3656 (tmm) cc_final: 0.2752 (mtm) outliers start: 251 outliers final: 178 residues processed: 1005 average time/residue: 0.8981 time to fit residues: 1563.3138 Evaluate side-chains 1009 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 822 time to evaluate : 4.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 15 LYS Chi-restraints excluded: chain W residue 20 LYS Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 53 HIS Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain 6 residue 6 LEU Chi-restraints excluded: chain 6 residue 22 ILE Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 36 CYS Chi-restraints excluded: chain 6 residue 54 HIS Chi-restraints excluded: chain 6 residue 76 ASP Chi-restraints excluded: chain 6 residue 78 ILE Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 7 residue 5 VAL Chi-restraints excluded: chain 7 residue 30 ASP Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 152 VAL Chi-restraints excluded: chain 7 residue 209 VAL Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 252 VAL Chi-restraints excluded: chain 7 residue 284 LEU Chi-restraints excluded: chain 7 residue 288 HIS Chi-restraints excluded: chain 8 residue 49 LEU Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 123 ASP Chi-restraints excluded: chain 8 residue 133 ILE Chi-restraints excluded: chain 9 residue 8 SER Chi-restraints excluded: chain 9 residue 26 GLU Chi-restraints excluded: chain 9 residue 28 TYR Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 41 ASP Chi-restraints excluded: chain 9 residue 88 ILE Chi-restraints excluded: chain 9 residue 111 HIS Chi-restraints excluded: chain 9 residue 167 MET Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 180 SER Chi-restraints excluded: chain 9 residue 205 ASN Chi-restraints excluded: chain 9 residue 291 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain b residue 5 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 235 optimal weight: 20.0000 chunk 629 optimal weight: 20.0000 chunk 138 optimal weight: 0.8980 chunk 410 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 699 optimal weight: 20.0000 chunk 580 optimal weight: 20.0000 chunk 323 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 367 optimal weight: 1.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN G 142 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN Q 13 HIS Q 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 107182 Z= 0.220 Angle : 0.591 11.106 159778 Z= 0.302 Chirality : 0.035 0.345 20348 Planarity : 0.004 0.081 9003 Dihedral : 23.531 178.434 52046 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 5.96 % Allowed : 24.19 % Favored : 69.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -1.69 (0.12), residues: 4280 helix: -0.38 (0.15), residues: 1125 sheet: -0.96 (0.18), residues: 754 loop : -1.55 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 9 46 HIS 0.011 0.001 HIS J 80 PHE 0.037 0.002 PHE K 112 TYR 0.046 0.002 TYR 9 310 ARG 0.008 0.001 ARG H 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 882 time to evaluate : 4.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 212 TRP cc_start: 0.7953 (p90) cc_final: 0.7508 (p90) REVERT: C 247 TRP cc_start: 0.8478 (m100) cc_final: 0.7954 (m100) REVERT: D 79 LEU cc_start: 0.8463 (tp) cc_final: 0.8241 (tp) REVERT: E 25 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7893 (tm-30) REVERT: E 154 ASP cc_start: 0.7784 (t0) cc_final: 0.7552 (t70) REVERT: E 199 MET cc_start: 0.9109 (ptm) cc_final: 0.8789 (ppp) REVERT: G 74 MET cc_start: 0.8044 (ptt) cc_final: 0.7568 (ptp) REVERT: G 124 CYS cc_start: 0.8270 (p) cc_final: 0.7883 (p) REVERT: G 166 GLU cc_start: 0.7219 (pp20) cc_final: 0.6572 (pp20) REVERT: J 102 GLU cc_start: 0.8031 (mp0) cc_final: 0.7493 (mp0) REVERT: J 106 LYS cc_start: 0.8428 (ptpt) cc_final: 0.7636 (ptpp) REVERT: N 99 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8715 (mttt) REVERT: Q 51 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7510 (tm-30) REVERT: Q 70 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8310 (tp-100) REVERT: Q 82 LEU cc_start: 0.9343 (mm) cc_final: 0.9127 (mm) REVERT: Q 101 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7397 (p0) REVERT: Q 110 GLU cc_start: 0.8736 (tt0) cc_final: 0.8223 (pt0) REVERT: R 62 GLU cc_start: 0.7485 (tp30) cc_final: 0.6845 (tt0) REVERT: S 1 MET cc_start: 0.5708 (ppp) cc_final: 0.5194 (ptm) REVERT: S 11 ARG cc_start: 0.6890 (mtt180) cc_final: 0.6563 (tpp80) REVERT: S 59 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7091 (mt-10) REVERT: S 95 ARG cc_start: 0.7202 (mmm160) cc_final: 0.6820 (mmm160) REVERT: T 28 ASN cc_start: 0.8927 (t0) cc_final: 0.8342 (t0) REVERT: V 5 ASN cc_start: 0.7729 (p0) cc_final: 0.7268 (t0) REVERT: W 22 PHE cc_start: 0.7967 (m-80) cc_final: 0.7645 (m-80) REVERT: W 52 ASP cc_start: 0.8730 (p0) cc_final: 0.8420 (p0) REVERT: W 64 LYS cc_start: 0.8516 (pttt) cc_final: 0.8291 (pttp) REVERT: Y 17 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8549 (tm-30) REVERT: Y 19 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8400 (mm) REVERT: Y 45 GLN cc_start: 0.8162 (pp30) cc_final: 0.7747 (pp30) REVERT: Y 49 ASP cc_start: 0.8123 (m-30) cc_final: 0.7817 (m-30) REVERT: Y 60 LYS cc_start: 0.8350 (ttmm) cc_final: 0.7890 (ttpt) REVERT: Z 5 LYS cc_start: 0.7094 (tptt) cc_final: 0.6771 (tptt) REVERT: 1 25 ASN