Starting phenix.real_space_refine on Mon Aug 25 10:35:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5l_19739/08_2025/8s5l_19739_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5l_19739/08_2025/8s5l_19739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8s5l_19739/08_2025/8s5l_19739_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5l_19739/08_2025/8s5l_19739_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s5l_19739/08_2025/8s5l_19739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5l_19739/08_2025/8s5l_19739.map" } resolution = 3.8 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 4 5.49 5 S 78 5.16 5 C 8650 2.51 5 N 2372 2.21 5 O 2578 1.98 5 H 13603 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27289 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5636 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 7904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7904 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Chain: "C" Number of atoms: 7909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7909 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Chain: "D" Number of atoms: 5636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5636 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'HEM': 1, 'PLP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'HEM': 1, 'PLP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 177 SG CYS A 52 79.352 132.334 41.782 1.00 56.77 S ATOM 21626 SG CYS D 52 47.665 28.331 41.717 1.00 56.13 S Time building chain proxies: 5.60, per 1000 atoms: 0.21 Number of scatterers: 27289 At special positions: 0 Unit cell: (127.958, 159.714, 83.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 78 16.00 P 4 15.00 O 2578 8.00 N 2372 7.00 C 8650 6.00 H 13603 1.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 934.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3196 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 14 sheets defined 45.6% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.463A pdb=" N ILE A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.875A pdb=" N VAL A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.535A pdb=" N LEU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 258 through 272 removed outlier: 3.813A pdb=" N ILE A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 328 through 343 removed outlier: 3.708A pdb=" N GLY A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 361 removed outlier: 3.709A pdb=" N LYS A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.735A pdb=" N MET A 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 99 removed outlier: 4.044A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 148 through 162 Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 226 through 235 removed outlier: 3.832A pdb=" N HIS B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.832A pdb=" N GLN B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 343 removed outlier: 3.570A pdb=" N ALA B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 361 removed outlier: 4.268A pdb=" N LYS B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.894A pdb=" N ASN B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET B 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 394 Processing helix chain 'B' and resid 398 through 405 removed outlier: 4.338A pdb=" N LYS B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 4.076A pdb=" N HIS B 411 " --> pdb=" O TRP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 430 through 441 removed outlier: 3.647A pdb=" N GLU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 535 through 548 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 93 through 99 removed outlier: 4.030A pdb=" N LYS C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 133 Processing helix chain 'C' and resid 148 through 162 Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.826A pdb=" N HIS C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 258 through 272 removed outlier: 3.542A pdb=" N LYS C 267 " --> pdb=" O GLY C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 removed outlier: 3.697A pdb=" N GLN C 295 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.771A pdb=" N VAL C 320 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 343 removed outlier: 3.655A pdb=" N ALA C 331 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 336 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 361 removed outlier: 4.218A pdb=" N LYS C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.853A pdb=" N ASN C 380 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET C 382 " --> pdb=" O ARG C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 395 Processing helix chain 'C' and resid 398 through 405 removed outlier: 4.288A pdb=" N LYS C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 removed outlier: 4.025A pdb=" N HIS C 411 " --> pdb=" O TRP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 430 through 442 removed outlier: 