Starting phenix.real_space_refine on Sat Aug 23 14:36:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bi5_44559/08_2025/9bi5_44559_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bi5_44559/08_2025/9bi5_44559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bi5_44559/08_2025/9bi5_44559_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bi5_44559/08_2025/9bi5_44559_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bi5_44559/08_2025/9bi5_44559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bi5_44559/08_2025/9bi5_44559.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.046 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: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 P 6 5.49 5 S 64 5.16 5 C 7827 2.51 5 N 2133 2.21 5 O 2379 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12413 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 3217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3217 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3237 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 27, 'TRANS': 383} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2631 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 324} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3262 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 27, 'TRANS': 384} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.63, per 1000 atoms: 0.21 Number of scatterers: 12413 At special positions: 0 Unit cell: (95.304, 111.549, 158.118, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 S 64 16.00 P 6 15.00 O 2379 8.00 N 2133 7.00 C 7827 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 513.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2966 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 21 sheets defined 29.3% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.523A pdb=" N THR D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 134 through 144 Proline residue: D 140 - end of helix Processing helix chain 'D' and resid 146 through 151 removed outlier: 3.914A pdb=" N LEU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 151' Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 171 through 178 removed outlier: 3.659A pdb=" N ASP D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 200 removed outlier: 3.687A pdb=" N ALA D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 209 removed outlier: 3.701A pdb=" N LEU D 204 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 208 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 1131 through 1136 Processing helix chain 'D' and resid 1145 through 1148 Processing helix chain 'D' and resid 1149 through 1158 removed outlier: 3.871A pdb=" N ASP D1154 " --> pdb=" O ASN D1150 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU D1155 " --> pdb=" O ARG D1151 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1221 removed outlier: 3.633A pdb=" N SER D1213 " --> pdb=" O LYS D1209 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D1215 " --> pdb=" O LEU D1211 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER D1221 " --> pdb=" O ARG D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1245 through 1259 removed outlier: 3.818A pdb=" N ALA D1249 " --> pdb=" O ILE D1245 " (cutoff:3.500A) Processing helix chain 'D' and resid 1273 through 1280 Processing helix chain 'D' and resid 1306 through 1310 Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.621A pdb=" N MET A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.514A pdb=" N ASP A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.619A pdb=" N LEU A 230 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 325 through 350 removed outlier: 3.694A pdb=" N GLN A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 393 through 396 removed outlier: 3.747A pdb=" N VAL A 396 " --> pdb=" O ASN A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 396' Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.817A pdb=" N ILE C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 4.157A pdb=" N ALA C 50 " --> pdb=" O CYS C 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.663A pdb=" N THR C 71 " --> pdb=" O ASP C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 Proline residue: C 140 - end of helix Processing helix chain 'C' and resid 167 through 180 removed outlier: 3.954A pdb=" N LEU C 171 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1150 through 1153 Processing helix chain 'C' and resid 1154 through 1160 Processing helix chain 'C' and resid 1208 through 1224 removed outlier: 5.041A pdb=" N GLU C1222 " --> pdb=" O LEU C1218 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C1224 " --> pdb=" O LEU C1220 " (cutoff:3.500A) Processing helix chain 'C' and resid 1241 through 1249 removed outlier: 4.368A pdb=" N SER C1247 " --> pdb=" O GLU C1243 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA C1249 " --> pdb=" O ILE C1245 " (cutoff:3.500A) Processing helix chain 'C' and resid 1249 through 1260 Processing helix chain 'C' and resid 1273 through 1278 Processing helix chain 'C' and resid 1281 through 1285 removed outlier: 3.672A pdb=" N PHE C1285 " --> pdb=" O ALA C1282 " (cutoff:3.500A) Processing helix chain 'C' and resid 1308 through 1310 No H-bonds generated for 'chain 'C' and resid 1308 through 1310' Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.603A pdb=" N ASN B 45 " --> pdb=" O MET B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 80 removed outlier: 4.048A pdb=" N LEU B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYS B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 181 through 191 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.640A pdb=" N PHE B 229 " --> pdb=" O PRO B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 322 through 350 Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.639A pdb=" N SER B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 9 Processing sheet with id=AA2, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'D' and