cc_start: 0.8580 (t0) cc_final: 0.7707 (t0) REVERT: I 135 MET cc_start: 0.5496 (ptm) cc_final: 0.5294 (ptt) REVERT: K 110 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8164 (tm-30) REVERT: K 112 PHE cc_start: 0.8273 (m-80) cc_final: 0.7954 (m-80) REVERT: P 8 GLU cc_start: 0.8884 (mp0) cc_final: 0.8642 (mp0) REVERT: P 26 GLU cc_start: 0.7979 (tp30) cc_final: 0.7746 (tp30) REVERT: P 67 GLU cc_start: 0.7874 (pp20) cc_final: 0.7410 (pp20) REVERT: 6 79 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8440 (p) REVERT: 7 44 ARG cc_start: 0.6478 (mtt180) cc_final: 0.5781 (mtm180) REVERT: 7 67 ILE cc_start: 0.6671 (mp) cc_final: 0.6346 (tt) REVERT: 7 137 ARG cc_start: 0.6717 (mmt180) cc_final: 0.6293 (mmt180) REVERT: 7 179 MET cc_start: 0.7767 (mmp) cc_final: 0.7197 (mmt) REVERT: 7 232 ARG cc_start: 0.5797 (mtt180) cc_final: 0.5289 (mmp-170) REVERT: 7 288 HIS cc_start: 0.3510 (OUTLIER) cc_final: 0.2811 (m-70) REVERT: 8 107 ARG cc_start: 0.8126 (mmp80) cc_final: 0.7585 (mmt180) REVERT: 9 26 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.5738 (tt0) REVERT: 9 71 GLN cc_start: 0.8357 (mm110) cc_final: 0.8061 (mm110) REVERT: 9 113 GLN cc_start: 0.7588 (mt0) cc_final: 0.7226 (mt0) REVERT: 9 122 TRP cc_start: 0.6298 (m-10) cc_final: 0.5163 (m100) REVERT: 9 158 LEU cc_start: 0.8196 (mp) cc_final: 0.7876 (mt) REVERT: 9 331 PHE cc_start: 0.8400 (t80) cc_final: 0.8033 (t80) REVERT: M 53 MET cc_start: 0.6175 (mtm) cc_final: 0.5030 (tmm) REVERT: M 105 MET cc_start: 0.7841 (tpp) cc_final: 0.7161 (tmm) REVERT: H 7 ASP cc_start: 0.8463 (t0) cc_final: 0.8213 (t0) REVERT: F 50 ASP cc_start: 0.7844 (m-30) cc_final: 0.7553 (m-30) REVERT: F 76 PHE cc_start: 0.6707 (m-80) cc_final: 0.5869 (t80) REVERT: F 99 PHE cc_start: 0.8471 (t80) cc_final: 0.7726 (t80) REVERT: F 100 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7781 (mm-30) REVERT: F 137 PHE cc_start: 0.7908 (m-80) cc_final: 0.7409 (m-80) REVERT: F 153 ILE cc_start: 0.8540 (pt) cc_final: 0.8325 (mt) REVERT: F 166 ARG cc_start: 0.8221 (tpp-160) cc_final: 0.7461 (mmt90) REVERT: b 1 MET cc_start: 0.3857 (tmm) cc_final: 0.2959 (mtm) outliers start: 211 outliers final: 158 residues processed: 997 average time/residue: 0.8980 time to fit residues: 1552.9550 Evaluate side-chains 1015 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 852 time to evaluate : 4.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 34 HIS Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 15 LYS Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 37 ARG Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain 6 residue 22 ILE Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 36 CYS Chi-restraints excluded: chain 6 residue 54 HIS Chi-restraints excluded: chain 6 residue 76 ASP Chi-restraints excluded: chain 6 residue 78 ILE Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 7 residue 30 ASP Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 209 VAL Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 252 VAL Chi-restraints excluded: chain 7 residue 284 LEU Chi-restraints excluded: chain 7 residue 288 HIS Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 114 LEU Chi-restraints excluded: chain 8 residue 123 ASP Chi-restraints excluded: chain 8 residue 133 ILE Chi-restraints excluded: chain 9 residue 8 SER Chi-restraints excluded: chain 9 residue 26 GLU Chi-restraints excluded: chain 9 residue 28 TYR Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 88 ILE Chi-restraints excluded: chain 9 residue 111 HIS Chi-restraints excluded: chain 9 residue 167 MET Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 180 SER Chi-restraints excluded: chain 9 residue 217 LEU Chi-restraints excluded: chain 9 residue 291 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 9 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 674 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 398 optimal weight: 20.0000 chunk 510 optimal weight: 10.0000 chunk 395 optimal weight: 10.0000 chunk 588 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 696 optimal weight: 30.0000 chunk 436 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 chunk 321 optimal weight: 9.9990 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 47 HIS ** 7 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 99 GLN ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 107182 Z= 0.427 Angle : 0.740 12.214 159778 Z= 0.373 Chirality : 0.041 0.361 20348 Planarity : 0.005 0.066 9003 Dihedral : 23.595 179.689 52046 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 6.44 % Allowed : 25.35 % Favored : 68.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -1.92 (0.12), residues: 4280 helix: -0.57 (0.15), residues: 1109 sheet: -1.11 (0.18), residues: 745 loop : -1.69 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP 9 46 HIS 0.013 0.002 HIS J 80 PHE 0.030 0.002 PHE K 112 TYR 0.040 0.003 TYR 9 310 ARG 0.024 0.001 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 867 time to evaluate : 4.