3.708A pdb=" N LYS C 441 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 470 Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.621A pdb=" N LYS C 481 " --> pdb=" O GLN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 535 through 548 Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 93 through 99 removed outlier: 3.559A pdb=" N LYS D 97 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 133 removed outlier: 4.478A pdb=" N ILE D 122 " --> pdb=" O VAL D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 162 Processing helix chain 'D' and resid 174 through 184 removed outlier: 3.864A pdb=" N VAL D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 214 Processing helix chain 'D' and resid 226 through 235 removed outlier: 3.517A pdb=" N LEU D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 245 Processing helix chain 'D' and resid 258 through 272 removed outlier: 3.856A pdb=" N LYS D 267 " --> pdb=" O GLY D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 328 through 343 removed outlier: 3.647A pdb=" N GLY D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 361 removed outlier: 3.715A pdb=" N LYS D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 378 through 382 removed outlier: 3.817A pdb=" N MET D 382 " --> pdb=" O ARG D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 394 Processing helix chain 'D' and resid 399 through 404 removed outlier: 3.905A pdb=" N GLU D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.680A pdb=" N LEU A 374 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 250 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER A 254 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU A 251 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL A 280 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ALA A 253 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 281 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 191 removed outlier: 3.675A pdb=" N THR A 191 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A 142 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL A 168 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU A 144 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR A 141 " --> pdb=" O HIS A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.684A pdb=" N MET B 250 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N SER B 254 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 251 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL B 280 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 253 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 322 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 190 removed outlier: 3.538A pdb=" N VAL B 168 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 423 through 425 removed outlier: 3.527A pdb=" N TYR C 518 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS C 488 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL C 512 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE C 490 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLU C 514 " --> pdb=" O ILE C 490 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 423 through 425 removed outlier: 3.527A pdb=" N TYR C 518 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA C 509 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL C 533 " --> pdb=" O ALA C 509 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL C 511 " --> pdb=" O PHE C 531 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 448 through 449 removed outlier: 3.662A pdb=" N GLY B 457 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 488 through 491 removed outlier: 6.653A pdb=" N ALA B 509 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL B 533 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B 511 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 525 " --> pdb=" O GLN B 517 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 488 through 491 removed outlier: 7.698A pdb=" N THR C 424 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE B 516 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 89 through 91 removed outlier: 6.253A pdb=" N MET C 250 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE C 373 " --> pdb=" O MET C 250 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL C 252 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU C 251 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL C 280 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA C 253 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N SER C 326 " --> pdb=" O GLY C 279 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP C 281 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 187 through 190 Processing sheet with id=AB3, first strand: chain 'C' and resid 448 through 449 removed outlier: 6.736A pdb=" N VAL C 448 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.274A pdb=" N GLU D 104 " --> pdb=" O CYS D 370 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL D 372 