Starting phenix.real_space_refine on Fri Jul 3 06:58:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bi5_44559/07_2026/9bi5_44559_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bi5_44559/07_2026/9bi5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bi5_44559/07_2026/9bi5_44559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bi5_44559/07_2026/9bi5_44559.map" model { file = "/net/cci-nas-00/data/ceres_data/9bi5_44559/07_2026/9bi5_44559_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bi5_44559/07_2026/9bi5_44559_neut.cif" } 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Time building chain proxies: 2.95, per 1000 atoms: 0.24 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: 1.01 Conformation dependent library (CDL) restraints added in 543.1 milliseconds 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: 0.33 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: 1.67 Time building geometry restraints manager: 1.32 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 3.060 nonbonded pdb=" OD1 ASP B 16 " pdb="MN MN B1001 " model vdw 2.135 3.060 nonbonded pdb=" OD2 ASP A 56 " pdb="MN MN A1001 " model vdw 2.178 3.060 nonbonded pdb=" NE2 HIS A 18 " pdb="MN MN A1001 " model vdw 2.179 3.140 nonbonded pdb=" OD1 ASN A 124 " pdb="MN MN A1002 " model vdw 2.182 3.060 ... (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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.930 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: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 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 are 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/Z covalent geometry : bond 0.00488 / 0.23 (12656) covalent geometry : angle 0.78212 / 0.44 (17142) hydrogen bonds : bond 0.24316 / 15.46 ( 311) hydrogen bonds : angle 8.69318 / 5.85 ( 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 : 0.505 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: 0.7712 (mtp) REVERT: B 409 TYR cc_start: 0.6055 (p90) cc_final: 0.5824 (p90) outliers start: 104 outliers final: 53 residues processed: 266 average time/residue: 0.0963 time to fit residues: 39.4420 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 : 0.493 ------------------------------------------------------------------------------- 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... 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4420 r_free = 0.4420 target = 0.156876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.133858 restraints weight = 23961.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.134659 restraints weight = 18523.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.135716 restraints weight = 17316.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.135991 restraints weight = 13003.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.136197 restraints weight = 13482.191| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12656 Z= 0.175 Angle : 0.682 8.381 17142 Z= 0.353 Chirality : 0.047 0.188 1934 Planarity : 0.005 0.051 2218 Dihedral : 10.793 87.298 1812 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.19 % Favored : 90.55 % Rotamer: Outliers : 5.55 % Allowed : 23.14 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -2.70 (0.20), residues: 1545 helix: -1.13 (0.25), residues: 394 sheet: -1.89 (0.29), residues: 312 loop : -2.09 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1188 TYR 0.017 0.002 TYR D1185 PHE 0.019 0.002 PHE B 257 TRP 0.012 0.002 TRP A 33 HIS 0.006 0.001 HIS D1279 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (12656) covalent geometry : angle 0.68226 / 0.35 (17142) hydrogen bonds : bond 0.04900 / 3.24 ( 311) hydrogen bonds : angle 6.23558 / 4.19 ( 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: symmetry clash REVERT: D 1146 MET cc_start: 0.6423 (tmm) cc_final: 0.5935 (tmm) REVERT: A 89 LEU cc_start: 0.4748 (OUTLIER) cc_final: 0.4480 (tt) REVERT: A 119 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6445 (p90) REVERT: A 205 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: A 283 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6397 (tt) REVERT: C 1253 HIS cc_start: 0.4709 (OUTLIER) cc_final: 0.4445 (m-70) REVERT: B 101 GLU cc_start: 0.5968 (OUTLIER) cc_final: 0.5728 (pt0) outliers start: 76 outliers final: 51 residues processed: 221 average time/residue: 0.1014 time to fit residues: 33.7635 Evaluate side-chains 192 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 135 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 1164 THR Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain D residue 1185 TYR 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 205 GLU 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 16 ASP 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 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: 0.9980 chunk 85 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 1 optimal weight: 0.0970 chunk 50 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 55 optimal weight: 0.1980 chunk 18 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN D1142 HIS ** D1264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1298 GLN 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.158133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.135330 restraints weight = 24074.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.136186 restraints weight = 17411.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.137131 restraints weight = 17239.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.137664 restraints weight = 12586.