resid 75 through 85 removed outlier: 3.859A pdb=" N PHE D 84 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL D 117 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR D 95 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN D 97 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLU D 113 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN D 99 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR D 111 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU D 101 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE D 109 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU D 116 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 1169 through 1171 removed outlier: 4.137A pdb=" N LYS D1170 " --> pdb=" O VAL D1190 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL D1190 " --> pdb=" O LYS D1170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 1229 through 1231 removed outlier: 6.766A pdb=" N GLY D1229 " --> pdb=" O GLN D1266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 146 through 148 removed outlier: 7.041A pdb=" N VAL A 118 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL A 51 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE A 121 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN A 53 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 9 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 292 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 146 through 148 removed outlier: 7.041A pdb=" N VAL A 118 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL A 51 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE A 121 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN A 53 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 9 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AA9, first strand: chain 'A' and resid 158 through 160 removed outlier: 6.972A pdb=" N ILE A 158 " --> pdb=" O THR A 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 173 through 175 removed outlier: 5.721A pdb=" N ALA A 173 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N CYS A 211 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR A 175 " --> pdb=" O CYS A 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 245 through 246 removed outlier: 4.692A pdb=" N GLN A 261 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 304 through 310 removed outlier: 6.704A pdb=" N LYS A 305 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ARG A 368 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS A 307 " --> pdb=" O ARG A 368 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ASP A 370 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ILE A 309 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLN A 407 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 367 " --> pdb=" O GLN A 407 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYR A 409 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL A 369 " --> pdb=" O TYR A 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 1231 through 1234 removed outlier: 6.387A pdb=" N ILE C1231 " --> pdb=" O ILE C1268 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE C1270 " --> pdb=" O ILE C1231 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU C1233 " --> pdb=" O ILE C1270 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LEU C 29 " --> pdb=" O HIS C1288 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N PHE C1290 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 31 " --> pdb=" O PHE C1290 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL C1292 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 33 " --> pdb=" O VAL C1292 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N ARG C1294 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C1293 " --> pdb=" O GLN C1301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1231 through 1234 removed outlier: 6.387A pdb=" N ILE C1231 " --> pdb=" O ILE C1268 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE C1270 " --> pdb=" O ILE C1231 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU C1233 " --> pdb=" O ILE C1270 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LEU C 29 " --> pdb=" O HIS C1288 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N PHE C1290 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 31 " --> pdb=" O PHE C1290 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL C1292 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 33 " --> pdb=" O VAL C1292 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N ARG C1294 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C1289 " --> pdb=" O VAL C1305 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL C1305 " --> pdb=" O PHE C1289 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.785A pdb=" N ILE C 98 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 92 through 93 removed outlier: 3.740A pdb=" N ILE C 93 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 117 " --> pdb=" O ILE C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 147 through 148 removed outlier: 6.543A pdb=" N VAL B 51 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG B 10 " --> pdb=" O MET B 50 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL B 52 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU B 12 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 147 through 148 removed outlier: 6.543A pdb=" N VAL B 51 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG B 10 " --> pdb=" O MET B 50 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL B 52 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU B 12 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 89 removed outlier: 3.536A pdb=" N LEU B 172 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 167 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 237 " --> pdb=" O ASP B 258 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 158 through 160 Processing sheet with id=AC3, first strand: chain 'B' and resid 304 through 