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU D 106 " --> pdb=" O VAL D 372 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU D 374 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS D 108 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER D 254 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU D 251 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL D 280 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA D 253 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 322 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 187 through 191 removed outlier: 3.648A pdb=" N THR D 191 " --> pdb=" O MET D 169 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE D 142 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL D 168 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU D 144 " --> pdb=" O VAL D 168 " (cutoff:3.500A) 545 hydrogen bonds defined for protein. 1479 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: 6.61 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 13533 1.08 - 1.32: 2459 1.32 - 1.56: 11441 1.56 - 1.81: 113 1.81 - 2.05: 25 Bond restraints: 27571 Sorted by residual: bond pdb=" C4' LLP A 119 " pdb="H4'1 LLP A 119 " ideal model delta sigma weight residual 0.930 1.084 -0.154 2.00e-02 2.50e+03 5.91e+01 bond pdb=" C4' LLP D 119 " pdb="H4'1 LLP D 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.84e+01 bond pdb=" C6 LLP D 119 " pdb=" H6 LLP D 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" C6 LLP A 119 " pdb=" H6 LLP A 119 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.81e+01 bond pdb=" N LLP D 119 " pdb=" H LLP D 119 " ideal model delta sigma weight residual 0.860 1.004 -0.144 2.00e-02 2.50e+03 5.17e+01 ... (remaining 27566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.38: 50016 7.38 - 14.77: 2 14.77 - 22.15: 0 22.15 - 29.54: 0 29.54 - 36.92: 2 Bond angle restraints: 50020 Sorted by residual: angle pdb=" O LLP A 119 " pdb=" C LLP A 119 " pdb=" N ASP A 120 " ideal model delta sigma weight residual 123.00 86.08 36.92 1.60e+00 3.91e-01 5.33e+02 angle pdb=" O LLP D 119 " pdb=" C LLP D 119 " pdb=" N ASP D 120 " ideal model delta sigma weight residual 123.00 87.69 35.31 1.60e+00 3.91e-01 4.87e+02 angle pdb=" OP1 LLP A 119 " pdb=" P LLP A 119 " pdb=" OP4 LLP A 119 " ideal model delta sigma weight residual 100.47 110.60 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" OP1 LLP D 119 " pdb=" P LLP D 119 " pdb=" OP4 LLP D 119 " ideal model delta sigma weight residual 100.47 110.28 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C LYS B 384 " pdb=" CA LYS B 384 " pdb=" CB LYS B 384 " ideal model delta sigma weight residual 110.42 115.84 -5.42 1.99e+00 2.53e-01 7.41e+00 ... (remaining 50015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 12328 35.03 - 70.05: 415 70.05 - 105.08: 41 105.08 - 140.10: 2 140.10 - 175.13: 1 Dihedral angle restraints: 12787 sinusoidal: 7201 harmonic: 5586 Sorted by residual: dihedral pdb=" C5A PLP C 602 " pdb=" O4P PLP C 602 " pdb=" P PLP C 602 " pdb=" O1P PLP C 602 " ideal model delta sinusoidal sigma weight residual 76.43 -98.70 175.13 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5 PLP B 602 " pdb=" C4 PLP B 602 " pdb=" C4A PLP B 602 " pdb=" O4A PLP B 602 " ideal model delta sinusoidal sigma weight residual 0.00 -137.31 137.31 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" C5A PLP B 602 " pdb=" O4P PLP B 602 " pdb=" P PLP B 602 " pdb=" O1P PLP B 602 " ideal model delta sinusoidal sigma weight residual 76.43 -58.43 134.86 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 12784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1405 0.036 - 0.073: 519 0.073 - 0.109: 131 0.109 - 0.146: 53 0.146 - 0.182: 4 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CA PRO A 375 " pdb=" N PRO A 375 " pdb=" C PRO A 375 " pdb=" CB PRO A 375 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CA PRO B 375 " pdb=" N PRO B 375 " pdb=" C PRO B 375 " pdb=" CB PRO B 375 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA PRO C 375 " pdb=" N PRO C 375 " pdb=" C PRO C 375 " pdb=" CB PRO C 375 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 2109 not shown) Planarity restraints: 4077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LLP A 119 " 0.137 2.00e-02 2.50e+03 2.22e-01 4.92e+02 pdb=" C LLP A 119 " -0.384 2.00e-02 2.50e+03 pdb=" O LLP A 119 " 0.135 2.00e-02 2.50e+03 pdb=" N ASP A 120 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP D 119 " -0.132 2.00e-02 2.50e+03 2.16e-01 4.66e+02 pdb=" C LLP D 119 " 0.374 2.00e-02 2.50e+03 pdb=" O LLP D 119 " -0.131 2.00e-02 2.50e+03 pdb=" N ASP D 120 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 374 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.12e+00 pdb=" N PRO A 375 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.025 5.00e-02 4.00e+02 ... (remaining 4074 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 914 2.14 - 2.75: 52195 2.75 - 3.37: 78159 3.37 - 3.98: 98302 3.98 - 4.60: 156215 