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7805 (mm110) REVERT: C 212 TRP cc_start: 0.8007 (p90) cc_final: 0.7684 (p90) REVERT: C 247 TRP cc_start: 0.8588 (m100) cc_final: 0.7945 (m100) REVERT: D 79 LEU cc_start: 0.8534 (tp) cc_final: 0.8278 (tp) REVERT: D 181 ASP cc_start: 0.7496 (t0) cc_final: 0.7225 (t0) REVERT: E 25 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7509 (tm-30) REVERT: E 154 ASP cc_start: 0.8034 (t0) cc_final: 0.7809 (t70) REVERT: E 173 THR cc_start: 0.8832 (m) cc_final: 0.8575 (p) REVERT: E 199 MET cc_start: 0.9083 (ptm) cc_final: 0.8821 (ppp) REVERT: G 74 MET cc_start: 0.7898 (ptt) cc_final: 0.7414 (ptp) REVERT: G 94 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7166 (mmp-170) REVERT: G 124 CYS cc_start: 0.8385 (p) cc_final: 0.7962 (p) REVERT: G 127 GLN cc_start: 0.8482 (pp30) cc_final: 0.7625 (pp30) REVERT: G 166 GLU cc_start: 0.7134 (pp20) cc_final: 0.6485 (pp20) REVERT: J 106 LYS cc_start: 0.8426 (ptpt) cc_final: 0.7621 (ptpp) REVERT: N 99 LYS cc_start: 0.9084 (mtmt) cc_final: 0.8874 (mttt) REVERT: O 69 ASP cc_start: 0.8992 (m-30) cc_final: 0.8332 (t0) REVERT: O 80 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7709 (pt0) REVERT: Q 70 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8346 (tp-100) REVERT: Q 82 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9124 (mm) REVERT: Q 101 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7581 (p0) REVERT: Q 110 GLU cc_start: 0.8798 (tt0) cc_final: 0.8296 (pt0) REVERT: S 1 MET cc_start: 0.5661 (ppp) cc_final: 0.5206 (ptm) REVERT: S 11 ARG cc_start: 0.6928 (mtt180) cc_final: 0.6676 (ttm170) REVERT: S 18 ARG cc_start: 0.8568 (mtm-85) cc_final: 0.8345 (mtm-85) REVERT: S 59 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7286 (mt-10) REVERT: S 95 ARG cc_start: 0.7311 (mmm160) cc_final: 0.6882 (mmm160) REVERT: T 28 ASN cc_start: 0.8967 (t0) cc_final: 0.8527 (t0) REVERT: V 85 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8590 (mmmt) REVERT: W 22 PHE cc_start: 0.8153 (m-80) cc_final: 0.7779 (m-80) REVERT: W 52 ASP cc_start: 0.8722 (p0) cc_final: 0.8464 (p0) REVERT: W 64 LYS cc_start: 0.8501 (pttt) cc_final: 0.8258 (pttp) REVERT: X 5 GLN cc_start: 0.8740 (mt0) cc_final: 0.8316 (mt0) REVERT: X 22 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8241 (m110) REVERT: Y 17 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8643 (tm-30) REVERT: Y 19 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8406 (mm) REVERT: Y 22 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7474 (tt) REVERT: Y 45 GLN cc_start: 0.8371 (pp30) cc_final: 0.7888 (pp30) REVERT: Y 49 ASP cc_start: 0.8215 (m-30) cc_final: 0.7906 (m-30) REVERT: Y 60 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8071 (ttpt) REVERT: 1 25 ASN cc_start: 0.8582 (t0) cc_final: 0.7653 (t0) REVERT: I 96 LYS cc_start: 0.6438 (mmpt) cc_final: 0.5694 (tmmt) REVERT: I 133 ARG cc_start: 0.5002 (OUTLIER) cc_final: 0.4700 (ptt90) REVERT: K 110 GLU cc_start: 0.8563 (tm-30) cc_final: 0.7994 (tm-30) REVERT: K 112 PHE cc_start: 0.8390 (m-80) cc_final: 0.7944 (m-80) REVERT: P 8 GLU cc_start: 0.8963 (mp0) cc_final: 0.8715 (mp0) REVERT: P 26 GLU cc_start: 0.8058 (tp30) cc_final: 0.7809 (tp30) REVERT: 6 79 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8290 (p) REVERT: 7 44 ARG cc_start: 0.6652 (mtt180) cc_final: 0.5944 (mtm180) REVERT: 7 67 ILE cc_start: 0.6383 (mp) cc_final: 0.6125 (tt) REVERT: 7 137 ARG cc_start: 0.6790 (mmt180) cc_final: 0.6523 (mmt180) REVERT: 7 179 MET cc_start: 0.7894 (mmp) cc_final: 0.7239 (mmt) REVERT: 7 232 ARG cc_start: 0.5792 (mtt180) cc_final: 0.5260 (mmp-170) REVERT: 7 288 HIS cc_start: 0.3345 (OUTLIER) cc_final: 0.2715 (m-70) REVERT: 7 307 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6692 (tm-30) REVERT: 8 45 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7709 (tm-30) REVERT: 8 99 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: 8 107 ARG cc_start: 0.8064 (mmp80) cc_final: 0.7681 (mmt90) REVERT: 9 26 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.5945 (tt0) REVERT: 9 71 GLN cc_start: 0.8380 (mm110) cc_final: 0.8046 (mm110) REVERT: 9 157 MET cc_start: 0.7621 (mmm) cc_final: 0.7387 (mmm) REVERT: 9 235 LEU cc_start: 0.8466 (mm) cc_final: 0.8264 (mm) REVERT: 9 331 PHE cc_start: 0.8441 (t80) cc_final: 0.8067 (t80) REVERT: M 53 MET cc_start: 0.6165 (mtm) cc_final: 0.4888 (tmm) REVERT: M 105 MET cc_start: 0.7973 (tpp) cc_final: 0.7220 (tmm) REVERT: H 7 ASP cc_start: 0.8526 (t0) cc_final: 0.8248 (t0) REVERT: e 1 MET cc_start: 0.1156 (OUTLIER) cc_final: 0.0921 (mmm) REVERT: F 50 ASP cc_start: 0.7757 (m-30) cc_final: 0.7509 (m-30) REVERT: F 76 PHE cc_start: 0.6672 (m-80) cc_final: 0.5842 (t80) REVERT: F 99 PHE cc_start: 0.8536 (t80) cc_final: 0.7813 (t80) REVERT: F 100 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7911 (mm-30) REVERT: F 137 PHE cc_start: 0.7889 (m-80) cc_final: 0.7387 (m-80) REVERT: F 153 ILE cc_start: 0.8481 (pt) cc_final: 0.8230 (mt) REVERT: F 166 ARG cc_start: 0.8154 (tpp-160) cc_final: 0.7379 (mmt90) REVERT: b 1 MET cc_start: 0.3993 (tmm) cc_final: 0.3109 (mtm) outliers start: 228 outliers final: 181 residues processed: 992 average time/residue: 0.9175 time to fit residues: 1575.6200 Evaluate side-chains 1035 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 840 time to evaluate : 4.