308 removed outlier: 6.730A pdb=" N LYS B 305 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ARG B 368 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS B 307 " --> pdb=" O ARG B 368 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLN B 407 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU B 367 " --> pdb=" O GLN B 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 332 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.03 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: 3387 1.33 - 1.45: 2126 1.45 - 1.57: 7027 1.57 - 1.70: 10 1.70 - 1.82: 106 Bond restraints: 12656 Sorted by residual: bond pdb=" C SER C 166 " pdb=" N GLU C 167 " ideal model delta sigma weight residual 1.327 1.354 -0.027 1.05e-02 9.07e+03 6.58e+00 bond pdb=" C TRP D 163 " pdb=" N PRO D 164 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.74e+00 bond pdb=" N CYS D1204 " pdb=" CA CYS D1204 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.41e-02 5.03e+03 4.13e+00 bond pdb=" C THR A 15 " pdb=" O THR A 15 " ideal model delta sigma weight residual 1.235 1.210 0.025 1.26e-02 6.30e+03 3.90e+00 bond pdb=" CA SER D1213 " pdb=" C SER D1213 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.27e-02 6.20e+03 3.78e+00 ... (remaining 12651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 16686 2.08 - 4.17: 406 4.17 - 6.25: 36 6.25 - 8.34: 9 8.34 - 10.42: 5 Bond angle restraints: 17142 Sorted by residual: angle pdb=" N CYS D1204 " pdb=" CA CYS D1204 " pdb=" C CYS D1204 " ideal model delta sigma weight residual 108.86 119.28 -10.42 1.41e+00 5.03e-01 5.46e+01 angle pdb=" N PHE D 64 " pdb=" CA PHE D 64 " pdb=" C PHE D 64 " ideal model delta sigma weight residual 114.04 105.67 8.37 1.24e+00 6.50e-01 4.56e+01 angle pdb=" N SER D1213 " pdb=" CA SER D1213 " pdb=" C SER D1213 " ideal model delta sigma weight residual 111.07 105.85 5.22 1.07e+00 8.73e-01 2.38e+01 angle pdb=" N SER D1205 " pdb=" CA SER D1205 " pdb=" C SER D1205 " ideal model delta sigma weight residual 109.06 116.87 -7.81 1.70e+00 3.46e-01 2.11e+01 angle pdb=" N GLY B 263 " pdb=" CA GLY B 263 " pdb=" C GLY B 263 " ideal model delta sigma weight residual 111.67 115.33 -3.66 9.20e-01 1.18e+00 1.58e+01 ... (remaining 17137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6630 17.78 - 35.56: 810 35.56 - 53.35: 216 53.35 - 71.13: 59 71.13 - 88.91: 21 Dihedral angle restraints: 7736 sinusoidal: 3176 harmonic: 4560 Sorted by residual: dihedral pdb=" CA LEU D 162 " pdb=" C LEU D 162 " pdb=" N TRP D 163 " pdb=" CA TRP D 163 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA SER D1136 " pdb=" C SER D1136 " pdb=" N ALA D1137 " pdb=" CA ALA D1137 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA VAL A 280 " pdb=" C VAL A 280 " pdb=" N PHE A 281 " pdb=" CA PHE A 281 " ideal model delta harmonic sigma weight residual 180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 7733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1417 0.051 - 0.101: 426 0.101 - 0.152: 81 0.152 - 0.203: 8 0.203 - 0.253: 2 Chirality restraints: 1934 Sorted by residual: chirality pdb=" CA VAL C 80 " pdb=" N VAL C 80 " pdb=" C VAL C 80 " pdb=" CB VAL C 80 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA GLN D1194 " pdb=" N GLN D1194 " pdb=" C GLN D1194 " pdb=" CB GLN D1194 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA GLU A 86 " pdb=" N GLU A 86 " pdb=" C GLU A 86 " pdb=" CB GLU A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1931 not shown) Planarity restraints: 2218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP D1401 " 0.005 2.00e-02 2.50e+03 1.84e-02 9.27e+00 pdb=" C2 ATP D1401 " -0.006 2.00e-02 2.50e+03 pdb=" C4 ATP D1401 " -0.000 2.00e-02 2.50e+03 pdb=" C5 ATP D1401 " 0.054 2.00e-02 2.50e+03 pdb=" C6 ATP D1401 " -0.000 2.00e-02 2.50e+03 pdb=" C8 ATP D1401 " -0.019 2.00e-02 2.50e+03 pdb=" N1 ATP D1401 " -0.009 2.00e-02 2.50e+03 pdb=" N3 ATP D1401 " -0.005 2.00e-02 2.50e+03 pdb=" N6 ATP D1401 " -0.005 2.00e-02 2.50e+03 pdb=" N7 ATP D1401 " -0.015 2.00e-02 2.50e+03 pdb=" N9 ATP D1401 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 360 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.12e+00 pdb=" N PRO A 361 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 387 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO A 388 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.027 5.00e-02 4.00e+02 ... (remaining 2215 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 231 2.61 - 3.19: 11195 3.19 - 3.76: 19873 3.76 - 4.33: 26263 4.33 - 4.90: 43244 Nonbonded interactions: 100806 Sorted by model distance: nonbonded pdb=" OD1 ASP A 16 " pdb="MN MN A1001 " model vdw 2.043 2.320 nonbonded pdb=" OD1 ASP B 16 " pdb="MN MN B1001 " model vdw 2.135 2.320 nonbonded pdb=" OD2 ASP A 56 " pdb="MN MN A1001 " model vdw 2.178 2.320 nonbonded pdb=" NE2 HIS A 18 " pdb="MN MN A1001 " model vdw 2.179 2.400 nonbonded pdb=" OD1 ASN A 124 " pdb="MN MN A1002 " model vdw 2.182 2.320 ... (remaining 100801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 40 or (resid 41 through 43 and (name N or name C \ A or name C or name O or name CB )) or resid 44 through 142 or (resid 143 and (n \ ame N or name CA or name C or name O or name CB )) or resid 144 through 1002)) selection = (chain 'B' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 20 or (resid 21 and (name N or name CA \ or name C or name O or name CB )) or resid 22 through 73 or (resid 74 and (name \ N or name CA or name C or name O or name CB )) or resid 75 through 145 or (resi \ d 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 304 or (resid 305 and (name N or name CA or name C or name O or name CB )) o \ r resid 306 through 355 or (resid 356 and (name N or name CA or name C or name O \ or name CB )) or resid 357 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.450 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 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 : 0.005 0.051 12656 Z= 0.229 Angle : 0.782 10.420 17142 