Starting phenix.real_space_refine on Thu Feb 5 08:07:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c13_45100/02_2026/9c13_45100.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c13_45100/02_2026/9c13_45100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c13_45100/02_2026/9c13_45100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c13_45100/02_2026/9c13_45100.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c13_45100/02_2026/9c13_45100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c13_45100/02_2026/9c13_45100.map" } resolution = 2.89 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= 0.002 sd= 0.051 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 P 12 5.49 5 Mg 4 5.21 5 S 115 5.16 5 C 9891 2.51 5 N 2675 2.21 5 O 3011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15708 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3364 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain: "D" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3364 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain: "A" Number of atoms: 3361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3361 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3355 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2132 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 254} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.84, per 1000 atoms: 0.24 Number of scatterers: 15708 At special positions: 0 Unit cell: (115.235, 105.397, 119.45, 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) S 115 16.00 P 12 15.00 Mg 4 11.99 O 3011 8.00 N 2675 7.00 C 9891 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: 1.38 Conformation dependent library (CDL) restraints added in 700.9 milliseconds 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3676 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 10 sheets defined 57.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.164A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 3.979A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 4.424A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.782A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.665A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.689A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.569A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.580A pdb=" N MET B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.581A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.132A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.982A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.575A pdb=" N GLU D 45 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 69 through 79 removed outlier: 3.960A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 108 through 125 removed outlier: 4.146A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 removed outlier: 3.668A pdb=" N GLY D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 4.099A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.745A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.597A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.537A pdb=" N LEU D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.632A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.576A pdb=" N PHE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 373 through 391 removed outlier: 4.078A pdb=" N LEU D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 3.951A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 427 removed outlier: 3.671A pdb=" N THR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.750A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 removed outlier: 4.105A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 removed outlier: 3.501A pdb=" N GLU A 113 " --> pdb=" O ILE A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.831A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 removed outlier: 4.489A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.411A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.555A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.616A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.615A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.659A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.937A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.900A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.017A pdb=" N ASN C 50 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 51' Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 111 through 129 removed outlier: 4.612A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.465A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.934A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.569A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.957A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.722A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.610A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 