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 15 LYS Chi-restraints excluded: chain W residue 53 HIS Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain 6 residue 6 LEU Chi-restraints excluded: chain 6 residue 22 ILE Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 36 CYS Chi-restraints excluded: chain 6 residue 76 ASP Chi-restraints excluded: chain 6 residue 78 ILE Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 7 residue 30 ASP Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 152 VAL Chi-restraints excluded: chain 7 residue 209 VAL Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 284 LEU Chi-restraints excluded: chain 7 residue 288 HIS Chi-restraints excluded: chain 8 residue 49 LEU Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 99 GLN Chi-restraints excluded: chain 8 residue 114 LEU Chi-restraints excluded: chain 8 residue 123 ASP Chi-restraints excluded: chain 8 residue 133 ILE Chi-restraints excluded: chain 9 residue 8 SER Chi-restraints excluded: chain 9 residue 26 GLU Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 88 ILE Chi-restraints excluded: chain 9 residue 108 MET Chi-restraints excluded: chain 9 residue 111 HIS Chi-restraints excluded: chain 9 residue 167 MET Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 180 SER Chi-restraints excluded: chain 9 residue 217 LEU Chi-restraints excluded: chain 9 residue 291 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 35 VAL Chi-restraints excluded: chain e residue 109 LYS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 41 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 431 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 416 optimal weight: 10.0000 chunk 209 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 443 optimal weight: 10.0000 chunk 474 optimal weight: 40.0000 chunk 344 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 547 optimal weight: 10.0000 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 99 GLN ** 8 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 107182 Z= 0.238 Angle : 0.612 12.625 159778 Z= 0.312 Chirality : 0.036 0.374 20348 Planarity : 0.005 0.074 9003 Dihedral : 23.584 179.194 52046 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.82 % Allowed : 26.50 % Favored : 67.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -1.78 (0.12), residues: 4280 helix: -0.40 (0.15), residues: 1108 sheet: -1.08 (0.18), residues: 747 loop : -1.60 (0.12), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP 9 46 HIS 0.012 0.001 HIS J 80 PHE 0.030 0.002 PHE K 112 TYR 0.036 0.002 TYR 9 310 ARG 0.007 0.001 ARG R 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 880 time to evaluate : 4.649 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: C 70 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7933 (mtpp) REVERT: C 114 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7638 (mm110) REVERT: C 117 SER cc_start: 0.7838 (p) cc_final: 0.7514 (p) REVERT: C 247 TRP cc_start: 0.8522 (m100) cc_final: 0.7866 (m100) REVERT: D 79 LEU cc_start: 0.8460 (tp) cc_final: 0.8203 (tp) REVERT: D 181 ASP cc_start: 0.7306 (t0) cc_final: 0.7024 (t0) REVERT: E 25 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7795 (tm-30) REVERT: E 154 ASP cc_start: 0.7957 (t0) cc_final: 0.7740 (t70) REVERT: E 199 MET cc_start: 0.9049 (ptm) cc_final: 0.8783 (ppp) REVERT: G 34 ARG cc_start: 0.8269 (tpt-90) cc_final: 0.7935 (tpt-90) REVERT: G 74 MET cc_start: 0.7900 (ptt) cc_final: 0.7356 (ptp) REVERT: G 124 CYS cc_start: 0.8172 (p) cc_final: 0.7805 (p) REVERT: G 127 GLN cc_start: 0.8365 (pp30) cc_final: 0.7955 (pp30) REVERT: G 166 GLU cc_start: 0.7109 (pp20) cc_final: 0.6423 (pp20) REVERT: J 102 GLU cc_start: 0.8087 (mp0) cc_final: 0.7496 (mp0) REVERT: J 106 LYS cc_start: 0.8381 (ptpt) cc_final: 0.7577 (ptpp) REVERT: L 69 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7584 (mmm-85) REVERT: N 99 LYS cc_start: 0.9076 (mtmt) cc_final: 0.8854 (mttt) REVERT: O 69 ASP cc_start: 0.8960 (m-30) cc_final: 0.8260 (t0) REVERT: Q 51 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7382 (tm-30) REVERT: Q 70 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8316 (tp-100) REVERT: Q 110 GLU cc_start: 0.8767 (tt0) cc_final: 0.8292 (pt0) REVERT: R 62 GLU cc_start: 0.7582 (tp30) cc_final: 0.6872 (tt0) REVERT: S 1 MET cc_start: 0.5607 (ppp) cc_final: 0.5126 (ptm) REVERT: S 11 ARG cc_start: 0.6763 (mtt180) cc_final: 0.6458 (ttm170) REVERT: S 18 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8251 (mtm-85) REVERT: S 59 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7018 (mt-10) REVERT: S 95 ARG cc_start: 0.7235 (mmm160) cc_final: 0.6837 (mmm160) REVERT: T 28 ASN cc_start: 0.8948 (t0) cc_final: 0.8361 (t0) REVERT: V 59 GLU cc_start: 0.8433 (pm20) cc_final: 0.8221 (pm20) REVERT: V 85 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8636 (mmmt) REVERT: W 52 ASP cc_start: 0.8712 (p0) cc_final: 0.8424 (p0) REVERT: W 64 LYS cc_start: 0.8523 (pttt) cc_final: 0.8287 (pttp) REVERT: Y 17 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8583 (tm-30) REVERT: Y 19 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8441 (mm) REVERT: Y 60 LYS cc_start: 0.8534 (ttmm) cc_final: 0.8063 (ttpt) REVERT: Z 5 LYS cc_start: 0.7158 (tptt) cc_final: 0.6759 (mptt) REVERT: 1 25 ASN cc_start: 0.8513 (t0) cc_final: 0.7727 (t0) REVERT: I 96 LYS cc_start: 0.6477 (mmpt) cc_final: 0.5657 (tmmt) REVERT: I 133 ARG cc_start: 0.4897 (OUTLIER) cc_final: 0.4597 (ptt90) REVERT: K 110 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7928 (tm-30) REVERT: K 112 PHE cc_start: 0.8323 (m-80) cc_final: 0.7904 (m-80) REVERT: P 8 GLU cc_start: 0.8934 (mp0) cc_final: 0.8551 (mp0) REVERT: P 26 GLU cc_start: 0.8023 (tp30) cc_final: 0.7776 (tp30) REVERT: P 67 GLU cc_start: 0.7817 (pp20) cc_final: 0.7334 (pp20) REVERT: 6 79 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8379 (p) REVERT: 7 44 ARG cc_start: 0.6516 (mtt180) cc_final: 0.5789 (mtm180) REVERT: 7 67 ILE cc_start: 0.6760 (mp) cc_final: 0.6458 (tt) REVERT: 7 137 ARG cc_start: 0.6711 (mmt180) cc_final: 0.6394 (mmt180) REVERT: 7 179 MET cc_start: 0.7849 (mmp) cc_final: 0.7092 (mmt) REVERT: 7 232 ARG cc_start: 0.5836 (mtt180) cc_final: 0.5256 (mmp-170) REVERT: 7 288 HIS cc_start: 0.3517 (OUTLIER) cc_final: 0.2901 (m-70) REVERT: 8 107 ARG cc_start: 0.8064 (mmp80) cc_final: 0.7776 (mmt90) REVERT: 9 26 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5655 (tt0) REVERT: 9 50 ASP cc_start: 0.8196 (t0) cc_final: 0.7935 (p0) REVERT: 9 71 GLN cc_start: 0.8378 (mm110) cc_final: 0.8025 (mm110) REVERT: 9 113 GLN cc_start: 0.7246 (mt0) cc_final: 0.7046 (mt0) REVERT: 9 158 LEU cc_start: 0.8211 (mp) cc_final: 0.7875 (mt) REVERT: 9 235 LEU cc_start: 0.8342 (mm) cc_final: 0.8113 (mm) REVERT: 9 331 PHE cc_start: 0.8412 (t80) cc_final: 0.8053 (t80) REVERT: M 53 MET cc_start: 0.6216 (mtm) cc_final: 0.4885 (tmm) REVERT: M 64 TRP cc_start: 0.5895 (m-90) cc_final: 0.5170 (m-90) REVERT: M 100 LYS cc_start: 0.4624 (pttp) cc_final: 0.3787 (mtmm) REVERT: M 105 MET cc_start: 0.7870 (tpp) cc_final: 0.7278 (tmm) REVERT: H 7 ASP cc_start: 0.8513 (t0) cc_final: 0.8248 (t0) REVERT: H 137 GLU cc_start: 0.5022 (OUTLIER) cc_final: 0.4533 (pp20) REVERT: e 52 MET cc_start: -0.2233 (tpt) cc_final: -0.2517 (tpt) REVERT: F 16 MET cc_start: 0.6785 (tpp) cc_final: 0.6528 (tpt) REVERT: F 25 MET cc_start: 0.7719 (tmm) cc_final: 0.7511 (tmm) REVERT: F 50 ASP cc_start: 0.7841 (m-30) cc_final: 0.7590 (m-30) REVERT: F 76 PHE cc_start: 0.6587 (m-80) cc_final: 0.5633 (t80) REVERT: F 99 PHE cc_start: 0.8489 (t80) cc_final: 0.7768 (t80) REVERT: F 100 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7730 (mm-30) REVERT: F 137 PHE cc_start: 0.7911 (m-80) cc_final: 0.7409 (m-80) REVERT: F 153 ILE cc_start: 0.8464 (pt) cc_final: 0.8230 (mt) REVERT: F 166 ARG cc_start: 0.8100 (tpp-160) cc_final: 0.7381 (mmt90) REVERT: b 1 MET cc_start: 0.3802 (tmm) cc_final: 0.2900 (mtm) outliers start: 206 outliers final: 170 residues processed: 985 average time/residue: 0.9224 time to fit residues: 1565.7820 Evaluate side-chains 1030 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 852 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 15 LYS Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain 6 residue 6 LEU Chi-restraints excluded: chain 6 residue 22 ILE Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 36 CYS Chi-restraints excluded: chain 6 residue 76 ASP Chi-restraints excluded: chain 6 residue 78 ILE Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 7 residue 30 ASP Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 209 VAL Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 284 LEU Chi-restraints excluded: chain 7 residue 288 HIS Chi-restraints excluded: chain 8 residue 49 LEU Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 114 LEU Chi-restraints excluded: chain 8 residue 123 ASP Chi-restraints excluded: chain 8 residue 133 ILE Chi-restraints excluded: chain 9 residue 8 SER Chi-restraints excluded: chain 9 residue 26 GLU Chi-restraints excluded: chain 9 residue 28 TYR Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 88 ILE Chi-restraints excluded: chain 9 residue 111 HIS Chi-restraints excluded: chain 9 residue 167 MET Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 180 SER Chi-restraints excluded: chain 9 residue 217 LEU Chi-restraints excluded: chain 9 residue 321 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 35 VAL Chi-restraints excluded: chain e residue 109 LYS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 41 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 633 optimal weight: 20.0000 chunk 667 optimal weight: 10.0000 chunk 609 optimal weight: 20.0000 chunk 649 optimal weight: 20.0000 chunk 390 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 509 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 586 optimal weight: 10.0000 chunk 614 optimal weight: 30.0000 chunk 647 optimal weight: 10.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN Q 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN U 73 ASN X 22 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 99 GLN ** 8 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 107182 Z= 0.425 Angle : 0.756 11.865 159778 Z= 0.381 Chirality : 0.042 0.365 20348 Planarity : 0.006 0.085 9003 Dihedral : 23.657 179.995 52046 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 6.36 % Allowed : 26.67 % Favored : 66.