Starting phenix.real_space_refine on Sun Jul 5 10:33:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5l_19739/07_2026/8s5l_19739_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5l_19739/07_2026/8s5l_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8s5l_19739/07_2026/8s5l_19739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5l_19739/07_2026/8s5l_19739.map" model { file = "/net/cci-nas-00/data/ceres_data/8s5l_19739/07_2026/8s5l_19739_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5l_19739/07_2026/8s5l_19739_trim.cif" } 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-dev-6108/lib/python3.11/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: 4.81, per 1000 atoms: 0.18 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: 2.52 Conformation dependent library (CDL) restraints added in 752.4 milliseconds 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: 0.66 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: 6.32 Time building geometry restraints manager: 3.47 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: 50014 7.38 - 14.77: 4 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=" O2P PLP C 602 " pdb=" P PLP C 602 " pdb=" O4P PLP C 602 " ideal model delta sigma weight residual 101.47 110.48 -9.01 3.00e+00 1.11e-01 9.01e+00 ... (remaining 50015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 11359 17.59 - 35.19: 974 35.19 - 52.78: 315 52.78 - 70.38: 107 70.38 - 87.97: 40 Dihedral angle restraints: 12795 sinusoidal: 7209 harmonic: 5586 Sorted by residual: dihedral pdb=" CA LYS B 384 " pdb=" C LYS B 384 " pdb=" N PHE B 385 " pdb=" CA PHE B 385 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA LYS C 384 " pdb=" C LYS C 384 " pdb=" N PHE C 385 " pdb=" CA PHE C 385 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LYS D 384 " pdb=" C LYS D 384 " pdb=" N PHE D 385 " pdb=" CA PHE D 385 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 12792 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.930 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: 0.190 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.880 Find NCS groups from input model: 0.400 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: 0.000 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: 0.000 Total: 37.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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= 0.266 Angle : 0.794 36.925 18972 Z= 0.432 Chirality : 0.043 0.182 2112 Planarity : 0.007 0.222 2432 Dihedral : 15.336 87.972 5222 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 are 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/Z covalent geometry : bond 0.00596 / 0.27 (13968) covalent geometry : angle 0.79439 / 0.43 (18972) hydrogen bonds : bond 0.18502 / 11.70 ( 541) hydrogen bonds : angle 6.69739 / 4.67 ( 1479) Misc. bond : bond 0.07693 / 4.73 ( 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 : 0.604 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: 0.2452 time to fit residues: 44.8246 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 : 0.654 ------------------------------------------------------------------------------- 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... C 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.108901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091629 restraints weight = 84673.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095747 restraints weight = 40573.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098491 restraints weight = 24908.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.100311 restraints weight = 17514.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101570 restraints weight = 13431.837| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 13973 Z= 0.132 Angle : 0.563 5.896 18972 Z= 0.282 Chirality : 0.042 0.144 2112 Planarity : 0.004 0.032 2432 Dihedral : 8.531 89.937 1924 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 0.96 % Allowed : 12.09 % Favored : 86.95 % 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 are not related in a simple way. whole: 0.17 (0.21), residues: 1726 helix: 0.55 (0.21), residues: 636 sheet: -0.83 (0.30), residues: 262 loop : 0.29 (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 A 323 HIS 0.004 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (13968) covalent geometry : angle 0.56251 / 0.28 (18972) hydrogen bonds : bond 0.03999 / 2.70 ( 541) hydrogen bonds : angle 5.12673 / 3.52 ( 1479) Misc. bond : bond 0.05142 / 3.19 ( 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 : 0.739 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: symmetry clash REVERT: C 234 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7697 (t0) REVERT: C 387 SER cc_start: 0.8888 (m) cc_final: 0.8396 (p) outliers start: 14 outliers final: 9 residues processed: 133 average time/residue: 0.2302 time to fit residues: 47.8713 Evaluate side-chains 120 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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: 2.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3509 r_free = 0.3509 target = 0.106687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.089408 restraints weight = 85519.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.093495 restraints weight = 41626.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096178 restraints weight = 25583.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097857 restraints weight = 18089.