Z= 0.439 Chirality : 0.049 0.253 1934 Planarity : 0.006 0.062 2218 Dihedral : 17.573 88.910 4770 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.00 % Favored : 90.68 % Rotamer: Outliers : 7.59 % Allowed : 19.34 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.04 (0.20), residues: 1545 helix: -1.72 (0.23), residues: 387 sheet: -2.03 (0.29), residues: 299 loop : -2.17 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1201 TYR 0.016 0.002 TYR A 409 PHE 0.021 0.002 PHE B 257 TRP 0.023 0.003 TRP C1157 HIS 0.006 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00488 (12656) covalent geometry : angle 0.78212 (17142) hydrogen bonds : bond 0.24316 ( 311) hydrogen bonds : angle 8.69318 ( 879) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 171 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1146 MET cc_start: 0.5885 (tmm) cc_final: 0.5642 (tmm) REVERT: A 119 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7103 (p90) REVERT: C 1149 ILE cc_start: 0.6595 (mp) cc_final: 0.6258 (mp) REVERT: B 80 MET cc_start: 0.7958 (mtp) cc_final: 0.7711 (mtp) REVERT: B 409 TYR cc_start: 0.6055 (p90) cc_final: 0.5825 (p90) outliers start: 104 outliers final: 53 residues processed: 266 average time/residue: 0.0821 time to fit residues: 33.2813 Evaluate side-chains 192 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 138 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain D residue 1214 ILE Chi-restraints excluded: chain D residue 1220 LEU Chi-restraints excluded: chain D residue 1252 LEU Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1289 PHE Chi-restraints excluded: chain D residue 1300 SER Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1165 ASP Chi-restraints excluded: chain C residue 1213 SER Chi-restraints excluded: chain C residue 1266 GLN Chi-restraints excluded: chain C residue 1269 VAL Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN D 97 ASN D 120 ASN D 121 ASN D 158 GLN D1147 GLN D1194 GLN ** D1264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 45 ASN A 95 GLN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 341 ASN ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN C1262 GLN ** C1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 98 HIS B 208 ASN B 214 GLN B 261 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.156395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.133792 restraints weight = 23538.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.134538 restraints weight = 17335.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.135533 restraints weight = 17306.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.135933 restraints weight = 12608.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.136404 restraints weight = 12038.221| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12656 Z= 0.176 Angle : 0.684 8.798 17142 Z= 0.355 Chirality : 0.047 0.186 1934 Planarity : 0.005 0.052 2218 Dihedral : 10.951 88.750 1812 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.32 % Favored : 90.42 % Rotamer: Outliers : 5.55 % Allowed : 23.36 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.20), residues: 1545 helix: -1.20 (0.24), residues: 398 sheet: -1.85 (0.29), residues: 305 loop : -2.13 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1188 TYR 0.017 0.002 TYR D1185 PHE 0.018 0.002 PHE D1289 TRP 0.012 0.002 TRP A 33 HIS 0.006 0.001 HIS D1279 Details of bonding type rmsd covalent geometry : bond 0.00399 (12656) covalent geometry : angle 0.68425 (17142) hydrogen bonds : bond 0.05156 ( 311) hydrogen bonds : angle 6.33624 ( 879) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 157 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 166 SER cc_start: 0.7705 (t) cc_final: 0.7381 (p) REVERT: D 194 ILE cc_start: -0.0105 (OUTLIER) cc_final: -0.0464 (mt) REVERT: D 1139 MET cc_start: 0.6277 (mmp) cc_final: 0.5942 (mmp) REVERT: D 1146 MET cc_start: 0.6332 (tmm) cc_final: 0.5882 (tmm) REVERT: A 89 LEU cc_start: 0.4707 (OUTLIER) cc_final: 0.4453 (tt) REVERT: A 119 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6424 (p90) REVERT: A 166 GLN cc_start: 0.6546 (tm-30) cc_final: 0.6269 (tm-30) REVERT: C 1253 HIS cc_start: 0.4807 (OUTLIER) cc_final: 0.4571 (m-70) REVERT: B 101 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.5672 (pt0) outliers start: 76 outliers final: 52 residues processed: 221 average time/residue: 0.0816 time to fit residues: 27.3112 Evaluate side-chains 197 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain D residue 1200 MET Chi-restraints excluded: chain D residue 1239 ASN Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain C residue 1253 HIS Chi-restraints excluded: chain C residue 1304 TRP Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 97 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 55 optimal weight: 0.0170 chunk 18 optimal weight: 7.9990 chunk 71 optimal weight: 0.0370 chunk 133 optimal weight: 0.1980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** D1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1298 GLN A 106 ASN A 147 ASN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN ** C1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 98 HIS B 401 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.159912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.137159 restraints weight = 23990.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.138400 restraints weight = 17172.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.139260 restraints weight = 16695.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.139798 restraints weight = 11939.