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.138226 restraints weight = 11802.340| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12656 Z= 0.137 Angle : 0.629 8.678 17142 Z= 0.323 Chirality : 0.045 0.175 1934 Planarity : 0.004 0.047 2218 Dihedral : 9.529 87.949 1767 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.41 % Favored : 91.39 % Rotamer: Outliers : 5.91 % Allowed : 23.72 % Favored : 70.36 % 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 are not related in a simple way. whole: -2.35 (0.21), residues: 1545 helix: -0.90 (0.25), residues: 402 sheet: -1.50 (0.31), residues: 282 loop : -1.92 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1188 TYR 0.012 0.001 TYR C 49 PHE 0.017 0.002 PHE B 257 TRP 0.013 0.002 TRP A 33 HIS 0.004 0.001 HIS D1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (12656) covalent geometry : angle 0.62921 / 0.32 (17142) hydrogen bonds : bond 0.04311 / 2.86 ( 311) hydrogen bonds : angle 5.95624 / 4.04 ( 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 241 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 160 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6695 (mp) REVERT: D 158 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7267 (mm-40) REVERT: A 89 LEU cc_start: 0.4729 (OUTLIER) cc_final: 0.4456 (tt) REVERT: A 119 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6377 (p90) REVERT: A 205 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: A 250 VAL cc_start: 0.5805 (t) cc_final: 0.5473 (t) REVERT: C 1 MET cc_start: 0.5595 (mtm) cc_final: 0.5387 (mtm) REVERT: C 1253 HIS cc_start: 0.4673 (OUTLIER) cc_final: 0.4391 (m-70) outliers start: 81 outliers final: 50 residues processed: 226 average time/residue: 0.0865 time to fit residues: 30.2752 Evaluate side-chains 199 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 158 GLN 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 1169 ILE Chi-restraints excluded: chain D residue 1185 TYR 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 96 VAL 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 205 GLU 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 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 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 1168 THR 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 16 ASP 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 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 266 VAL 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: 2.9990 chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 0.3980 chunk 135 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 GLN D 158 GLN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN ** C1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1298 GLN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.156731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.133915 restraints weight = 23885.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.134613 restraints weight = 17521.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.135430 restraints weight = 17920.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.135959 restraints weight = 13239.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.136537 restraints weight = 12277.144| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12656 Z= 0.155 Angle : 0.634 8.551 17142 Z= 0.323 Chirality : 0.045 0.168 1934 Planarity : 0.005 0.053 2218 Dihedral : 8.912 83.437 1761 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.87 % Favored : 91.00 % Rotamer: Outliers : 6.86 % Allowed : 23.65 % 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 are not related in a simple way. whole: -2.26 (0.21), residues: 1545 helix: -0.77 (0.26), residues: 397 sheet: -1.52 (0.30), residues: 297 loop : -1.86 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 96 TYR 0.014 0.001 TYR B 409 PHE 0.023 0.002 PHE B 391 TRP 0.012 0.002 TRP C1157 HIS 0.006 0.001 HIS D1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (12656) covalent geometry : angle 0.63440 / 0.32 (17142) hydrogen bonds : bond 0.04120 / 2.74 ( 311) hydrogen bonds : angle 5.77289 / 3.91 ( 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 246 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 152 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6696 (mp) REVERT: D 158 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6986 (mm-40) REVERT: A 119 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.6498 (p90) REVERT: A 186 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6983 (t80) REVERT: A 205 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 250 VAL cc_start: 0.6049 (t) cc_final: 0.5811 (t) REVERT: B 101 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.5608 (pt0) outliers start: 94 outliers final: 61 residues processed: 230 average time/residue: 0.0954 time to fit residues: 33.7113 Evaluate side-chains 203 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 136 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 79 GLN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 158 GLN 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 1169 ILE Chi-restraints excluded: chain D residue 1185 TYR 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 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 119 PHE 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 205 GLU 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 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 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 107 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1169 ILE Chi-restraints excluded: chain C residue 1237 THR Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain C residue 1250 LYS Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 LEU 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 293 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 73 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 GLN D 158 GLN D1142 HIS ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN C1266 GLN C1298 GLN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.157276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.134430 restraints weight = 24025.