Nonbonded interactions: 385785 Sorted by model distance: nonbonded pdb=" OD2 ASP C 249 " pdb=" H ARG C 369 " model vdw 1.525 2.450 nonbonded pdb=" OD2 ASP B 249 " pdb=" H ARG B 369 " model vdw 1.536 2.450 nonbonded pdb=" OE1 GLU D 201 " pdb=" H GLU D 201 " model vdw 1.546 2.450 nonbonded pdb=" OE1 GLU B 399 " pdb=" H GLU B 399 " model vdw 1.546 2.450 nonbonded pdb=" OE1 GLU A 201 " pdb=" H GLU A 201 " model vdw 1.550 2.450 ... (remaining 385780 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 42 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 120 through 602)) } 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: 9.690 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: 0.180 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.430 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.040 Total: 39.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.006 0.111 13973 Z= 0.259 Angle : 0.782 36.925 18972 Z= 0.430 Chirality : 0.043 0.182 2112 Planarity : 0.007 0.222 2432 Dihedral : 15.676 175.125 5214 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.56 % Favored : 94.21 % Rotamer: Outliers : 0.14 % Allowed : 12.70 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.21), residues: 1726 helix: 0.05 (0.20), residues: 656 sheet: -1.07 (0.29), residues: 262 loop : 0.30 (0.24), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 209 TYR 0.015 0.002 TYR D 233 PHE 0.012 0.002 PHE A 324 TRP 0.009 0.001 TRP B 323 HIS 0.005 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00583 (13968) covalent geometry : angle 0.78182 (18972) hydrogen bonds : bond 0.18502 ( 541) hydrogen bonds : angle 6.69739 ( 1479) Misc. bond : bond 0.07693 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 119 average time/residue: 0.2634 time to fit residues: 47.5033 Evaluate side-chains 113 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 387 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.091562 restraints weight = 84713.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095672 restraints weight = 40634.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098427 restraints weight = 24988.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.100239 restraints weight = 17537.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.101487 restraints weight = 13442.297| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 13973 Z= 0.134 Angle : 0.568 6.130 18972 Z= 0.284 Chirality : 0.042 0.144 2112 Planarity : 0.004 0.031 2432 Dihedral : 9.485 131.800 1916 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 0.96 % Allowed : 12.16 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.21), residues: 1726 helix: 0.55 (0.21), residues: 636 sheet: -0.83 (0.29), residues: 262 loop : 0.28 (0.24), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.007 0.001 TYR B 518 PHE 0.007 0.001 PHE C 531 TRP 0.005 0.001 TRP C 409 HIS 0.004 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00324 (13968) covalent geometry : angle 0.56795 (18972) hydrogen bonds : bond 0.04067 ( 541) hydrogen bonds : angle 5.15030 ( 1479) Misc. bond : bond 0.05312 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 234 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7692 (t0) REVERT: C 387 SER cc_start: 0.8886 (m) cc_final: 0.8395 (p) outliers start: 14 outliers final: 9 residues processed: 133 average time/residue: 0.2476 time to fit residues: 50.9256 Evaluate side-chains 119 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 316 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 107 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 ASN D 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.089278 restraints weight = 85611.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.093296 restraints weight = 41170.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.095935 restraints weight = 25301.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.097543 restraints weight = 17920.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098798 restraints weight = 14060.025| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 13973 Z= 0.229 Angle : 0.603 7.597 18972 Z= 0.305 Chirality : 0.043 0.159 2112 Planarity : 0.004 0.034 2432 Dihedral : 9.187 114.124 1915 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.50 % Rotamer: Outliers : 1.23 % Allowed : 13.93 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.21), residues: 1726 helix: 0.38 (0.21), residues: 642 sheet: -1.05 (0.29), residues: 264 loop : -0.01 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.013 0.001 TYR D 233 PHE 0.011 0.001 PHE A 324 TRP 0.005 0.001 TRP C 409 HIS 0.006 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00553 (13968) covalent geometry : angle 0.60280 (18972) hydrogen bonds : bond 0.04021 ( 541) hydrogen bonds : angle 5.07872 ( 1479) Misc. bond : bond 0.09993 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 234 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7752 (t0) REVERT: C 387 SER cc_start: 0.8898 (m) cc_final: 0.8408 (p) REVERT: D 184 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8730 (mp) outliers start: 18 outliers final: 11 residues processed: 124 average time/residue: 0.2351 time to fit residues: 45.7257 Evaluate side-chains 122 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 316 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.0980 chunk 159 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 ASN C 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.108556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.091381 restraints weight = 84397.