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.12), residues: 4280 helix: -0.65 (0.15), residues: 1106 sheet: -1.30 (0.17), residues: 799 loop : -1.74 (0.12), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP 9 46 HIS 0.014 0.002 HIS J 80 PHE 0.041 0.003 PHE Q 78 TYR 0.033 0.003 TYR 9 310 ARG 0.009 0.001 ARG R 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 859 time to evaluate : 4.614 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: C 94 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7904 (tp) REVERT: C 114 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7942 (mm110) REVERT: C 117 SER cc_start: 0.7758 (p) cc_final: 0.7406 (p) REVERT: C 247 TRP cc_start: 0.8646 (m100) cc_final: 0.8023 (m100) REVERT: D 181 ASP cc_start: 0.7710 (t0) cc_final: 0.7440 (t0) REVERT: E 173 THR cc_start: 0.8870 (m) cc_final: 0.8558 (p) REVERT: E 199 MET cc_start: 0.9088 (ptm) cc_final: 0.8864 (ppp) REVERT: G 74 MET cc_start: 0.7908 (ptt) cc_final: 0.7366 (ptp) REVERT: G 94 ARG cc_start: 0.7363 (mmt180) cc_final: 0.6829 (mmt180) REVERT: G 124 CYS cc_start: 0.8338 (p) cc_final: 0.7945 (p) REVERT: G 127 GLN cc_start: 0.8273 (pp30) cc_final: 0.7644 (pp30) REVERT: G 166 GLU cc_start: 0.7110 (pp20) cc_final: 0.6486 (pp20) REVERT: J 102 GLU cc_start: 0.8188 (mp0) cc_final: 0.7697 (mp0) REVERT: J 106 LYS cc_start: 0.8515 (ptpt) cc_final: 0.7717 (ptpp) REVERT: N 99 LYS cc_start: 0.9130 (mtmt) cc_final: 0.8857 (mttt) REVERT: O 69 ASP cc_start: 0.9019 (m-30) cc_final: 0.8366 (t0) REVERT: O 80 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: Q 51 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7725 (tm-30) REVERT: Q 70 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8383 (tp-100) REVERT: Q 110 GLU cc_start: 0.8840 (tt0) cc_final: 0.8339 (pt0) REVERT: R 62 GLU cc_start: 0.7635 (tp30) cc_final: 0.7053 (tt0) REVERT: S 18 ARG cc_start: 0.8631 (mtm-85) cc_final: 0.8364 (mtm-85) REVERT: S 59 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7290 (mt-10) REVERT: S 95 ARG cc_start: 0.7322 (mmm160) cc_final: 0.6889 (mmm160) REVERT: T 28 ASN cc_start: 0.8988 (t0) cc_final: 0.8555 (t0) REVERT: V 85 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8847 (mmmt) REVERT: W 52 ASP cc_start: 0.8720 (p0) cc_final: 0.8484 (p0) REVERT: W 64 LYS cc_start: 0.8516 (pttt) cc_final: 0.8270 (pttp) REVERT: Y 17 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8604 (tm-30) REVERT: Y 19 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8382 (mm) REVERT: Y 49 ASP cc_start: 0.8233 (m-30) cc_final: 0.7897 (m-30) REVERT: Y 60 LYS cc_start: 0.8662 (ttmm) cc_final: 0.8185 (ttpt) REVERT: 1 25 ASN cc_start: 0.8624 (t0) cc_final: 0.8382 (t0) REVERT: I 96 LYS cc_start: 0.6545 (mmpt) cc_final: 0.5638 (tmmt) REVERT: I 133 ARG cc_start: 0.4628 (OUTLIER) cc_final: 0.4249 (ptt90) REVERT: K 110 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7878 (tm-30) REVERT: K 112 PHE cc_start: 0.8464 (m-80) cc_final: 0.7957 (m-80) REVERT: P 26 GLU cc_start: 0.8016 (tp30) cc_final: 0.7802 (tp30) REVERT: P 67 GLU cc_start: 0.7869 (pp20) cc_final: 0.7276 (pp20) REVERT: 6 79 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8270 (p) REVERT: 7 67 ILE cc_start: 0.6551 (mp) cc_final: 0.6348 (tt) REVERT: 7 137 ARG cc_start: 0.6592 (mmt180) cc_final: 0.6352 (mmt180) REVERT: 7 232 ARG cc_start: 0.5963 (mtt180) cc_final: 0.5475 (mmp-170) REVERT: 7 235 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7073 (tp40) REVERT: 7 239 HIS cc_start: 0.6257 (OUTLIER) cc_final: 0.4763 (m90) REVERT: 7 288 HIS cc_start: 0.3552 (OUTLIER) cc_final: 0.2912 (m-70) REVERT: 7 307 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6701 (tm-30) REVERT: 8 99 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: 8 107 ARG cc_start: 0.7892 (mmp80) cc_final: 0.7533 (mmt90) REVERT: 9 26 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5897 (tt0) REVERT: 9 116 LEU cc_start: 0.8329 (tp) cc_final: 0.8031 (tt) REVERT: 9 158 LEU cc_start: 0.8288 (mp) cc_final: 0.7943 (mt) REVERT: 9 331 PHE cc_start: 0.8451 (t80) cc_final: 0.8070 (t80) REVERT: M 53 MET cc_start: 0.6075 (mtm) cc_final: 0.4783 (tmm) REVERT: M 64 TRP cc_start: 0.6012 (m-90) cc_final: 0.5117 (m-90) REVERT: M 100 LYS cc_start: 0.4977 (pttp) cc_final: 0.4461 (mtmm) REVERT: M 105 MET cc_start: 0.7985 (tpp) cc_final: 0.7302 (tmm) REVERT: H 7 ASP cc_start: 0.8536 (t0) cc_final: 0.8258 (t0) REVERT: H 48 GLU cc_start: 0.6113 (OUTLIER) cc_final: 0.5762 (pp20) REVERT: H 137 GLU cc_start: 0.5023 (OUTLIER) cc_final: 0.4512 (pp20) REVERT: e 52 MET cc_start: -0.1719 (tpt) cc_final: -0.1972 (tpt) REVERT: F 16 MET cc_start: 0.6731 (tpp) cc_final: 0.6505 (tpt) REVERT: F 25 MET cc_start: 0.7919 (tmm) cc_final: 0.7614 (tmm) REVERT: F 31 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7905 (mm-30) REVERT: F 50 ASP cc_start: 0.7782 (m-30) cc_final: 0.7535 (m-30) REVERT: F 76 PHE cc_start: 0.6545 (m-80) cc_final: 0.5956 (t80) REVERT: F 93 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7288 (mm-30) REVERT: F 99 PHE cc_start: 0.8553 (t80) cc_final: 0.8018 (t80) REVERT: F 100 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7909 (mm-30) REVERT: F 137 PHE cc_start: 0.7904 (m-80) cc_final: 0.7413 (m-80) REVERT: F 166 ARG cc_start: 0.8159 (tpp-160) cc_final: 0.7257 (mmt90) REVERT: b 1 MET cc_start: 0.3863 (tmm) cc_final: 0.2904 (mtm) outliers start: 225 outliers final: 183 residues processed: 979 average time/residue: 0.9697 time to fit residues: 1648.5401 Evaluate side-chains 1039 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 843 time to evaluate : 4.