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.140119 restraints weight = 11061.933| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12656 Z= 0.121 Angle : 0.619 8.771 17142 Z= 0.318 Chirality : 0.045 0.172 1934 Planarity : 0.004 0.050 2218 Dihedral : 9.473 84.898 1769 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.22 % Favored : 91.59 % Rotamer: Outliers : 5.33 % Allowed : 23.72 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.21), residues: 1545 helix: -0.90 (0.25), residues: 399 sheet: -1.33 (0.31), residues: 272 loop : -1.99 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 96 TYR 0.011 0.001 TYR C 49 PHE 0.016 0.001 PHE B 257 TRP 0.013 0.002 TRP A 33 HIS 0.009 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00271 (12656) covalent geometry : angle 0.61863 (17142) hydrogen bonds : bond 0.04233 ( 311) hydrogen bonds : angle 5.94447 ( 879) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6661 (mp) REVERT: D 1139 MET cc_start: 0.6302 (mmp) cc_final: 0.6040 (mmp) REVERT: D 1146 MET cc_start: 0.6147 (tmm) cc_final: 0.5915 (tmm) REVERT: A 89 LEU cc_start: 0.4466 (OUTLIER) cc_final: 0.4164 (tt) REVERT: A 119 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6568 (p90) REVERT: A 250 VAL cc_start: 0.5590 (t) cc_final: 0.5280 (t) REVERT: A 283 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6565 (tt) REVERT: C 1146 MET cc_start: 0.7101 (tpt) cc_final: 0.6732 (tpt) REVERT: C 1253 HIS cc_start: 0.4567 (OUTLIER) cc_final: 0.4298 (m-70) outliers start: 73 outliers final: 44 residues processed: 219 average time/residue: 0.0821 time to fit residues: 27.3900 Evaluate side-chains 191 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain D residue 1239 ASN Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1300 SER Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1237 THR Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain C residue 1253 HIS Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 4.9990 chunk 130 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 96 optimal weight: 0.2980 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1194 GLN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN C1266 GLN B 98 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.160316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.137229 restraints weight = 23714.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.137771 restraints weight = 17969.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.139089 restraints weight = 16828.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.139583 restraints weight = 12920.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.140218 restraints weight = 13269.745| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12656 Z= 0.118 Angle : 0.603 8.630 17142 Z= 0.308 Chirality : 0.044 0.161 1934 Planarity : 0.004 0.045 2218 Dihedral : 8.729 89.781 1760 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.41 % Favored : 91.46 % Rotamer: Outliers : 5.99 % Allowed : 23.80 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.21), residues: 1545 helix: -0.61 (0.26), residues: 391 sheet: -1.34 (0.31), residues: 290 loop : -1.88 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 96 TYR 0.015 0.001 TYR B 409 PHE 0.026 0.001 PHE B 391 TRP 0.011 0.001 TRP A 33 HIS 0.011 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00269 (12656) covalent geometry : angle 0.60310 (17142) hydrogen bonds : bond 0.03863 ( 311) hydrogen bonds : angle 5.64933 ( 879) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 157 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: D 44 ILE cc_start: 0.6975 (OUTLIER) cc_final: 0.6675 (mp) REVERT: D 1146 MET cc_start: 0.6142 (tmm) cc_final: 0.5937 (tmm) REVERT: D 1203 ARG cc_start: 0.5945 (OUTLIER) cc_final: 0.4343 (ttm-80) REVERT: A 89 LEU cc_start: 0.4474 (OUTLIER) cc_final: 0.4215 (tt) REVERT: A 119 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.6749 (p90) REVERT: A 186 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6818 (t80) REVERT: C 1188 ARG cc_start: 0.6839 (ptt-90) cc_final: 0.6160 (ptt-90) REVERT: B 101 GLU cc_start: 0.5741 (OUTLIER) cc_final: 0.5521 (pt0) outliers start: 82 outliers final: 51 residues processed: 227 average time/residue: 0.0849 time to fit residues: 29.5229 Evaluate side-chains 201 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 144 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1203 ARG Chi-restraints excluded: chain D residue 1239 ASN Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1300 SER Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1237 THR Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain C residue 1266 GLN Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 73 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 21 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.0060 chunk 100 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1194 GLN ** D1272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN C1266 GLN B 98 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.160139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.137401 restraints weight = 24147.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.138504 restraints weight = 17599.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.139524 restraints weight = 16361.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.139796 restraints weight = 12160.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.140060 restraints weight = 12159.030| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12656 Z= 0.121 Angle : 0.602 9.950 17142 Z= 0.305 Chirality : 0.044 0.231 1934 Planarity : 0.004 0.044 2218 Dihedral : 8.084 71.405 1754 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.28 % Favored : 91.59 % Rotamer: Outliers : 5.84 % Allowed : 23.72 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.21), residues: 1545 helix: -0.47 (0.26), residues: 392 sheet: -1.23 (0.31), residues: 290 loop : -1.78 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 96 TYR 0.009 0.001 TYR B 371 PHE 0.019 0.001 PHE B 391 TRP 0.011 0.001 TRP A 33 HIS 0.007 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00277 (12656) covalent geometry : angle 0.60178 (17142) hydrogen bonds : bond 0.03714 ( 311) hydrogen bonds : angle 5.54636 ( 879) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 