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095495 restraints weight = 40713.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098251 restraints weight = 25002.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.099969 restraints weight = 17551.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.101306 restraints weight = 13570.446| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 13973 Z= 0.117 Angle : 0.529 6.717 18972 Z= 0.261 Chirality : 0.041 0.155 2112 Planarity : 0.004 0.033 2432 Dihedral : 8.758 104.404 1914 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 1.09 % Allowed : 14.21 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.21), residues: 1726 helix: 0.64 (0.21), residues: 638 sheet: -0.89 (0.29), residues: 262 loop : 0.07 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.008 0.001 TYR B 233 PHE 0.010 0.001 PHE B 443 TRP 0.005 0.001 TRP A 323 HIS 0.004 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00290 (13968) covalent geometry : angle 0.52866 (18972) hydrogen bonds : bond 0.03259 ( 541) hydrogen bonds : angle 4.72124 ( 1479) Misc. bond : bond 0.05772 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8930 (mp) REVERT: C 234 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7733 (t0) REVERT: C 382 MET cc_start: 0.8919 (mmt) cc_final: 0.8642 (mmt) REVERT: C 387 SER cc_start: 0.8937 (m) cc_final: 0.8464 (p) outliers start: 16 outliers final: 11 residues processed: 139 average time/residue: 0.2544 time to fit residues: 55.2733 Evaluate side-chains 131 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 184 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 10 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 101 optimal weight: 0.0020 chunk 106 optimal weight: 1.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 ASN C 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.106936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.089730 restraints weight = 84845.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.093786 restraints weight = 41203.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.096494 restraints weight = 25361.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098078 restraints weight = 17868.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099417 restraints weight = 14103.929| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 13973 Z= 0.186 Angle : 0.565 8.117 18972 Z= 0.281 Chirality : 0.042 0.158 2112 Planarity : 0.004 0.035 2432 Dihedral : 8.698 96.476 1914 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.64 % Allowed : 14.41 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.21), residues: 1726 helix: 0.46 (0.21), residues: 654 sheet: -1.02 (0.29), residues: 268 loop : -0.13 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.017 0.001 TYR C 381 PHE 0.010 0.001 PHE A 324 TRP 0.004 0.001 TRP C 408 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00447 (13968) covalent geometry : angle 0.56522 (18972) hydrogen bonds : bond 0.03447 ( 541) hydrogen bonds : angle 4.77217 ( 1479) Misc. bond : bond 0.09484 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8968 (mp) REVERT: C 234 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7818 (t0) REVERT: C 387 SER cc_start: 0.8939 (m) cc_final: 0.8462 (p) REVERT: D 86 ASP cc_start: 0.7781 (t0) cc_final: 0.7554 (t0) REVERT: D 184 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8713 (mp) outliers start: 24 outliers final: 14 residues processed: 139 average time/residue: 0.2435 time to fit residues: 53.1914 Evaluate side-chains 134 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 126 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 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 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.089816 restraints weight = 85080.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093794 restraints weight = 41056.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096438 restraints weight = 25409.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098286 restraints weight = 18085.