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 15 LYS Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain 6 residue 6 LEU Chi-restraints excluded: chain 6 residue 22 ILE Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 36 CYS Chi-restraints excluded: chain 6 residue 76 ASP Chi-restraints excluded: chain 6 residue 78 ILE Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 7 residue 5 VAL Chi-restraints excluded: chain 7 residue 30 ASP Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 194 THR Chi-restraints excluded: chain 7 residue 209 VAL Chi-restraints excluded: chain 7 residue 235 GLN Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 239 HIS Chi-restraints excluded: chain 7 residue 284 LEU Chi-restraints excluded: chain 7 residue 288 HIS Chi-restraints excluded: chain 8 residue 49 LEU Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 99 GLN Chi-restraints excluded: chain 8 residue 114 LEU Chi-restraints excluded: chain 8 residue 123 ASP Chi-restraints excluded: chain 8 residue 133 ILE Chi-restraints excluded: chain 9 residue 8 SER Chi-restraints excluded: chain 9 residue 26 GLU Chi-restraints excluded: chain 9 residue 28 TYR Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 88 ILE Chi-restraints excluded: chain 9 residue 111 HIS Chi-restraints excluded: chain 9 residue 167 MET Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 180 SER Chi-restraints excluded: chain 9 residue 217 LEU Chi-restraints excluded: chain 9 residue 291 VAL Chi-restraints excluded: chain 9 residue 321 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 35 VAL Chi-restraints excluded: chain e residue 109 LYS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain b residue 5 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 426 optimal weight: 10.0000 chunk 686 optimal weight: 0.9990 chunk 419 optimal weight: 20.0000 chunk 325 optimal weight: 0.9990 chunk 477 optimal weight: 10.0000 chunk 720 optimal weight: 30.0000 chunk 662 optimal weight: 10.0000 chunk 573 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 443 optimal weight: 10.0000 chunk 351 optimal weight: 0.8980 overall best weight: 3.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 148 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN X 22 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** 7 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 107182 Z= 0.196 Angle : 0.598 15.471 159778 Z= 0.305 Chirality : 0.035 0.365 20348 Planarity : 0.004 0.071 9003 Dihedral : 23.612 179.388 52046 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.55 % Allowed : 28.34 % Favored : 67.11 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.12), residues: 4280 helix: -0.35 (0.15), residues: 1112 sheet: -1.22 (0.18), residues: 739 loop : -1.54 (0.12), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP 9 46 HIS 0.009 0.001 HIS J 80 PHE 0.026 0.002 PHE H 46 TYR 0.031 0.002 TYR 9 310 ARG 0.018 0.001 ARG H 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 892 time to evaluate : 4.545 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: C 70 LYS cc_start: 0.8301 (mtpp) cc_final: 0.7966 (mtpp) REVERT: C 94 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7758 (tp) REVERT: C 114 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7774 (mm110) REVERT: C 117 SER cc_start: 0.7664 (p) cc_final: 0.7337 (p) REVERT: C 216 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.6956 (mtm-85) REVERT: C 247 TRP cc_start: 0.8526 (m100) cc_final: 0.7911 (m100) REVERT: D 79 LEU cc_start: 0.8431 (tp) cc_final: 0.8179 (tp) REVERT: D 181 ASP cc_start: 0.7496 (t0) cc_final: 0.7167 (t0) REVERT: E 129 PRO cc_start: 0.9197 (Cg_endo) cc_final: 0.8972 (Cg_exo) REVERT: E 199 MET cc_start: 0.9062 (ptm) cc_final: 0.8816 (ppp) REVERT: G 34 ARG cc_start: 0.8264 (tpt-90) cc_final: 0.7951 (tpt-90) REVERT: G 71 LEU cc_start: 0.8494 (mm) cc_final: 0.8255 (mm) REVERT: G 74 MET cc_start: 0.7601 (ptt) cc_final: 0.7024 (ptp) REVERT: G 94 ARG cc_start: 0.7260 (mmt180) cc_final: 0.6675 (mmt180) REVERT: G 124 CYS cc_start: 0.8162 (p) cc_final: 0.7827 (p) REVERT: G 127 GLN cc_start: 0.8005 (pp30) cc_final: 0.7403 (pp30) REVERT: G 166 GLU cc_start: 0.7097 (pp20) cc_final: 0.6430 (pp20) REVERT: J 106 LYS cc_start: 0.8400 (ptpt) cc_final: 0.7566 (ptpp) REVERT: N 24 MET cc_start: 0.7240 (tpp) cc_final: 0.6971 (ttm) REVERT: N 99 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8820 (mttt) REVERT: O 69 ASP cc_start: 0.8961 (m-30) cc_final: 0.8264 (t0) REVERT: Q 70 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8384 (tp-100) REVERT: Q 110 GLU cc_start: 0.8759 (tt0) cc_final: 0.8341 (pt0) REVERT: R 11 GLN cc_start: 0.8437 (pt0) cc_final: 0.8163 (pt0) REVERT: R 62 GLU cc_start: 0.7653 (tp30) cc_final: 0.6792 (tt0) REVERT: S 59 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6861 (mt-10) REVERT: S 95 ARG cc_start: 0.7288 (mmm160) cc_final: 0.6901 (mmm160) REVERT: T 28 ASN cc_start: 0.8934 (t0) cc_final: 0.8359 (t0) REVERT: V 85 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8775 (mmmt) REVERT: W 22 PHE cc_start: 0.8096 (m-80) cc_final: 0.7644 (m-80) REVERT: W 52 ASP cc_start: 0.8721 (p0) cc_final: 0.8371 (p0) REVERT: W 64 LYS cc_start: 0.8528 (pttt) cc_final: 0.8292 (pttp) REVERT: Y 17 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8440 (tm-30) REVERT: Y 19 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8362 (mm) REVERT: Y 49 ASP cc_start: 0.8150 (m-30) cc_final: 0.7791 (m-30) REVERT: Y 60 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8156 (ttpt) REVERT: I 96 LYS cc_start: 0.6442 (mmpt) cc_final: 0.5471 (tmmt) REVERT: I 133 ARG cc_start: 0.4669 (OUTLIER) cc_final: 0.4338 (ptt90) REVERT: K 110 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7972 (tm-30) REVERT: K 112 PHE cc_start: 0.8303 (m-80) cc_final: 