152 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6703 (mp) REVERT: D 1146 MET cc_start: 0.6085 (tmm) cc_final: 0.5875 (tmm) REVERT: D 1203 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.4308 (ttm-80) REVERT: A 89 LEU cc_start: 0.4611 (OUTLIER) cc_final: 0.4315 (tt) REVERT: A 119 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6593 (p90) REVERT: A 186 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6808 (t80) REVERT: B 101 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.5532 (pt0) outliers start: 80 outliers final: 51 residues processed: 218 average time/residue: 0.0829 time to fit residues: 27.4545 Evaluate side-chains 197 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 1139 MET Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1203 ARG Chi-restraints excluded: chain D residue 1239 ASN Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1272 HIS Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1300 SER Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 47 optimal weight: 0.0670 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN C1298 GLN B 98 HIS B 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.160163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.137185 restraints weight = 23607.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.138008 restraints weight = 17303.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.138869 restraints weight = 17507.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.139348 restraints weight = 12683.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.140007 restraints weight = 11904.249| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12656 Z= 0.119 Angle : 0.601 11.211 17142 Z= 0.303 Chirality : 0.044 0.189 1934 Planarity : 0.004 0.047 2218 Dihedral : 7.649 65.513 1746 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.28 % Favored : 91.59 % Rotamer: Outliers : 5.55 % Allowed : 24.31 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.22), residues: 1545 helix: -0.37 (0.27), residues: 392 sheet: -1.09 (0.31), residues: 293 loop : -1.71 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 96 TYR 0.010 0.001 TYR C 49 PHE 0.018 0.001 PHE C1224 TRP 0.011 0.001 TRP A 33 HIS 0.006 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00276 (12656) covalent geometry : angle 0.60102 (17142) hydrogen bonds : bond 0.03571 ( 311) hydrogen bonds : angle 5.45024 ( 879) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 145 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6674 (mp) REVERT: D 1146 MET cc_start: 0.6136 (tmm) cc_final: 0.5880 (tmm) REVERT: D 1203 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.4058 (ttm-80) REVERT: A 89 LEU cc_start: 0.4642 (OUTLIER) cc_final: 0.4355 (tt) REVERT: A 119 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.6691 (p90) REVERT: A 186 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6861 (t80) REVERT: B 101 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5525 (pt0) outliers start: 76 outliers final: 59 residues processed: 210 average time/residue: 0.0879 time to fit residues: 28.3472 Evaluate side-chains 203 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 138 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 1139 MET Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1203 ARG Chi-restraints excluded: chain D residue 1239 ASN Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1272 HIS Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1300 SER Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1204 CYS Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1237 THR Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain C residue 1280 MET Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 153 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 114 optimal weight: 0.0670 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 HIS ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN C1298 GLN B 98 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.160092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.137146 restraints weight = 23659.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.137805 restraints weight = 17710.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.138928 restraints weight = 16770.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.139187 restraints weight = 12804.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.139421 restraints weight = 13050.427| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12656 Z= 0.123 Angle : 0.608 12.381 17142 Z= 0.305 Chirality : 0.044 0.170 1934 Planarity : 0.004 0.048 2218 Dihedral : 7.430 61.604 1744 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.09 % Favored : 91.84 % Rotamer: Outliers : 5.91 % Allowed : 24.60 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.22), residues: 1545 helix: -0.28 (0.27), residues: 391 sheet: -1.05 (0.30), residues: 298 loop : -1.66 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 96 TYR 0.016 0.001 TYR B 409 PHE 0.019 0.001 PHE C1224 TRP 0.010 0.001 TRP A 33 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00285 (12656) covalent geometry : angle 0.60764 (17142) hydrogen bonds : bond 0.03520 ( 311) hydrogen bonds : angle 5.35636 ( 879) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 147 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.6974 (OUTLIER) cc_final: 0.6688 (mp) REVERT: D 1146 MET cc_start: 0.6256 (tmm) cc_final: 0.6006 (tmm) REVERT: D 1203 ARG cc_start: 0.5617 (OUTLIER) cc_final: 0.3974 (ttm-80) REVERT: A 119 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6681 (p90) REVERT: A 186 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6807 (t80) REVERT: A 250 VAL cc_start: 0.5824 (t) cc_final: 0.5583 (t) REVERT: C 35 MET cc_start: 0.7268 (mmp) cc_final: 0.6707 (mmp) REVERT: C 1222 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7178 (mm-30) REVERT: B 33 TRP cc_start: 0.6314 (OUTLIER) cc_final: 0.5976 (p-90) REVERT: B 101 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.5521 (pt0) outliers start: 81 outliers final: 62 residues processed: 217 average time/residue: 0.0818 time to fit residues: 27.2648 Evaluate side-chains 207 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 138 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 1139 MET Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1203 ARG Chi-restraints excluded: chain D residue 1239 ASN Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1272 HIS Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1204 CYS Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1237 THR Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain C residue 1280 MET Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 TRP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 39 optimal weight: 0.0770 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 HIS ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN B 98 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.160530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.137690 restraints weight = 23662.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.138554 restraints weight = 17320.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.139550 restraints weight = 16718.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.139911 restraints weight = 12402.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.140063 restraints weight = 12181.693| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12656 Z= 0.119 Angle : 0.610 13.133 17142 Z= 0.307 Chirality : 0.044 0.179 1934 Planarity : 0.004 0.044 2218 Dihedral : 7.193 57.556 1744 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.16 % Favored : 91.78 % Rotamer: Outliers : 6.28 % Allowed : 24.45 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.22), residues: 1545 helix: -0.31 (0.27), residues: 398 sheet: -0.98 (0.31), residues: 298 loop : -1.57 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 96 TYR 0.009 0.001 TYR C 49 PHE 0.019 0.001 PHE C1224 TRP 0.012 0.001 TRP A 33 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00277 (12656) covalent geometry : angle 0.61022 (17142) hydrogen bonds : bond 0.03414 ( 311) hydrogen bonds : angle 5.28611 ( 879) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 151 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6694 (mp) REVERT: D 94 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8352 (m) REVERT: D 1146 MET cc_start: 0.6258 (tmm) cc_final: 0.6007 (tmm) REVERT: D 1209 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6511 (ttpp) REVERT: A 89 LEU cc_start: 0.4600 (OUTLIER) cc_final: 0.4285 (tt) REVERT: A 119 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.6625 (p90) REVERT: A 186 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6843 (t80) REVERT: A 250 VAL cc_start: 0.5786 (t) cc_final: 0.5506 (t) REVERT: C 35 MET cc_start: 0.7254 (mmp) cc_final: 0.6740 (mmp) REVERT: C 1222 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6272 (mm-30) REVERT: B 33 TRP cc_start: 0.6319 (OUTLIER) cc_final: 0.5937 (p-90) REVERT: B 101 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.5487 (pt0) outliers start: 86 outliers final: 59 residues processed: 223 average time/residue: 0.0834 time to fit residues: 28.4170 Evaluate side-chains 210 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 142 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 1139 MET Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1168 THR Chi-restraints excluded: chain D residue 1203 ARG Chi-restraints excluded: chain D residue 1209 LYS Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1272 HIS Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1204 CYS Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1237 THR Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 TRP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 95 optimal weight: 0.1980 chunk 3 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 HIS ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1147 GLN ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN B 98 HIS B 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.160216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.137303 restraints weight = 23654.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.138152 restraints weight = 17226.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.139082 restraints weight = 17225.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.139476 restraints weight = 12501.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.140094 restraints weight = 12008.314| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12656 Z= 0.127 Angle : 0.626 13.391 17142 Z= 0.312 Chirality : 0.044 0.164 1934 Planarity : 0.004 0.044 2218 Dihedral : 7.067 61.014 1744 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.90 % Favored : 92.04 % Rotamer: Outliers : 5.62 % Allowed : 25.26 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.22), residues: 1545 helix: -0.18 (0.27), residues: 390 sheet: -0.92 (0.31), residues: 298 loop : -1.58 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.011 0.001 TYR C 49 PHE 0.022 0.001 PHE D 64 TRP 0.010 0.001 TRP A 33 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00297 (12656) covalent geometry : angle 0.62620 (17142) hydrogen bonds : bond 0.03475 ( 311) hydrogen bonds : angle 5.27433 ( 879) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 146 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6692 (mp) REVERT: D 1146 MET cc_start: 0.6244 (tmm) cc_final: 0.5982 (tmm) REVERT: D 1192 TYR cc_start: 0.5703 (m-80) cc_final: 0.5084 (m-80) REVERT: D 1203 ARG cc_start: 0.5630 (OUTLIER) cc_final: 0.4143 (ttm-80) REVERT: D 1209 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6508 (ttpp) REVERT: A 89 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.4304 (tt) REVERT: A 119 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.6530 (p90) REVERT: A 186 