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.135242 restraints weight = 17276.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.136267 restraints weight = 16766.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.136663 restraints weight = 12470.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.137177 restraints weight = 12014.795| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12656 Z= 0.137 Angle : 0.628 10.601 17142 Z= 0.319 Chirality : 0.045 0.233 1934 Planarity : 0.004 0.048 2218 Dihedral : 8.456 75.658 1760 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.74 % Favored : 91.13 % Rotamer: Outliers : 6.42 % Allowed : 24.23 % Favored : 69.34 % 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 are not related in a simple way. whole: -2.11 (0.21), residues: 1545 helix: -0.70 (0.26), residues: 403 sheet: -1.39 (0.31), residues: 291 loop : -1.76 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 96 TYR 0.017 0.001 TYR C 49 PHE 0.019 0.001 PHE B 391 TRP 0.013 0.002 TRP A 33 HIS 0.004 0.001 HIS D 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (12656) covalent geometry : angle 0.62786 / 0.32 (17142) hydrogen bonds : bond 0.03867 / 2.56 ( 311) hydrogen bonds : angle 5.66955 / 3.84 ( 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 236 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 148 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6687 (mp) REVERT: D 1139 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6284 (mmp) REVERT: D 1146 MET cc_start: 0.4968 (tmm) cc_final: 0.4617 (tmm) REVERT: D 1203 ARG cc_start: 0.5784 (OUTLIER) cc_final: 0.4361 (ttm-80) REVERT: A 86 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6552 (mm-30) REVERT: A 89 LEU cc_start: 0.4642 (OUTLIER) cc_final: 0.4346 (tt) REVERT: A 119 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.6507 (p90) REVERT: A 186 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6988 (t80) REVERT: A 205 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: A 250 VAL cc_start: 0.5899 (t) cc_final: 0.5646 (t) REVERT: C 1146 MET cc_start: 0.7139 (tpt) cc_final: 0.6829 (tpt) REVERT: C 1250 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7641 (mmtm) outliers start: 88 outliers final: 63 residues processed: 220 average time/residue: 0.0835 time to fit residues: 28.3007 Evaluate side-chains 213 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 141 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 79 GLN 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 1169 ILE Chi-restraints excluded: chain D residue 1185 TYR 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 1305 VAL Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 86 GLU 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 205 GLU 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 67 ASP 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 105 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1169 ILE Chi-restraints excluded: chain C residue 1237 THR Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain C residue 1250 LYS Chi-restraints excluded: chain C residue 1266 GLN Chi-restraints excluded: chain C residue 1280 MET Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 LEU 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 234 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 45 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 GLN ** 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 C1266 GLN B 125 HIS ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.158585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.135576 restraints weight = 23746.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.136375 restraints weight = 17562.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.137505 restraints weight = 16879.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.137799 restraints weight = 12494.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.138289 restraints weight = 12428.778| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12656 Z= 0.124 Angle : 0.610 11.166 17142 Z= 0.309 Chirality : 0.045 0.184 1934 Planarity : 0.004 0.046 2218 Dihedral : 8.069 68.574 1760 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.80 % Favored : 91.13 % Rotamer: Outliers : 6.13 % Allowed : 24.67 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -1.96 (0.21), residues: 1545 helix: -0.58 (0.26), residues: 403 sheet: -1.33 (0.30), residues: 298 loop : -1.65 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.016 0.001 TYR C 49 PHE 0.018 0.001 PHE C1224 TRP 0.013 0.002 TRP A 33 HIS 0.004 0.001 HIS D 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (12656) covalent geometry : angle 0.61009 / 0.31 (17142) hydrogen bonds : bond 0.03653 / 2.42 ( 311) hydrogen bonds : angle 5.56556 / 3.79 ( 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 238 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 154 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6721 (mp) REVERT: D 1139 MET cc_start: 0.6265 (mmp) cc_final: 0.5837 (mmp) REVERT: D 1203 ARG cc_start: 0.5590 (OUTLIER) cc_final: 0.4136 (ttm-80) REVERT: A 86 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6490 (mm-30) REVERT: A 89 LEU cc_start: 0.4586 (OUTLIER) cc_final: 0.4281 (tt) REVERT: A 119 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6620 (p90) REVERT: A 186 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6872 (t80) REVERT: A 250 VAL cc_start: 0.5857 (t) cc_final: 0.5565 (t) REVERT: C 35 MET cc_start: 0.7167 (mmp) cc_final: 0.6656 (mmp) REVERT: C 49 TYR cc_start: 0.6325 (t80) cc_final: 0.6019 (t80) outliers start: 84 outliers final: 58 residues processed: 225 average time/residue: 0.0887 time to fit residues: 30.3486 Evaluate side-chains 206 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 142 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 79 GLN 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 1164 THR Chi-restraints excluded: chain D residue 1168 THR Chi-restraints excluded: chain D residue 1185 TYR 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 1305 VAL Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 86 GLU 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 323 ASP Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 67 ASP 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 106 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1168 THR 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 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: 1.9990 chunk 22 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 120 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 GLN D 120 ASN A 106 ASN ** 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 B 111 ASN B 113 ASN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.158401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.135580 restraints weight = 23741.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.136364 restraints weight = 17757.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.137434 restraints weight = 17085.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.137768 restraints weight = 12643.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.138153 restraints weight = 12645.964| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12656 Z= 0.129 Angle : 0.618 12.468 17142 Z= 0.312 Chirality : 0.044 0.160 1934 Planarity : 0.004 0.045 2218 Dihedral : 7.531 64.743 1747 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.61 % Favored : 91.33 % Rotamer: Outliers : 6.20 % Allowed : 24.96 % Favored : 68.83 % 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 are not related in a simple way. whole: -1.84 (0.22), residues: 1545 helix: -0.49 (0.26), residues: 403 sheet: -1.12 (0.31), residues: 292 loop : -1.62 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 96 TYR 0.016 0.001 TYR B 409 PHE 0.019 0.001 PHE C1224 TRP 0.012 0.002 TRP A 33 HIS 0.004 0.001 HIS D1272 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (12656) covalent geometry : angle 0.61836 / 0.31 (17142) hydrogen bonds : bond 0.03603 / 2.39 ( 311) hydrogen bonds : angle 5.47583 / 3.73 ( 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 236 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 151 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6728 (mp) REVERT: D 1203 ARG cc_start: 0.5606 (OUTLIER) cc_final: 0.4207 (ttm-80) REVERT: A 86 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6527 (mm-30) REVERT: A 89 LEU cc_start: 0.4633 (OUTLIER) cc_final: 0.4358 (tt) REVERT: A 119 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.6569 (p90) REVERT: A 186 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6874 (t80) REVERT: A 250 VAL cc_start: 0.5899 (t) cc_final: 0.5647 (t) REVERT: C 35 MET cc_start: 0.7141 (mmp) cc_final: 0.6712 (mmp) REVERT: C 49 TYR cc_start: 0.6339 (t80) cc_final: 0.6076 (t80) REVERT: B 33 TRP cc_start: 0.6391 (OUTLIER) cc_final: 0.6089 (p-90) outliers start: 85 outliers final: 65 residues processed: 221 average time/residue: 0.0893 time to fit residues: 30.4700 Evaluate side-chains 216 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 144 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 79 GLN 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 1164 THR Chi-restraints excluded: chain D residue 1168 THR Chi-restraints excluded: chain D residue 1185 TYR 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 1305 VAL Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 86 GLU 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 205 GLU 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 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 A residue 406 VAL Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 67 ASP 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 106 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 1168 THR 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 14 THR 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 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: 2.9990 chunk 32 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 119 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 GLN A 47 ASN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1147 GLN ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN B 98 HIS ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.154362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.131842 restraints weight = 24064.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.132656 restraints weight = 19291.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.133443 restraints weight = 19174.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.134053 restraints weight = 13449.