4.243A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.035A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.936A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 1200 through 1210 Processing helix chain 'E' and resid 1222 through 1234 removed outlier: 3.949A pdb=" N ILE E1226 " --> pdb=" O ARG E1222 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER E1234 " --> pdb=" O LYS E1230 " (cutoff:3.500A) Processing helix chain 'E' and resid 1238 through 1246 removed outlier: 4.426A pdb=" N GLU E1244 " --> pdb=" O TRP E1240 " (cutoff:3.500A) Processing helix chain 'E' and resid 1249 through 1263 removed outlier: 3.561A pdb=" N GLN E1253 " --> pdb=" O ASP E1249 " (cutoff:3.500A) Processing helix chain 'E' and resid 1267 through 1274 Processing helix chain 'E' and resid 1274 through 1285 removed outlier: 3.525A pdb=" N LEU E1284 " --> pdb=" O LYS E1280 " (cutoff:3.500A) Processing helix chain 'E' and resid 1290 through 1311 removed outlier: 3.843A pdb=" N LEU E1294 " --> pdb=" O ASN E1290 " (cutoff:3.500A) Processing helix chain 'E' and resid 1316 through 1328 Proline residue: E1325 - end of helix Processing helix chain 'E' and resid 1336 through 1349 removed outlier: 3.805A pdb=" N LYS E1340 " --> pdb=" O ASP E1336 " (cutoff:3.500A) Processing helix chain 'E' and resid 1354 through 1365 removed outlier: 3.575A pdb=" N MET E1358 " --> pdb=" O PRO E1354 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN E1360 " --> pdb=" O SER E1356 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE E1361 " --> pdb=" O LYS E1357 " (cutoff:3.500A) Processing helix chain 'E' and resid 1366 through 1368 No H-bonds generated for 'chain 'E' and resid 1366 through 1368' Processing helix chain 'E' and resid 1370 through 1389 Processing helix chain 'E' and resid 1396 through 1404 Processing helix chain 'E' and resid 1405 through 1410 Processing helix chain 'E' and resid 1413 through 1431 removed outlier: 3.661A pdb=" N VAL E1429 " --> pdb=" O THR E1425 " (cutoff:3.500A) Processing helix chain 'E' and resid 1433 through 1438 Processing helix chain 'E' and resid 1444 through 1457 removed outlier: 3.638A pdb=" N MET E1448 " --> pdb=" O LYS E1444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.902A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.615A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.578A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.856A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 90 through 92 removed outlier: 7.971A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY D 132 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER D 138 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N HIS D 137 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.703A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 13.717A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.765A pdb=" N LYS D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.204A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 94 removed outlier: 7.937A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS C 200 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 273 800 hydrogen bonds defined for protein. 2331 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: 2.99 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4795 1.34 - 1.46: 3213 1.46 - 1.58: 7848 1.58 - 1.70: 7 1.70 - 1.82: 190 Bond restraints: 16053 Sorted by residual: bond pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sigma weight residual 1.610 1.822 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " ideal model delta sigma weight residual 1.610 1.820 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" O5' G2P D 501 " pdb=" PA G2P D 501 " ideal model delta sigma weight residual 1.656 1.818 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" O5' G2P B 501 " pdb=" PA G2P B 501 " ideal model delta sigma weight residual 1.656 1.814 -0.158 2.00e-02 2.50e+03 6.24e+01 bond pdb=" C3A G2P B 501 " pdb=" PA G2P B 501 " ideal model delta sigma weight residual 1.818 1.663 0.155 2.00e-02 2.50e+03 6.00e+01 ... (remaining 16048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 21530 3.90 - 7.80: 203 7.80 - 11.69: 24 11.69 - 15.59: 17 15.59 - 19.49: 4 Bond angle restraints: 21778 Sorted by residual: angle pdb=" O1A G2P D 501 " pdb=" PA G2P D 501 " pdb=" O5' G2P D 501 " ideal model delta sigma weight residual 109.23 89.74 19.49 3.00e+00 1.11e-01 4.22e+01 angle pdb=" O1A G2P B 501 " pdb=" PA G2P B 501 " pdb=" O5' G2P B 501 " ideal model delta sigma weight residual 109.23 89.93 19.30 3.00e+00 1.11e-01 4.14e+01 angle pdb=" O2B GTP A 501 " pdb=" PB GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sigma weight residual 109.50 92.77 16.73 3.00e+00 1.11e-01 3.11e+01 angle pdb=" O2B GTP C 501 " pdb=" PB GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sigma weight residual 109.50 92.95 16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" C1' GTP C 501 " pdb=" C2' GTP C 501 " pdb=" C3' GTP C 501 " ideal model delta sigma weight