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.099142 restraints weight = 14100.871| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 13973 Z= 0.209 Angle : 0.586 6.294 18972 Z= 0.296 Chirality : 0.043 0.160 2112 Planarity : 0.004 0.033 2432 Dihedral : 8.458 89.958 1923 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.33 % Favored : 94.61 % Rotamer: Outliers : 1.30 % Allowed : 13.59 % Favored : 85.11 % 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 are not related in a simple way. whole: -0.11 (0.21), residues: 1726 helix: 0.45 (0.21), residues: 638 sheet: -1.00 (0.29), residues: 264 loop : 0.01 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 45 TYR 0.012 0.001 TYR D 233 PHE 0.010 0.001 PHE A 324 TRP 0.005 0.001 TRP A 323 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (13968) covalent geometry : angle 0.58571 / 0.30 (18972) hydrogen bonds : bond 0.03912 / 2.67 ( 541) hydrogen bonds : angle 5.00292 / 3.44 ( 1479) Misc. bond : bond 0.09462 / 5.68 ( 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 139 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.737 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: 0.9193 (OUTLIER) cc_final: 0.8979 (mp) REVERT: C 234 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7747 (t0) REVERT: C 387 SER cc_start: 0.8904 (m) cc_final: 0.8412 (p) outliers start: 19 outliers final: 12 residues processed: 132 average time/residue: 0.2266 time to fit residues: 47.4690 Evaluate side-chains 127 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS 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: 0.2980 chunk 159 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3529 r_free = 0.3529 target = 0.107909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.090686 restraints weight = 84684.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.094759 restraints weight = 40987.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.097484 restraints weight = 25350.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.099251 restraints weight = 17826.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.100504 restraints weight = 13732.172| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 13973 Z= 0.141 Angle : 0.535 5.594 18972 Z= 0.267 Chirality : 0.042 0.155 2112 Planarity : 0.004 0.032 2432 Dihedral : 8.199 89.076 1922 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 1.16 % Allowed : 14.21 % Favored : 84.63 % 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 are not related in a simple way. whole: 0.02 (0.21), residues: 1726 helix: 0.61 (0.21), residues: 638 sheet: -0.96 (0.29), residues: 264 loop : 0.05 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.008 0.001 TYR D 163 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/Z covalent geometry : bond 0.00345 / 0.14 (13968) covalent geometry : angle 0.53514 / 0.27 (18972) hydrogen bonds : bond 0.03359 / 2.29 ( 541) hydrogen bonds : angle 4.74913 / 3.26 ( 1479) Misc. bond : bond 0.07326 / 4.39 ( 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 140 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.761 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: symmetry clash REVERT: C 234 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7760 (t0) REVERT: C 382 MET cc_start: 0.8947 (mmt) cc_final: 0.8678 (mmt) REVERT: C 387 SER cc_start: 0.8946 (m) cc_final: 0.8460 (p) REVERT: D 184 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8735 (mp) outliers start: 17 outliers final: 12 residues processed: 135 average time/residue: 0.2338 time to fit residues: 49.5176 Evaluate side-chains 129 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 C residue 425 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 316 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 10 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3513 r_free = 0.3513 target = 0.106778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.089532 restraints weight = 84978.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093513 restraints weight = 40872.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.096234 restraints weight = 25242.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098031 restraints weight = 17826.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.099151 restraints weight = 13727.537| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 13973 Z= 0.185 Angle : 0.557 6.059 18972 Z= 0.280 Chirality : 0.042 0.159 2112 Planarity : 0.004 0.035 2432 Dihedral : 8.174 89.234 1922 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.45 % Favored : 94.44 % Rotamer: Outliers : 1.50 % Allowed : 14.48 % Favored : 84.02 % 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 are not related in a simple way. whole: -0.29 (0.21), residues: 1726 helix: 0.38 (0.21), residues: 664 sheet: -1.04 (0.30), residues: 268 loop : -0.22 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.011 0.001 TYR D 163 PHE 0.010 0.001 PHE A 324 TRP 0.004 0.001 TRP A 323 HIS 0.005 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 (13968) covalent geometry : angle 0.55739 / 0.28 (18972) hydrogen bonds : bond 0.03467 / 2.36 ( 541) hydrogen bonds : angle 4.76804 / 3.27 ( 1479) Misc. bond : bond 0.09901 / 5.78 ( 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 142 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.797 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: 0.9178 (OUTLIER) cc_final: 0.8974 (mp) REVERT: C 234 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7871 (t0) REVERT: C 387 SER cc_start: 0.8906 (m) cc_final: 0.8418 (p) REVERT: D 184 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8744 (mp) outliers start: 22 outliers final: 14 residues processed: 135 average time/residue: 0.2353 time to fit residues: 50.4357 Evaluate side-chains 133 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 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 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: 0.0020 chunk 151 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3524 r_free = 0.3524 target = 0.107577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.090177 restraints weight = 84969.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.094297 restraints weight = 41059.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.097071 restraints weight = 25180.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.098875 restraints weight = 17697.