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.134476 restraints weight = 12429.070| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12656 Z= 0.206 Angle : 0.697 13.218 17142 Z= 0.352 Chirality : 0.047 0.153 1934 Planarity : 0.005 0.042 2218 Dihedral : 7.898 70.035 1747 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.77 % Favored : 90.16 % Rotamer: Outliers : 6.28 % Allowed : 25.77 % Favored : 67.96 % 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 are not related in a simple way. whole: -2.04 (0.22), residues: 1545 helix: -0.59 (0.26), residues: 399 sheet: -1.42 (0.30), residues: 303 loop : -1.70 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 96 TYR 0.012 0.002 TYR B 107 PHE 0.019 0.002 PHE B 257 TRP 0.015 0.002 TRP C1157 HIS 0.007 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (12656) covalent geometry : angle 0.69655 / 0.35 (17142) hydrogen bonds : bond 0.04170 / 2.78 ( 311) hydrogen bonds : angle 5.64059 / 3.81 ( 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 234 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 148 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6700 (mp) REVERT: D 203 LYS cc_start: 0.5765 (mmtm) cc_final: 0.5470 (mmtt) REVERT: D 1209 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6831 (ttpt) REVERT: A 89 LEU cc_start: 0.5224 (OUTLIER) cc_final: 0.4965 (tt) REVERT: A 119 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.6587 (p90) REVERT: A 250 VAL cc_start: 0.6187 (t) cc_final: 0.5938 (t) REVERT: C 1188 ARG cc_start: 0.6732 (ptt-90) cc_final: 0.6156 (ptt-90) outliers start: 86 outliers final: 70 residues processed: 220 average time/residue: 0.0889 time to fit residues: 30.5048 Evaluate side-chains 216 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 142 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 31 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1168 THR Chi-restraints excluded: chain D residue 1185 TYR 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 1288 HIS 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 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 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 A residue 406 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 95 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 1168 THR 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 1280 MET Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 19 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 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 Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 95 optimal weight: 0.0270 chunk 3 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 GLN D1235 GLN ** 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 ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.158089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.135117 restraints weight = 23768.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.135142 restraints weight = 18135.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.135825 restraints weight = 19386.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.136822 restraints weight = 14454.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.137127 restraints weight = 12683.249| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.3054 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 : 0.636 13.597 17142 Z= 0.319 Chirality : 0.045 0.173 1934 Planarity : 0.004 0.043 2218 Dihedral : 7.486 68.352 1747 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.03 % Favored : 91.91 % Rotamer: Outliers : 5.18 % Allowed : 27.01 % Favored : 67.81 % 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 are not related in a simple way. whole: -1.77 (0.22), residues: 1545 helix: -0.39 (0.27), residues: 398 sheet: -1.19 (0.30), residues: 304 loop : -1.55 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 96 TYR 0.017 0.001 TYR C 49 PHE 0.022 0.001 PHE C1224 TRP 0.017 0.002 TRP A 33 HIS 0.007 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12656) covalent geometry : angle 0.63571 / 0.32 (17142) hydrogen bonds : bond 0.03536 / 2.37 ( 311) hydrogen bonds : angle 5.45390 / 3.71 ( 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 225 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 154 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6790 (mp) REVERT: D 1192 TYR cc_start: 0.5911 (m-80) cc_final: 0.5230 (m-80) REVERT: D 1203 ARG cc_start: 0.5578 (OUTLIER) cc_final: 0.4124 (ttm-80) REVERT: D 1209 LYS cc_start: 0.6776 (OUTLIER) cc_final: 0.6548 (ttpt) REVERT: D 1235 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6177 (mm-40) REVERT: A 89 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4659 (tt) REVERT: A 119 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.6519 (p90) REVERT: A 205 GLU cc_start: 0.7171 (mp0) cc_final: 0.6668 (mp0) REVERT: A 250 VAL cc_start: 0.5861 (t) cc_final: 0.5569 (t) REVERT: C 29 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7510 (tt) REVERT: C 35 MET cc_start: 0.7219 (mmp) cc_final: 0.6908 (mpp) REVERT: C 49 TYR cc_start: 0.6270 (t80) cc_final: 0.6013 (t80) REVERT: B 244 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7232 (tt0) outliers start: 71 outliers final: 55 residues processed: 212 average time/residue: 0.0952 time to fit residues: 31.0544 Evaluate side-chains 211 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 149 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 79 GLN 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 1185 TYR 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 1239 ASN Chi-restraints excluded: chain D residue 1248 LEU 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 