residual 111.00 96.28 14.72 3.00e+00 1.11e-01 2.41e+01 ... (remaining 21773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.36: 9429 33.36 - 66.72: 173 66.72 - 100.09: 21 100.09 - 133.45: 3 133.45 - 166.81: 5 Dihedral angle restraints: 9631 sinusoidal: 3909 harmonic: 5722 Sorted by residual: dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -123.92 -166.81 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -125.01 -165.72 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -59.45 164.05 1 2.00e+01 2.50e-03 4.71e+01 ... (remaining 9628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1963 0.071 - 0.141: 383 0.141 - 0.212: 33 0.212 - 0.282: 4 0.282 - 0.353: 8 Chirality restraints: 2391 Sorted by residual: chirality pdb=" C3' GTP A 501 " pdb=" C2' GTP A 501 " pdb=" C4' GTP A 501 " pdb=" O3' GTP A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.82 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C3' GTP C 501 " pdb=" C2' GTP C 501 " pdb=" C4' GTP C 501 " pdb=" O3' GTP C 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.82 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB VAL E1331 " pdb=" CA VAL E1331 " pdb=" CG1 VAL E1331 " pdb=" CG2 VAL E1331 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 2388 not shown) Planarity restraints: 2819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E1222 " 0.258 9.50e-02 1.11e+02 1.16e-01 8.38e+00 pdb=" NE ARG E1222 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E1222 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG E1222 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E1222 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E1224 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C GLU E1224 " -0.038 2.00e-02 2.50e+03 pdb=" O GLU E1224 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR E1225 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E1240 " -0.014 2.00e-02 2.50e+03 1.37e-02 4.72e+00 pdb=" CG TRP E1240 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP E1240 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E1240 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E1240 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E1240 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E1240 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP E1240 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E1240 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E1240 " -0.000 2.00e-02 2.50e+03 ... (remaining 2816 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 182 2.62 - 3.19: 13519 3.19 - 3.76: 25981 3.76 - 4.33: 36085 4.33 - 4.90: 59878 Nonbonded interactions: 135645 Sorted by model distance: nonbonded pdb=" O2G G2P B 501 " pdb="MG MG B 502 " model vdw 2.053 2.170 nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 2.062 2.170 nonbonded pdb=" O2G G2P D 501 " pdb="MG MG D 502 " model vdw 2.079 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 2.082 2.170 nonbonded pdb=" O2B G2P D 501 " pdb="MG MG D 502 " model vdw 2.085 2.170 ... (remaining 135640 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 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 4 through 55 or (resid 56 and (name N or name CA \ or name C or name O or name CB )) or resid 57 through 502)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.980 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.212 16053 Z= 0.318 Angle : 1.034 19.489 21778 Z= 0.497 Chirality : 0.057 0.353 2391 Planarity : 0.006 0.116 2819 Dihedral : 14.429 166.812 5955 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.06 % Allowed : 0.65 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.98 (0.17), residues: 1962 helix: -0.44 (0.16), residues: 925 sheet: 0.37 (0.33), residues: 262 loop : -1.12 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 64 TYR 0.024 0.002 TYR C 24 PHE 0.027 0.002 PHE E1359 TRP 0.037 0.003 TRP E1240 HIS 0.010 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00683 (16053) covalent geometry : angle 1.03415 (21778) hydrogen bonds : bond 0.17115 ( 800) hydrogen bonds : angle 7.21049 ( 2331) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 362 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ASN cc_start: 0.8499 (t0) cc_final: 0.8186 (t0) REVERT: B 69 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7531 (mt-10) REVERT: B 73 MET cc_start: 0.9214 (mmp) cc_final: 0.8972 (mpm) REVERT: B 111 GLU cc_start: 0.8508 (pm20) cc_final: 0.8297 (pm20) REVERT: B 114 ASP cc_start: 0.8928 (m-30) cc_final: 0.8452 (m-30) REVERT: B 174 LYS cc_start: 0.9359 (mmpt) cc_final: 0.9133 (mmmm) REVERT: B 177 ASP cc_start: 0.8697 (t70) cc_final: 0.8406 (t0) REVERT: B 279 GLN cc_start: 0.9104 (tt0) cc_final: 0.8672 (tm-30) REVERT: B 291 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8682 (tm-30) REVERT: B 321 MET cc_start: 0.8619 (mtp) cc_final: 0.8117 (mtm) REVERT: B 406 MET cc_start: 0.8900 (tpt) cc_final: 0.8322 (tpp) REVERT: B 407 GLU cc_start: 0.7627 (pm20) cc_final: 0.6830 (pm20) REVERT: B 410 GLU cc_start: 0.8578 (mp0) cc_final: 0.8059 (pm20) REVERT: B 412 GLU cc_start: 0.8266 (tp30) cc_final: 0.8058 (tm-30) REVERT: D 26 ASP cc_start: 0.9210 (t0) cc_final: 0.8779 (OUTLIER) REVERT: D 55 THR cc_start: 0.8546 (m) cc_final: 0.8207 (t) REVERT: D 88 ASP cc_start: 0.9278 (m-30) cc_final: 0.9068 (m-30) REVERT: D 94 GLN cc_start: 0.8643 (pm20) cc_final: 0.8380 (pm20) REVERT: D 209 ASP cc_start: 0.8772 (m-30) cc_final: 0.8558 (m-30) REVERT: D 279 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8397 (tm-30) REVERT: D 320 ARG cc_start: 0.9041 (mmm160) cc_final: 0.8836 (mmm-85) REVERT: D 323 MET cc_start: 0.9199 (mmm) cc_final: 0.8776 (mmm) REVERT: D 328 GLU cc_start: 0.8167 (pp20) cc_final: 0.7630 (pp20) REVERT: D 332 ASN cc_start: 0.8996 (m-40) cc_final: 0.8578 (m110) REVERT: D 412 GLU cc_start: 0.8507 (tp30) cc_final: 0.7924 (tp30) REVERT: D 416 ASN cc_start: 0.9188 (m-40) cc_final: 0.8191 (m-40) REVERT: A 36 MET cc_start: 0.9464 (ttm) cc_final: 0.9002 (ttp) REVERT: A 161 TYR cc_start: 0.9157 (m-80) cc_final: 0.8869 (m-80) REVERT: A 285 GLN cc_start: 0.8397 (tt0) cc_final: 0.7829 (mm110) REVERT: A 342 GLN cc_start: 0.8905 (pt0) cc_final: 0.8270 (pm20) REVERT: A 377 MET cc_start: 0.8973 (tmm) cc_final: 0.8737 (tmm) REVERT: A 390 ARG cc_start: 0.8363 (ptp-170) cc_final: 0.8030 (ptt-90) REVERT: A 411 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8471 (tp30) REVERT: A 423 GLU cc_start: 0.8676 (mp0) cc_final: 0.8250 (mp0) REVERT: C 77 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8507 (mt-10) REVERT: C 98 ASP cc_start: 0.8617 (p0) cc_final: 0.8382 (p0) REVERT: C 116 ASP cc_start: 0.8725 (m-30) cc_final: 0.8523 (m-30) REVERT: C 163 LYS cc_start: 0.9276 (ptpp) cc_final: 0.9057 (mmmt) REVERT: C 251 ASP cc_start: 0.7596 (t0) cc_final: 0.7315 (t0) REVERT: C 290 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7845 (mt-10) REVERT: C 434 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8672 (tm-30) REVERT: E 1242 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7755 (mm-40) REVERT: E 1247 HIS cc_start: 0.8608 (t-90) cc_final: 0.8272 (t70) REVERT: E 1284 LEU cc_start: 0.9538 (mm) cc_final: 0.9260 (mm) REVERT: E 1285 ARG cc_start: 0.9474 (mmp80) cc_final: 0.8935 (mmm160) REVERT: E 1294 LEU cc_start: 0.9560 (mt) cc_final: 0.9313 (mt) REVERT: E 1301 LEU cc_start: 0.9573 (mm) cc_final: 0.8715 (mm) REVERT: E 1326 TYR cc_start: 0.8561 (m-80) cc_final: 0.8303 (m-80) REVERT: E 1341 ASP cc_start: 0.9145 (t0) cc_final: 0.8895 (t0) REVERT: E 1346 LEU cc_start: 0.9401 (tp) cc_final: 0.9121 (tm) REVERT: E 1388 TYR cc_start: 0.8545 (m-80) cc_final: 0.8270 (m-80) REVERT: E 1401 LEU cc_start: 0.9210 (mm) cc_final: 0.8983 (mm) REVERT: E 1417 ASN cc_start: 0.9226 (m-40) cc_final: 0.8584 (m-40) REVERT: E 1432 GLU cc_start: 0.8756 (mp0) cc_final: 0.8404 (tp30) REVERT: E 1450 GLU cc_start: 0.9231 (mp0) cc_final: 0.8568 (mp0) REVERT: E 1454 LYS cc_start: 0.9470 (mmpt) cc_final: 0.9240 (mmmt) REVERT: E 1455 ARG cc_start: 0.8942 (mtt-85) cc_final: 0.8427 (mtt-85) outliers start: 1 outliers final: 3 residues processed: 362 average time/residue: 0.7896 time to fit residues: 309.6405 Evaluate side-chains 281 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 279 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1214 LEU Chi-restraints excluded: chain E residue 1260 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.0060 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 131 GLN B 137 HIS B 332 ASN B 396 HIS B 416 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 131 GLN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS C 192 HIS E1310 GLN E1373 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075625 restraints weight = 25272.288| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.54 r_work: 0.2850 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16053 Z= 0.166 Angle : 0.644 10.165 21778 Z= 0.331 Chirality : 0.046 0.190 2391 Planarity : 0.005 0.043 2819 Dihedral : 11.398 179.146 2241 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.06 % Allowed : 9.78 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.02 (0.19), residues: 1962 helix: 0.56 (0.17), residues: 963 sheet: 0.23 (0.32), residues: 262 loop : -0.74 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E1343 TYR 0.012 0.001 TYR C 24 PHE 0.027 0.001 PHE C 255 TRP 0.018 0.002 TRP E1281 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00370 (16053) covalent geometry : angle 0.64443 (21778) hydrogen bonds : bond 0.04985 ( 800) hydrogen bonds : angle 5.10339 ( 2331) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ASN cc_start: 0.8461 (t0) cc_final: 0.8142 (t0) REVERT: B 69 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7974 (tm-30) REVERT: B 73 MET cc_start: 0.9222 (mmp) cc_final: 0.8981 (mpm) REVERT: B 108 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8644 (mm-30) REVERT: B 114 ASP cc_start: 0.8649 (m-30) cc_final: 0.8335 (m-30) REVERT: B 157 