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.099407 restraints weight = 13926.687| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 13973 Z= 0.173 Angle : 0.556 7.848 18972 Z= 0.276 Chirality : 0.042 0.164 2112 Planarity : 0.004 0.034 2432 Dihedral : 8.609 95.565 1914 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.21 % Favored : 94.73 % Rotamer: Outliers : 1.64 % Allowed : 14.21 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.21), residues: 1726 helix: 0.41 (0.21), residues: 664 sheet: -1.12 (0.29), residues: 264 loop : -0.19 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.017 0.001 TYR C 381 PHE 0.009 0.001 PHE A 324 TRP 0.005 0.001 TRP C 408 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00415 (13968) covalent geometry : angle 0.55557 (18972) hydrogen bonds : bond 0.03335 ( 541) hydrogen bonds : angle 4.71007 ( 1479) Misc. bond : bond 0.09845 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8964 (mp) REVERT: C 234 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7886 (t0) REVERT: C 387 SER cc_start: 0.8952 (m) cc_final: 0.8484 (p) REVERT: D 184 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8714 (mp) outliers start: 24 outliers final: 18 residues processed: 141 average time/residue: 0.2335 time to fit residues: 51.9863 Evaluate side-chains 139 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 158 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 138 optimal weight: 0.0770 chunk 141 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.107547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.090247 restraints weight = 84385.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094345 restraints weight = 40613.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097069 restraints weight = 24938.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.098852 restraints weight = 17616.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.099977 restraints weight = 13590.995| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 13973 Z= 0.149 Angle : 0.539 8.027 18972 Z= 0.266 Chirality : 0.042 0.161 2112 Planarity : 0.004 0.033 2432 Dihedral : 8.432 93.228 1914 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.50 % Allowed : 14.89 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.21), residues: 1726 helix: 0.60 (0.21), residues: 652 sheet: -1.14 (0.29), residues: 264 loop : -0.11 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.018 0.001 TYR C 381 PHE 0.007 0.001 PHE A 324 TRP 0.005 0.001 TRP C 408 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00360 (13968) covalent geometry : angle 0.53931 (18972) hydrogen bonds : bond 0.03179 ( 541) hydrogen bonds : angle 4.59725 ( 1479) Misc. bond : bond 0.08808 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8951 (mp) REVERT: C 234 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7906 (t0) REVERT: C 387 SER cc_start: 0.8921 (m) cc_final: 0.8480 (p) REVERT: D 184 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8722 (mp) outliers start: 22 outliers final: 18 residues processed: 138 average time/residue: 0.2372 time to fit residues: 51.5924 Evaluate side-chains 139 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 4 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.107803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.090520 restraints weight = 84246.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094543 restraints weight = 41047.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.097246 restraints weight = 25397.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099001 restraints weight = 17962.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.100264 restraints weight = 13977.505| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 13973 Z= 0.126 Angle : 0.527 7.747 18972 Z= 0.258 Chirality : 0.041 0.159 2112 Planarity : 0.004 0.037 2432 Dihedral : 8.278 90.351 1914 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.71 % Allowed : 15.03 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.21), residues: 1726 helix: 0.67 (0.21), residues: 656 sheet: -0.99 (0.30), residues: 260 loop : -0.06 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 132 TYR 0.016 0.001 TYR B 518 PHE 0.006 0.001 PHE A 324 TRP 0.005 0.001 TRP C 408 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00309 (13968) covalent geometry : angle 0.52745 (18972) hydrogen bonds : bond 0.03055 ( 541) hydrogen bonds : angle 4.51643 ( 1479) Misc. bond : bond 0.07671 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8919 (mp) REVERT: C 234 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7822 (t0) REVERT: C 382 MET cc_start: 0.8950 (mmt) cc_final: 0.8728 (mmt) REVERT: C 387 SER cc_start: 0.8966 (m) cc_final: 0.8531 (p) REVERT: D 184 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8751 (mp) outliers start: 25 outliers final: 20 residues processed: 143 average time/residue: 0.2432 time to fit residues: 54.2390 Evaluate side-chains 142 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.105791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.088175 restraints weight = 86111.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.092182 restraints weight = 42120.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.094884 restraints weight = 26197.