180 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 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 A residue 406 VAL Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 29 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 95 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 1169 ILE 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 1304 TRP 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 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 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: 0.7980 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 116 optimal weight: 0.0570 chunk 45 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 69 optimal weight: 0.0030 chunk 140 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1235 GLN 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 ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.158775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.135761 restraints weight = 23818.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.135925 restraints weight = 18063.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.136911 restraints weight = 19362.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.137482 restraints weight = 13749.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.138004 restraints weight = 12665.525| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12656 Z= 0.123 Angle : 0.651 14.024 17142 Z= 0.326 Chirality : 0.045 0.348 1934 Planarity : 0.004 0.043 2218 Dihedral : 7.296 69.285 1745 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.35 % Favored : 91.59 % Rotamer: Outliers : 4.82 % Allowed : 27.88 % Favored : 67.30 % 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 are not related in a simple way. whole: -1.67 (0.22), residues: 1545 helix: -0.26 (0.27), residues: 392 sheet: -0.97 (0.32), residues: 288 loop : -1.57 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.016 0.001 TYR C 49 PHE 0.021 0.001 PHE C1224 TRP 0.016 0.002 TRP A 33 HIS 0.010 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (12656) covalent geometry : angle 0.65119 / 0.33 (17142) hydrogen bonds : bond 0.03470 / 2.32 ( 311) hydrogen bonds : angle 5.38196 / 3.67 ( 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 218 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 152 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6696 (mp) REVERT: D 1203 ARG cc_start: 0.5551 (OUTLIER) cc_final: 0.4012 (ttm-80) REVERT: D 1209 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.6297 (ttpp) REVERT: A 89 LEU cc_start: 0.4740 (OUTLIER) cc_final: 0.4426 (tt) REVERT: A 119 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.6600 (p90) REVERT: A 205 GLU cc_start: 0.7179 (mp0) cc_final: 0.6709 (mp0) REVERT: A 250 VAL cc_start: 0.5749 (t) cc_final: 0.5469 (t) REVERT: C 35 MET cc_start: 0.7204 (mmp) cc_final: 0.6664 (mmm) REVERT: C 102 MET cc_start: 0.5439 (mtm) cc_final: 0.4669 (mtt) REVERT: B 244 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7267 (tt0) REVERT: B 271 CYS cc_start: 0.7841 (p) cc_final: 0.7635 (m) outliers start: 66 outliers final: 54 residues processed: 211 average time/residue: 0.0918 time to fit residues: 30.0170 Evaluate side-chains 207 residues out of total 1411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 148 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1168 THR Chi-restraints excluded: chain D residue 1185 TYR 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 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 180 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 406 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 95 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 1169 ILE Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain C residue 1304 TRP 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 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 230 LEU 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 89 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1279 HIS ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1254 ASN B 98 HIS ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.157507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.134569 restraints weight = 23872.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.134444 restraints weight = 18488.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.135198 restraints weight = 19375.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.135969 restraints weight = 14838.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.136340 restraints weight = 13746.505| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12656 Z= 0.143 Angle : 0.663 13.780 17142 Z= 0.332 Chirality : 0.045 0.164 1934 Planarity : 0.004 0.043 2218 Dihedral : 7.242 68.319 1742 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.54 % Favored : 91.39 % Rotamer: Outliers : 4.67 % Allowed : 28.03 % Favored : 67.30 % 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 are not related in a simple way. whole: -1.68 (0.22), residues: 1545 helix: -0.26 (0.27), residues: 391 sheet: -1.06 (0.31), residues: 299 loop : -1.55 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 96 TYR 0.019 0.001 TYR B 409 PHE 0.021 0.001 PHE C1224 TRP 0.014 0.002 TRP C1304 HIS 0.007 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (12656) covalent geometry : angle 0.66328 / 0.33 (17142) hydrogen bonds : bond 0.03599 / 2.41 ( 311) hydrogen bonds : angle 5.38081 / 3.65 ( 879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2224.85 seconds wall clock time: 39 minutes 24.94 seconds (2364.94 seconds total)