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 177 ASP cc_start: 0.9130 (t70) cc_final: 0.8877 (t70) REVERT: B 284 LEU cc_start: 0.8472 (mm) cc_final: 0.8187 (mm) REVERT: B 291 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8694 (tm-30) REVERT: B 403 MET cc_start: 0.8860 (mtm) cc_final: 0.8355 (ttm) REVERT: B 406 MET cc_start: 0.8578 (tpt) cc_final: 0.7917 (tpp) REVERT: B 407 GLU cc_start: 0.7822 (pm20) cc_final: 0.7531 (pt0) REVERT: B 412 GLU cc_start: 0.8606 (tp30) cc_final: 0.8288 (tp30) REVERT: D 26 ASP cc_start: 0.9221 (t0) cc_final: 0.8805 (OUTLIER) REVERT: D 88 ASP cc_start: 0.9158 (m-30) cc_final: 0.8948 (m-30) REVERT: D 149 THR cc_start: 0.9087 (m) cc_final: 0.8696 (p) REVERT: D 209 ASP cc_start: 0.8836 (m-30) cc_final: 0.8635 (m-30) REVERT: D 279 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8283 (tm-30) REVERT: D 320 ARG cc_start: 0.9048 (mmm160) cc_final: 0.8750 (mmm-85) REVERT: D 323 MET cc_start: 0.9037 (mmm) cc_final: 0.8657 (mmm) REVERT: D 328 GLU cc_start: 0.8080 (pp20) cc_final: 0.7485 (pp20) REVERT: D 332 ASN cc_start: 0.8846 (m-40) cc_final: 0.8454 (m110) REVERT: A 36 MET cc_start: 0.9284 (ttm) cc_final: 0.8893 (ttp) REVERT: A 161 TYR cc_start: 0.9021 (m-80) cc_final: 0.8744 (m-80) REVERT: A 285 GLN cc_start: 0.8320 (tt0) cc_final: 0.7613 (mm110) REVERT: A 313 MET cc_start: 0.9300 (mtm) cc_final: 0.8976 (mtp) REVERT: A 342 GLN cc_start: 0.8897 (pt0) cc_final: 0.8300 (pm20) REVERT: A 390 ARG cc_start: 0.8271 (ptp-170) cc_final: 0.8017 (ptt-90) REVERT: A 392 ASP cc_start: 0.9270 (m-30) cc_final: 0.8902 (m-30) REVERT: A 411 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8508 (tp30) REVERT: A 433 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: C 196 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7462 (pm20) REVERT: C 251 ASP cc_start: 0.7878 (t0) cc_final: 0.7503 (t0) REVERT: C 339 ARG cc_start: 0.8675 (mmm160) cc_final: 0.8173 (tpm170) REVERT: C 434 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8632 (tm-30) REVERT: E 1242 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8138 (mm110) REVERT: E 1247 HIS cc_start: 0.8436 (t-90) cc_final: 0.7970 (t-90) REVERT: E 1257 LEU cc_start: 0.9533 (pp) cc_final: 0.9285 (pp) REVERT: E 1285 ARG cc_start: 0.9538 (mmp80) cc_final: 0.9256 (mmm160) REVERT: E 1290 ASN cc_start: 0.8915 (t0) cc_final: 0.8623 (t0) REVERT: E 1294 LEU cc_start: 0.9549 (mt) cc_final: 0.9295 (mt) REVERT: E 1301 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9216 (mm) REVERT: E 1305 PHE cc_start: 0.9370 (m-80) cc_final: 0.9049 (m-80) REVERT: E 1328 MET cc_start: 0.9266 (mmp) cc_final: 0.8945 (mmp) REVERT: E 1424 VAL cc_start: 0.9376 (p) cc_final: 0.9139 (m) REVERT: E 1435 PHE cc_start: 0.9164 (m-80) cc_final: 0.8879 (m-80) REVERT: E 1448 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8117 (mtp) REVERT: E 1451 GLU cc_start: 0.8546 (pp20) cc_final: 0.8046 (pp20) outliers start: 35 outliers final: 13 residues processed: 315 average time/residue: 0.7552 time to fit residues: 258.9589 Evaluate side-chains 279 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 262 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain D residue 324 LYS Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain E residue 1232 GLN Chi-restraints excluded: chain E residue 1260 MET Chi-restraints excluded: chain E residue 1301 LEU Chi-restraints excluded: chain E residue 1413 THR Chi-restraints excluded: chain E residue 1414 THR Chi-restraints excluded: chain E residue 1448 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 145 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 GLN B 298 ASN B 332 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS D 423 GLN A 128 GLN C 226 ASN C 309 HIS ** E1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1373 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.074708 restraints weight = 25670.625| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.51 r_work: 0.2840 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16053 Z= 0.170 Angle : 0.637 10.736 21778 Z= 0.321 Chirality : 0.045 0.158 2391 Planarity : 0.004 0.049 2819 Dihedral : 11.056 176.715 2239 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.47 % Allowed : 12.67 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: 0.27 (0.19), residues: 1962 helix: 0.91 (0.17), residues: 963 sheet: 0.09 (0.32), residues: 262 loop : -0.64 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E1343 TYR 0.010 0.001 TYR C 24 PHE 0.022 0.001 PHE A 255 TRP 0.017 0.002 TRP E1281 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00389 (16053) covalent geometry : angle 0.63662 (21778) hydrogen bonds : bond 0.04486 ( 800) hydrogen bonds : angle 4.81753 ( 2331) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 278 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ASN cc_start: 0.8469 (t0) cc_final: 0.8195 (t0) REVERT: B 73 MET cc_start: 0.9265 (mmp) cc_final: 0.9052 (mpm) REVERT: B 108 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8648 (mm-30) REVERT: B 114 ASP cc_start: 0.8637 (m-30) cc_final: 0.8374 (m-30) REVERT: B 174 LYS cc_start: 0.9210 (mmpt) cc_final: 0.8980 (mmmm) REVERT: B 194 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8346 (pm20) REVERT: B 284 LEU cc_start: 0.8542 (mm) cc_final: 0.8240 (mm) REVERT: B 291 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8686 (tm-30) REVERT: B 332 ASN cc_start: 0.9012 (m-40) cc_final: 0.8741 (t0) REVERT: B 406 MET cc_start: 0.8889 (tpt) cc_final: 0.8544 (tpp) REVERT: B 410 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7963 (mm-30) REVERT: B 412 GLU cc_start: 0.8629 (tp30) cc_final: 0.8324 (tp30) REVERT: D 26 ASP cc_start: 0.9227 (t0) cc_final: 0.8808 (OUTLIER) REVERT: D 149 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8834 (p) REVERT: D 279 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8295 (tm-30) REVERT: D 284 LEU cc_start: 0.8880 (mm) cc_final: 0.8671 (mt) REVERT: D 320 ARG cc_start: 0.9043 (mmm160) cc_final: 0.8725 (mmm-85) REVERT: D 323 MET cc_start: 0.9057 (mmm) cc_final: 0.8756 (mmm) REVERT: D 328 GLU cc_start: 0.8148 (pp20) cc_final: 0.7567 (pp20) REVERT: D 332 ASN cc_start: 0.8902 (m-40) cc_final: 0.8436 (m110) REVERT: D 376 GLU cc_start: 0.8574 (pt0) cc_final: 0.8043 (pp20) REVERT: A 36 MET cc_start: 0.9278 (ttm) cc_final: 0.8975 (ttp) REVERT: A 161 TYR cc_start: 0.9022 (m-80) cc_final: 0.8707 (m-80) REVERT: A 285 GLN cc_start: 0.8116 (tt0) cc_final: 0.7325 (mm110) REVERT: A 313 MET cc_start: 0.9297 (mtm) cc_final: 0.8948 (mtp) REVERT: A 342 GLN cc_start: 0.8896 (pt0) cc_final: 0.8303 (pm20) REVERT: A 411 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8297 (tp30) REVERT: A 433 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: C 251 ASP cc_start: 0.7980 (t0) cc_final: 0.7564 (t0) REVERT: C 339 ARG cc_start: 0.8659 (mmm160) cc_final: 0.8149 (tpm170) REVERT: C 425 MET cc_start: 0.8868 (tpt) cc_final: 0.8653 (tpt) REVERT: C 434 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8689 (tm-30) REVERT: E 1247 HIS cc_start: 0.8660 (t-90) cc_final: 0.8262 (t-90) REVERT: E 1301 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9240 (mm) REVERT: E 1305 PHE cc_start: 0.9341 (m-80) cc_final: 0.9104 (m-80) REVERT: E 1328 MET cc_start: 0.9312 (mmp) cc_final: 0.9111 (mmp) REVERT: E 1401 LEU cc_start: 0.9221 (mm) cc_final: 0.8959 (mm) REVERT: E 1454 LYS cc_start: 0.9270 (mmmt) cc_final: 0.9050 (mmmt) outliers start: 42 outliers final: 15 residues processed: 297 average time/residue: 0.6875 time to fit residues: 223.8831 Evaluate side-chains 275 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain E residue 1232 GLN Chi-restraints excluded: chain E residue 1301 LEU Chi-restraints excluded: chain E residue 1413 THR Chi-restraints excluded: chain E residue 1414 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 167 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN B 298 ASN ** E1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.101038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.071895 restraints weight = 25551.621| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.48 r_work: 0.2806 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16053 Z= 0.223 Angle : 0.667 12.405 21778 Z= 0.333 Chirality : 0.047 0.205 2391 Planarity : 0.004 0.037 2819 Dihedral : 10.950 176.501 2236 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.48 % Allowed : 13.91 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: 0.30 (0.19), residues: 1962 helix: 0.94 (0.17), residues: 963 sheet: 0.06 (0.32), residues: 264 loop : -0.63 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 320 TYR 0.011 0.001 TYR A 185 PHE 0.022 0.002 PHE A 255 TRP 0.018 0.002 TRP E1281 HIS 0.006 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00513 (16053) covalent geometry : angle 0.66673 (21778) hydrogen bonds : bond 0.04578 ( 800) hydrogen bonds : angle 4.81085 ( 2331) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 268 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ASN cc_start: 0.8513 (t0) cc_final: 0.8262 (t0) REVERT: B 69 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7974 (tp30) REVERT: B 108 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8703 (mm-30) REVERT: B 114 ASP cc_start: 0.8606 (m-30) cc_final: 0.8303 (m-30) REVERT: B 157 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7720 (mm-30) REVERT: B 174 LYS cc_start: 0.9229 (mmpt) cc_final: 0.8997 (mmmm) REVERT: B 194 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: B 284 LEU cc_start: 0.8635 (mm) cc_final: 0.8337 (mm) REVERT: B 291 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8662 (tm-30) REVERT: B 403 MET cc_start: 0.8701 (ttm) cc_final: 0.8351 (ttp) REVERT: B 406 MET cc_start: 0.9037 (tpt) cc_final: 0.8361 (tpp) REVERT: B 410 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8303 (mm-30) REVERT: B 412 GLU cc_start: 0.8679 (tp30) cc_final: 0.8361 (tp30) REVERT: D 26 ASP cc_start: 0.9308 (t0) cc_final: 0.8905 (OUTLIER) REVERT: D 149 