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.099917 restraints weight = 13624.798| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 13973 Z= 0.142 Angle : 0.529 5.624 18972 Z= 0.263 Chirality : 0.041 0.154 2112 Planarity : 0.004 0.033 2432 Dihedral : 8.028 89.199 1922 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 1.30 % Allowed : 14.48 % Favored : 84.22 % 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 are not related in a simple way. whole: -0.16 (0.21), residues: 1726 helix: 0.50 (0.21), residues: 664 sheet: -1.07 (0.29), residues: 264 loop : -0.12 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 132 TYR 0.009 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/Z covalent geometry : bond 0.00344 / 0.14 (13968) covalent geometry : angle 0.52851 / 0.26 (18972) hydrogen bonds : bond 0.03211 / 2.19 ( 541) hydrogen bonds : angle 4.62052 / 3.17 ( 1479) Misc. bond : bond 0.08365 / 4.86 ( 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 145 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.770 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: 0.9145 (OUTLIER) cc_final: 0.8943 (mp) REVERT: C 234 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7865 (t0) REVERT: C 387 SER cc_start: 0.8942 (m) cc_final: 0.8481 (p) REVERT: D 184 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8711 (mp) outliers start: 19 outliers final: 15 residues processed: 140 average time/residue: 0.2195 time to fit residues: 48.7737 Evaluate side-chains 138 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 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 D residue 184 LEU 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: 0.1980 chunk 37 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 138 optimal weight: 0.0980 chunk 141 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.090446 restraints weight = 84298.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.094516 restraints weight = 40634.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.097235 restraints weight = 24980.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.099033 restraints weight = 17614.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100097 restraints weight = 13565.940| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 13973 Z= 0.144 Angle : 0.528 5.524 18972 Z= 0.261 Chirality : 0.042 0.159 2112 Planarity : 0.004 0.033 2432 Dihedral : 7.960 89.431 1922 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.50 % Allowed : 14.96 % Favored : 83.54 % 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 are not related in a simple way. whole: -0.03 (0.21), residues: 1726 helix: 0.64 (0.21), residues: 656 sheet: -1.08 (0.29), residues: 264 loop : -0.04 (0.24), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.011 0.001 TYR C 381 PHE 0.007 0.001 PHE A 332 TRP 0.004 0.001 TRP A 323 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (13968) covalent geometry : angle 0.52797 / 0.26 (18972) hydrogen bonds : bond 0.03159 / 2.15 ( 541) hydrogen bonds : angle 4.56879 / 3.14 ( 1479) Misc. bond : bond 0.08353 / 4.82 ( 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 148 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.657 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: C 234 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7891 (t0) REVERT: C 382 MET cc_start: 0.8991 (mmt) cc_final: 0.8786 (mmt) REVERT: C 387 SER cc_start: 0.8916 (m) cc_final: 0.8434 (p) REVERT: D 184 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8753 (mp) outliers start: 22 outliers final: 16 residues processed: 141 average time/residue: 0.2054 time to fit residues: 45.7580 Evaluate side-chains 135 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.108484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091823 restraints weight = 83314.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095650 restraints weight = 41060.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098297 restraints weight = 25676.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.100044 restraints weight = 18238.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.101143 restraints weight = 14110.210| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 13973 Z= 0.141 Angle : 0.529 5.557 18972 Z= 0.262 Chirality : 0.041 0.157 2112 Planarity : 0.004 0.033 2432 Dihedral : 7.914 89.989 1922 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.57 % Allowed : 15.10 % Favored : 83.33 % 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 are not related in a simple way. whole: -0.01 (0.21), residues: 1726 helix: 0.64 (0.21), residues: 656 sheet: -0.99 (0.30), residues: 260 loop : -0.04 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.015 0.001 TYR B 518 PHE 0.007 0.001 PHE A 324 TRP 0.005 0.001 TRP C 408 HIS 0.005 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (13968) covalent geometry : angle 0.52883 / 0.26 (18972) hydrogen bonds : bond 0.03126 / 2.12 ( 541) hydrogen bonds : angle 4.55901 / 3.13 ( 1479) Misc. bond : bond 0.08230 / 4.75 ( 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 142 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 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: C 234 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7772 (t0) REVERT: C 382 MET cc_start: 0.8918 (mmt) cc_final: 0.8714 (mmt) REVERT: C 387 SER cc_start: 0.9006 (m) cc_final: 0.8550 (p) REVERT: D 184 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8711 (mp) outliers start: 23 outliers final: 20 residues processed: 135 average time/residue: 0.2285 time to fit residues: 48.9631 Evaluate side-chains 140 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 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 380 ASN 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: 0.7980 chunk 50 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 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: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.107845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.091175 restraints weight = 84094.