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6828 (t80) REVERT: A 250 VAL cc_start: 0.5812 (t) cc_final: 0.5568 (t) REVERT: C 35 MET cc_start: 0.7322 (mmp) cc_final: 0.6787 (mmp) REVERT: B 33 TRP cc_start: 0.6326 (OUTLIER) cc_final: 0.5991 (p-90) REVERT: B 101 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5445 (pt0) outliers start: 77 outliers final: 60 residues processed: 214 average time/residue: 0.0780 time to fit residues: 25.6853 Evaluate side-chains 209 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 141 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 1139 MET Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1168 THR Chi-restraints excluded: chain D residue 1203 ARG Chi-restraints excluded: chain D residue 1209 LYS Chi-restraints excluded: chain D residue 1239 ASN Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1272 HIS Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1169 ILE Chi-restraints excluded: chain C residue 1204 CYS Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1237 THR Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 TRP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 144 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 0.0570 chunk 116 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 15 optimal weight: 0.0020 overall best weight: 0.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1235 GLN ** D1272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 HIS ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN B 98 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.161819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.139142 restraints weight = 23600.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.140013 restraints weight = 16698.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.140854 restraints weight = 16953.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.141331 restraints weight = 12301.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.141877 restraints weight = 11672.147| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12656 Z= 0.114 Angle : 0.619 13.795 17142 Z= 0.310 Chirality : 0.044 0.157 1934 Planarity : 0.004 0.044 2218 Dihedral : 6.872 62.216 1744 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.64 % Favored : 92.30 % Rotamer: Outliers : 4.96 % Allowed : 25.91 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.22), residues: 1545 helix: -0.03 (0.28), residues: 385 sheet: -0.81 (0.31), residues: 298 loop : -1.57 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.017 0.001 TYR B 409 PHE 0.022 0.001 PHE D 64 TRP 0.014 0.001 TRP A 33 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00261 (12656) covalent geometry : angle 0.61946 (17142) hydrogen bonds : bond 0.03321 ( 311) hydrogen bonds : angle 5.19501 ( 879) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 151 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6655 (mp) REVERT: D 1146 MET cc_start: 0.6237 (tmm) cc_final: 0.5987 (tmm) REVERT: D 1203 ARG cc_start: 0.5501 (OUTLIER) cc_final: 0.3948 (ttm-80) REVERT: D 1209 LYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6349 (ttpp) REVERT: D 1235 GLN cc_start: 0.6814 (OUTLIER) cc_final: 0.6058 (mm-40) REVERT: A 89 LEU cc_start: 0.4562 (OUTLIER) cc_final: 0.4254 (tt) REVERT: A 119 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.6701 (p90) REVERT: A 186 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6709 (t80) REVERT: A 250 VAL cc_start: 0.5663 (t) cc_final: 0.5412 (t) REVERT: C 35 MET cc_start: 0.7315 (mmp) cc_final: 0.6779 (mmp) REVERT: B 33 TRP cc_start: 0.6186 (OUTLIER) cc_final: 0.5818 (p-90) outliers start: 68 outliers final: 56 residues processed: 211 average time/residue: 0.0881 time to fit residues: 28.1571 Evaluate side-chains 212 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 148 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 1139 MET Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1168 THR Chi-restraints excluded: chain D residue 1203 ARG Chi-restraints excluded: chain D residue 1209 LYS Chi-restraints excluded: chain D residue 1235 GLN Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1272 HIS Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1169 ILE Chi-restraints excluded: chain C residue 1204 CYS Chi-restraints excluded: chain C residue 1237 THR Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 TRP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.0570 chunk 121 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1235 GLN ** D1272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.161575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.138856 restraints weight = 23665.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.139840 restraints weight = 16684.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.140633 restraints weight = 16960.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.141164 restraints weight = 12292.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.141638 restraints weight = 11607.670| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 12656 Z= 0.184 Angle : 0.876 59.199 17142 Z= 0.481 Chirality : 0.050 0.952 1934 Planarity : 0.004 0.078 2218 Dihedral : 6.870 62.228 1744 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.64 % Favored : 92.30 % Rotamer: Outliers : 4.89 % Allowed : 25.62 % Favored : 69.49 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.22), residues: 1545 helix: -0.03 (0.28), residues: 385 sheet: -0.81 (0.31), residues: 298 loop : -1.57 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 96 TYR 0.009 0.001 TYR B 175 PHE 0.020 0.001 PHE C1224 TRP 0.013 0.001 TRP A 33 HIS 0.086 0.002 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00392 (12656) covalent geometry : angle 0.87554 (17142) hydrogen bonds : bond 0.03322 ( 311) hydrogen bonds : angle 5.19293 ( 879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1952.32 seconds wall clock time: 34 minutes 35.44 seconds (2075.44 seconds total)