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.8948 (p) REVERT: D 279 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8306 (tm-30) REVERT: D 284 LEU cc_start: 0.8874 (mm) cc_final: 0.8631 (mt) REVERT: D 320 ARG cc_start: 0.9045 (mmm160) cc_final: 0.8679 (mmm-85) REVERT: D 323 MET cc_start: 0.9116 (mmm) cc_final: 0.8817 (mmm) REVERT: D 328 GLU cc_start: 0.8251 (pp20) cc_final: 0.7730 (pp20) REVERT: D 332 ASN cc_start: 0.8846 (m-40) cc_final: 0.8365 (m110) REVERT: D 376 GLU cc_start: 0.8652 (pt0) cc_final: 0.8127 (pp20) REVERT: A 36 MET cc_start: 0.9314 (ttm) cc_final: 0.8978 (ttp) REVERT: A 161 TYR cc_start: 0.9060 (m-80) cc_final: 0.8743 (m-80) REVERT: A 196 GLU cc_start: 0.7934 (pm20) cc_final: 0.7158 (pm20) REVERT: A 285 GLN cc_start: 0.8122 (tt0) cc_final: 0.7255 (mm110) REVERT: A 313 MET cc_start: 0.9386 (mtm) cc_final: 0.9149 (mtp) REVERT: A 342 GLN cc_start: 0.8915 (pt0) cc_final: 0.8277 (pm20) REVERT: A 392 ASP cc_start: 0.9242 (m-30) cc_final: 0.8920 (m-30) REVERT: C 88 HIS cc_start: 0.8570 (p90) cc_final: 0.5958 (m-70) REVERT: C 116 ASP cc_start: 0.8810 (p0) cc_final: 0.8510 (m-30) REVERT: C 251 ASP cc_start: 0.8124 (t0) cc_final: 0.7754 (t0) REVERT: C 253 THR cc_start: 0.9032 (p) cc_final: 0.8604 (t) REVERT: C 285 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7399 (pm20) REVERT: C 339 ARG cc_start: 0.8691 (mmm160) cc_final: 0.8142 (tpm170) REVERT: C 425 MET cc_start: 0.8916 (tpt) cc_final: 0.8687 (tpt) REVERT: C 434 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8668 (tm-30) REVERT: E 1227 GLU cc_start: 0.8974 (mp0) cc_final: 0.8636 (mp0) REVERT: E 1229 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9066 (mm) REVERT: E 1247 HIS cc_start: 0.8725 (t-90) cc_final: 0.8433 (t-90) REVERT: E 1284 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8899 (mm) REVERT: E 1298 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8935 (tm) REVERT: E 1301 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9318 (mm) REVERT: E 1307 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8562 (mmm) REVERT: E 1326 TYR cc_start: 0.8891 (m-80) cc_final: 0.8637 (m-80) outliers start: 59 outliers final: 25 residues processed: 303 average time/residue: 0.6931 time to fit residues: 230.2007 Evaluate side-chains 282 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 420 GLU Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain E residue 1229 LEU Chi-restraints excluded: chain E residue 1232 GLN Chi-restraints excluded: chain E residue 1276 ASP Chi-restraints excluded: chain E residue 1284 LEU Chi-restraints excluded: chain E residue 1298 LEU Chi-restraints excluded: chain E residue 1301 LEU Chi-restraints excluded: chain E residue 1307 MET Chi-restraints excluded: chain E residue 1356 SER Chi-restraints excluded: chain E residue 1413 THR Chi-restraints excluded: chain E residue 1414 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 66 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN B 298 ASN D 375 GLN D 423 GLN C 300 ASN C 309 HIS ** E1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1373 GLN ** 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 = 0.3454 r_free = 0.3454 target = 0.101797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.072595 restraints weight = 25403.957| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.50 r_work: 0.2809 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16053 Z= 0.168 Angle : 0.651 14.830 21778 Z= 0.323 Chirality : 0.046 0.194 2391 Planarity : 0.004 0.040 2819 Dihedral : 10.870 176.248 2236 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.12 % Allowed : 15.97 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: 0.39 (0.19), residues: 1962 helix: 1.05 (0.17), residues: 957 sheet: -0.01 (0.32), residues: 262 loop : -0.59 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 320 TYR 0.019 0.001 TYR E1300 PHE 0.022 0.001 PHE A 255 TRP 0.019 0.002 TRP E1281 HIS 0.006 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00388 (16053) covalent geometry : angle 0.65094 (21778) hydrogen bonds : bond 0.04266 ( 800) hydrogen bonds : angle 4.69778 ( 2331) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 284 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ASN cc_start: 0.8511 (t0) cc_final: 0.8268 (t0) REVERT: B 69 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: B 108 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8765 (mm-30) REVERT: B 114 ASP cc_start: 0.8588 (m-30) cc_final: 0.8286 (m-30) REVERT: B 125 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8370 (mm-30) REVERT: B 194 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: B 284 LEU cc_start: 0.8614 (mm) cc_final: 0.8319 (mm) REVERT: B 291 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8699 (tm-30) REVERT: B 406 MET cc_start: 0.8972 (tpt) cc_final: 0.8692 (tpp) REVERT: B 407 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: B 410 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8387 (mm-30) REVERT: B 412 