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095030 restraints weight = 41323.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097599 restraints weight = 25807.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.099314 restraints weight = 18435.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100524 restraints weight = 14328.066| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 13973 Z= 0.177 Angle : 0.552 6.202 18972 Z= 0.275 Chirality : 0.042 0.161 2112 Planarity : 0.004 0.035 2432 Dihedral : 7.947 89.450 1922 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.78 % Allowed : 14.96 % 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 are not related in a simple way. whole: -0.10 (0.21), residues: 1726 helix: 0.61 (0.21), residues: 656 sheet: -1.05 (0.30), residues: 264 loop : -0.12 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.013 0.001 TYR B 518 PHE 0.009 0.001 PHE A 324 TRP 0.005 0.001 TRP C 408 HIS 0.012 0.001 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (13968) covalent geometry : angle 0.55221 / 0.28 (18972) hydrogen bonds : bond 0.03231 / 2.19 ( 541) hydrogen bonds : angle 4.62673 / 3.17 ( 1479) Misc. bond : bond 0.09772 / 5.61 ( 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: 26 poor density : 116 time to evaluate : 0.587 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: C 234 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7752 (t0) REVERT: C 382 MET cc_start: 0.8913 (mmt) cc_final: 0.8689 (mmt) REVERT: C 387 SER cc_start: 0.8990 (m) cc_final: 0.8541 (p) REVERT: D 184 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8704 (mp) outliers start: 26 outliers final: 23 residues processed: 134 average time/residue: 0.2112 time to fit residues: 44.9484 Evaluate side-chains 140 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 380 ASN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 425 VAL 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 C residue 380 ASN Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 144 GLU 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: 0.8980 chunk 103 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 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 = 0.3544 r_free = 0.3544 target = 0.108572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.091533 restraints weight = 83599.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095549 restraints weight = 39961.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098287 restraints weight = 24528.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100065 restraints weight = 17201.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.101221 restraints weight = 13242.334| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 13973 Z= 0.120 Angle : 0.524 7.067 18972 Z= 0.258 Chirality : 0.041 0.156 2112 Planarity : 0.004 0.033 2432 Dihedral : 7.812 89.135 1922 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.57 % Allowed : 15.37 % Favored : 83.06 % 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 are not related in a simple way. whole: 0.03 (0.21), residues: 1726 helix: 0.68 (0.21), residues: 656 sheet: -0.93 (0.30), residues: 264 loop : -0.03 (0.24), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 498 TYR 0.012 0.001 TYR B 518 PHE 0.006 0.001 PHE A 324 TRP 0.005 0.001 TRP C 408 HIS 0.006 0.001 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (13968) covalent geometry : angle 0.52360 / 0.26 (18972) hydrogen bonds : bond 0.03028 / 2.05 ( 541) hydrogen bonds : angle 4.51320 / 3.10 ( 1479) Misc. bond : bond 0.07678 / 4.44 ( 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 146 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.766 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: 0.8086 (OUTLIER) cc_final: 0.7838 (t0) REVERT: C 382 MET cc_start: 0.8975 (mmt) cc_final: 0.8758 (mmt) REVERT: C 387 SER cc_start: 0.8926 (m) cc_final: 0.8486 (p) REVERT: D 184 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8719 (mp) outliers start: 23 outliers final: 21 residues processed: 137 average time/residue: 0.2220 time to fit residues: 47.4049 Evaluate side-chains 144 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 B residue 425 VAL 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 C residue 501 HIS Chi-restraints excluded: chain D residue 144 GLU 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 114 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 0.0470 chunk 67 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.109233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.092269 restraints weight = 82525.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096300 restraints weight = 39582.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.098977 restraints weight = 24278.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100788 restraints weight = 17154.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.102022 restraints weight = 13141.028| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 0.097 13973 Z= 0.103 Angle : 0.511 7.199 18972 Z= 0.250 Chirality : 0.041 0.157 2112 Planarity : 0.004 0.039 2432 Dihedral : 7.693 89.206 1922 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.43 % Allowed : 15.57 % Favored : 82.99 % 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 are not related in a simple way. whole: 0.14 (0.21), residues: 1726 helix: 0.75 (0.21), residues: 656 sheet: -0.91 (0.30), residues: 260 loop : 0.05 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.011 0.001 TYR B 518 PHE 0.005 0.001 PHE B 443 TRP 0.005 0.001 TRP B 408 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.10 (13968) covalent geometry : angle 0.51127 / 0.25 (18972) hydrogen bonds : bond 0.02915 / 1.97 ( 541) hydrogen bonds : angle 4.43240 / 3.04 ( 1479) Misc. bond : bond 0.06158 / 3.54 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3863.85 seconds wall clock time: 67 minutes 1.65 seconds (4021.65 seconds total)