0.7855 (m-80) REVERT: P 26 GLU cc_start: 0.8006 (tp30) cc_final: 0.7766 (tp30) REVERT: P 67 GLU cc_start: 0.7805 (pp20) cc_final: 0.7272 (pp20) REVERT: 6 79 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8309 (p) REVERT: 7 44 ARG cc_start: 0.6641 (mtt180) cc_final: 0.6044 (mtm180) REVERT: 7 67 ILE cc_start: 0.6806 (mp) cc_final: 0.6546 (tt) REVERT: 7 137 ARG cc_start: 0.6635 (mmt180) cc_final: 0.6378 (mmt180) REVERT: 7 179 MET cc_start: 0.7527 (mmp) cc_final: 0.7024 (mmt) REVERT: 7 204 MET cc_start: 0.7825 (tmm) cc_final: 0.7278 (tpp) REVERT: 7 232 ARG cc_start: 0.5935 (mtt180) cc_final: 0.5404 (mmp-170) REVERT: 7 235 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7508 (tp40) REVERT: 7 288 HIS cc_start: 0.3312 (OUTLIER) cc_final: 0.2720 (m-70) REVERT: 8 107 ARG cc_start: 0.7927 (mmp80) cc_final: 0.7613 (mmt90) REVERT: 8 147 GLN cc_start: 0.7935 (pp30) cc_final: 0.7364 (mt0) REVERT: 8 148 LEU cc_start: 0.7035 (tt) cc_final: 0.6337 (tp) REVERT: 9 26 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.5460 (tt0) REVERT: 9 158 LEU cc_start: 0.8131 (mp) cc_final: 0.7849 (mt) REVERT: 9 209 PHE cc_start: 0.6418 (p90) cc_final: 0.6213 (p90) REVERT: 9 331 PHE cc_start: 0.8407 (t80) cc_final: 0.8012 (t80) REVERT: M 53 MET cc_start: 0.5912 (mtm) cc_final: 0.4750 (tmm) REVERT: M 64 TRP cc_start: 0.5874 (m-90) cc_final: 0.5262 (m-90) REVERT: M 105 MET cc_start: 0.7755 (tpp) cc_final: 0.7249 (tmm) REVERT: H 7 ASP cc_start: 0.8529 (t0) cc_final: 0.8239 (t0) REVERT: F 16 MET cc_start: 0.6838 (tpp) cc_final: 0.6511 (tpt) REVERT: F 25 MET cc_start: 0.7760 (tmm) cc_final: 0.7495 (tmm) REVERT: F 50 ASP cc_start: 0.7825 (m-30) cc_final: 0.7563 (m-30) REVERT: F 76 PHE cc_start: 0.6513 (m-80) cc_final: 0.5934 (t80) REVERT: F 93 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7172 (mm-30) REVERT: F 96 TRP cc_start: 0.6733 (m-90) cc_final: 0.6481 (m-10) REVERT: F 99 PHE cc_start: 0.8461 (t80) cc_final: 0.7750 (t80) REVERT: F 100 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7805 (mm-30) REVERT: F 129 MET cc_start: 0.7010 (mpp) cc_final: 0.6587 (mpp) REVERT: F 137 PHE cc_start: 0.7795 (m-80) cc_final: 0.7336 (m-80) REVERT: F 166 ARG cc_start: 0.8164 (tpp-160) cc_final: 0.7144 (mmt90) REVERT: b 1 MET cc_start: 0.3429 (tmm) cc_final: 0.2644 (mtm) outliers start: 161 outliers final: 139 residues processed: 974 average time/residue: 0.9180 time to fit residues: 1543.0787 Evaluate side-chains 1008 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 860 time to evaluate : 4.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 15 LYS Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain 6 residue 6 LEU Chi-restraints excluded: chain 6 residue 22 ILE Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 36 CYS Chi-restraints excluded: chain 6 residue 78 ILE Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 7 residue 30 ASP Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 209 VAL Chi-restraints excluded: chain 7 residue 235 GLN Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 284 LEU Chi-restraints excluded: chain 7 residue 288 HIS Chi-restraints excluded: chain 8 residue 49 LEU Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 8 residue 123 ASP Chi-restraints excluded: chain 9 residue 26 GLU Chi-restraints excluded: chain 9 residue 28 TYR Chi-restraints excluded: chain 9 residue 38 ASP Chi-restraints excluded: chain 9 residue 111 HIS Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 180 SER Chi-restraints excluded: chain 9 residue 217 LEU Chi-restraints excluded: chain 9 residue 321 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 35 VAL Chi-restraints excluded: chain e residue 109 LYS Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain b residue 5 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 455 optimal weight: 20.0000 chunk 610 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 528 optimal weight: 20.0000 chunk 84 optimal weight: 0.0370 chunk 159 optimal weight: 2.9990 chunk 574 optimal weight: 20.0000 chunk 240 optimal weight: 30.0000 chunk 589 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 overall best weight: 5.6068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** 7 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 99 GLN ** 8 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 71 GLN ** 9 234 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 = 0.3842 r_free = 0.3842 target = 0.108080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.086628 restraints weight = 304519.192| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.04 r_work: 0.3362 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 107182 Z= 0.259 Angle : 0.621 12.862 159778 Z= 0.317 Chirality : 0.036 0.339 20348 Planarity : 0.005 0.104 9003 Dihedral : 23.564 179.349 52046 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 4.69 % Allowed : 28.12 % Favored : 67.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.12), residues: 4280 helix: -0.32 (0.15), residues: 1117 sheet: -1.20 (0.18), residues: 776 loop : -1.58 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP 9 46 HIS 0.012 0.001 HIS J 80 PHE 0.067 0.002 PHE Q 78 TYR 0.044 0.002 TYR F 127 ARG 0.009 0.001 ARG V 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24384.53 seconds wall clock time: 431 minutes 9.26 seconds (25869.26 seconds total)