GLU cc_start: 0.8695 (tp30) cc_final: 0.8159 (tp30) REVERT: D 26 ASP cc_start: 0.9253 (t0) cc_final: 0.8824 (OUTLIER) REVERT: D 149 THR cc_start: 0.9340 (m) cc_final: 0.9019 (p) REVERT: D 191 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8170 (mt0) REVERT: D 194 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8253 (pm20) REVERT: D 279 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8341 (tm-30) REVERT: D 320 ARG cc_start: 0.9014 (mmm160) cc_final: 0.8635 (mmm-85) REVERT: D 323 MET cc_start: 0.9110 (mmm) cc_final: 0.8710 (mmm) REVERT: D 328 GLU cc_start: 0.8206 (pp20) cc_final: 0.7697 (pp20) REVERT: D 332 ASN cc_start: 0.8830 (m-40) cc_final: 0.8362 (m110) REVERT: D 376 GLU cc_start: 0.8637 (pt0) cc_final: 0.8151 (pp20) REVERT: A 36 MET cc_start: 0.9317 (ttm) cc_final: 0.8939 (ttp) REVERT: A 161 TYR cc_start: 0.8976 (m-80) cc_final: 0.8643 (m-80) REVERT: A 196 GLU cc_start: 0.8008 (pm20) cc_final: 0.7207 (pm20) REVERT: A 285 GLN cc_start: 0.8042 (tt0) cc_final: 0.7079 (mm110) REVERT: A 313 MET cc_start: 0.9384 (mtm) cc_final: 0.9155 (mtp) REVERT: A 342 GLN cc_start: 0.8932 (pt0) cc_final: 0.8300 (pm20) REVERT: A 392 ASP cc_start: 0.9239 (m-30) cc_final: 0.8607 (m-30) REVERT: C 88 HIS cc_start: 0.8412 (p90) cc_final: 0.5853 (m-70) REVERT: C 116 ASP cc_start: 0.8786 (p0) cc_final: 0.8451 (m-30) REVERT: C 163 LYS cc_start: 0.9251 (ptpp) cc_final: 0.9042 (mmmt) REVERT: C 251 ASP cc_start: 0.8123 (t0) cc_final: 0.7788 (t0) REVERT: C 253 THR cc_start: 0.9024 (p) cc_final: 0.8588 (t) REVERT: C 254 GLU cc_start: 0.8370 (tt0) cc_final: 0.7460 (tp30) REVERT: C 285 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: C 434 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8694 (tm-30) REVERT: E 1229 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9115 (mm) REVERT: E 1242 GLN cc_start: 0.8673 (mm110) cc_final: 0.8388 (mm110) REVERT: E 1247 HIS cc_start: 0.8751 (t-90) cc_final: 0.8397 (t70) REVERT: E 1281 TRP cc_start: 0.9591 (t60) cc_final: 0.9290 (t-100) REVERT: E 1285 ARG cc_start: 0.9620 (mmp80) cc_final: 0.9124 (mmm160) REVERT: E 1294 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9338 (mm) REVERT: E 1301 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9281 (mm) REVERT: E 1326 TYR cc_start: 0.8772 (m-80) cc_final: 0.8458 (m-80) REVERT: E 1416 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8841 (ttp-170) REVERT: E 1452 ARG cc_start: 0.8858 (tpp80) cc_final: 0.8635 (tpp80) REVERT: E 1455 ARG cc_start: 0.8656 (mtt-85) cc_final: 0.8455 (mtt-85) outliers start: 53 outliers final: 23 residues processed: 317 average time/residue: 0.6538 time to fit residues: 226.8016 Evaluate side-chains 293 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1229 LEU Chi-restraints excluded: chain E residue 1232 GLN Chi-restraints excluded: chain E residue 1276 ASP Chi-restraints excluded: chain E residue 1291 THR Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1301 LEU Chi-restraints excluded: chain E residue 1328 MET Chi-restraints excluded: chain E residue 1413 THR Chi-restraints excluded: chain E residue 1414 THR Chi-restraints excluded: chain E residue 1416 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.127 > 50: distance: 69 - 75: 3.977 distance: 75 - 76: 8.404 distance: 75 - 81: 12.873 distance: 76 - 77: 6.254 distance: 76 - 79: 11.865 distance: 77 - 78: 20.912 distance: 77 - 82: 7.780 distance: 79 - 80: 12.359 distance: 80 - 81: 10.166 distance: 82 - 83: 21.388 distance: 82 - 88: 13.481 distance: 83 - 84: 13.459 distance: 83 - 86: 17.625 distance: 84 - 85: 26.312 distance: 84 - 89: 19.907 distance: 86 - 87: 25.982 distance: 87 - 88: 28.459 distance: 89 - 90: 13.911 distance: 90 - 91: 18.224 distance: 90 - 93: 30.922 distance: 91 - 92: 17.666 distance: 91 - 96: 18.766 distance: 93 - 94: 3.947 distance: 93 - 95: 14.291 distance: 96 - 97: 9.783 distance: 97 - 98: 10.893 distance: 97 - 100: 15.182 distance: 98 - 99: 8.418 distance: 98 - 103: 7.529 distance: 100 - 101: 8.630 distance: 100 - 102: 12.158 distance: 103 - 104: 25.948 distance: 104 - 105: 23.941 distance: 105 - 106: 15.060 distance: 105 - 110: 32.319 distance: 107 - 108: 10.772 distance: 107 - 109: 15.891 distance: 110 - 111: 16.058 distance: 110 - 116: 16.830 distance: 111 - 112: 21.209 distance: 111 - 114: 3.264 distance: 112 - 113: 13.992 distance: 112 - 117: 24.677 distance: 114 - 115: 21.794 distance: 115 - 116: 21.338 distance: 117 - 118: 10.556 distance: 118 - 119: 8.399 distance: 119 - 120: 3.254 distance: 119 - 121: 16.775 distance: 121 - 122: 9.565 distance: 122 - 123: 6.022 distance: 123 - 124: 8.868 distance: 123 - 125: 7.086 distance: 125 - 126: 10.241 distance: 126 - 127: 6.793 distance: 126 - 129: 11.071 distance: 127 - 128: 21.988 distance: 127 - 130: 5.725 distance: 130 - 131: 10.795 distance: 131 - 132: 4.856 distance: 131 - 134: 6.308 distance: 132 - 133: 6.959 distance: 132 - 138: 7.617 distance: 134 - 135: 13.084 distance: 135 - 136: 9.504 distance: 135 - 137: 16.413