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096757 restraints weight = 18758.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097983 restraints weight = 14503.026| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 13973 Z= 0.224 Angle : 0.596 9.484 18972 Z= 0.298 Chirality : 0.043 0.180 2112 Planarity : 0.004 0.037 2432 Dihedral : 8.467 90.564 1914 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.97 % Favored : 93.97 % Rotamer: Outliers : 1.64 % Allowed : 15.51 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.21), residues: 1726 helix: 0.49 (0.21), residues: 656 sheet: -1.26 (0.29), residues: 268 loop : -0.25 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 132 TYR 0.014 0.002 TYR C 381 PHE 0.011 0.002 PHE A 324 TRP 0.004 0.001 TRP C 408 HIS 0.005 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00533 (13968) covalent geometry : angle 0.59585 (18972) hydrogen bonds : bond 0.03500 ( 541) hydrogen bonds : angle 4.75690 ( 1479) Misc. bond : bond 0.12782 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7767 (t0) cc_final: 0.7515 (t0) REVERT: A 184 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8964 (mp) REVERT: C 119 LYS cc_start: 0.8533 (mmtp) cc_final: 0.8314 (mtpp) REVERT: C 234 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7927 (t0) REVERT: C 382 MET cc_start: 0.8990 (mmt) cc_final: 0.8749 (mmt) REVERT: C 387 SER cc_start: 0.8939 (m) cc_final: 0.8499 (p) REVERT: D 184 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8780 (mp) outliers start: 24 outliers final: 19 residues processed: 135 average time/residue: 0.2334 time to fit residues: 49.6333 Evaluate side-chains 136 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 146 optimal weight: 0.3980 chunk 119 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.108941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.091970 restraints weight = 83342.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.096013 restraints weight = 39635.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.098721 restraints weight = 24218.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100545 restraints weight = 17019.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.101682 restraints weight = 13027.441| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 13973 Z= 0.103 Angle : 0.521 7.211 18972 Z= 0.253 Chirality : 0.041 0.156 2112 Planarity : 0.004 0.038 2432 Dihedral : 8.105 88.641 1914 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.43 % Allowed : 15.44 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.21), residues: 1726 helix: 0.72 (0.21), residues: 656 sheet: -0.97 (0.30), residues: 260 loop : -0.05 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.012 0.001 TYR C 381 PHE 0.006 0.001 PHE B 443 TRP 0.006 0.001 TRP C 408 HIS 0.004 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00252 (13968) covalent geometry : angle 0.52068 (18972) hydrogen bonds : bond 0.02927 ( 541) hydrogen bonds : angle 4.46218 ( 1479) Misc. bond : bond 0.06449 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7553 (t0) cc_final: 0.7338 (t0) REVERT: B 381 TYR cc_start: 0.8669 (m-80) cc_final: 0.8466 (m-10) REVERT: C 234 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7830 (t0) REVERT: C 387 SER cc_start: 0.9029 (m) cc_final: 0.8598 (p) REVERT: D 184 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8744 (mp) outliers start: 21 outliers final: 17 residues processed: 138 average time/residue: 0.2441 time to fit residues: 53.2434 Evaluate side-chains 140 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 114 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.108344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.091441 restraints weight = 82850.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.095466 restraints weight = 39687.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098155 restraints weight = 24250.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099917 restraints weight = 17061.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101142 restraints weight = 13101.493| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 13973 Z= 0.134 Angle : 0.535 7.934 18972 Z= 0.260 Chirality : 0.042 0.161 2112 Planarity : 0.004 0.035 2432 Dihedral : 8.042 89.370 1914 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.23 % Allowed : 15.98 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.21), residues: 1726 helix: 0.73 (0.21), residues: 656 sheet: -0.96 (0.30), residues: 264 loop : -0.10 (0.24), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 132 TYR 0.011 0.001 TYR B 518 PHE 0.007 0.001 PHE A 332 TRP 0.005 0.001 TRP C 408 HIS 0.005 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00326 (13968) covalent geometry : angle 0.53533 (18972) hydrogen bonds : bond 0.03022 ( 541) hydrogen bonds : angle 4.48321 ( 1479) Misc. bond : bond 0.07980 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3972.25 seconds wall clock time: 69 minutes 5.95 seconds (4145.95 seconds total)