Starting phenix.real_space_refine on Mon Jun 23 16:15:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5l_19739/06_2025/8s5l_19739_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5l_19739/06_2025/8s5l_19739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s5l_19739/06_2025/8s5l_19739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5l_19739/06_2025/8s5l_19739.map" model { file = "/net/cci-nas-00/data/ceres_data/8s5l_19739/06_2025/8s5l_19739_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5l_19739/06_2025/8s5l_19739_trim.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.43, per 1000 atoms: 0.53 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: 8.07 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.72 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: 10.72 Time building geometry restraints manager: 9.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 13533 1.08 - 1.32: 2459 1.32 - 1.56: 11441 1.56 - 1.81: 113 1.81 - 2.05: 25 Bond restraints: 27571 Sorted by residual: bond pdb=" C4' LLP A 119 " pdb="H4'1 LLP A 119 " ideal model delta sigma weight residual 0.930 1.084 -0.154 2.00e-02 2.50e+03 5.91e+01 bond pdb=" C4' LLP D 119 " pdb="H4'1 LLP D 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.84e+01 bond pdb=" C6 LLP D 119 " pdb=" H6 LLP D 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" C6 LLP A 119 " pdb=" H6 LLP A 119 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.81e+01 bond pdb=" N LLP D 119 " pdb=" H LLP D 119 " ideal model delta sigma weight residual 0.860 1.004 -0.144 2.00e-02 2.50e+03 5.17e+01 ... (remaining 27566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.38: 50016 7.38 - 14.77: 2 14.77 - 22.15: 0 22.15 - 29.54: 0 29.54 - 36.92: 2 Bond angle restraints: 50020 Sorted by residual: angle pdb=" O LLP A 119 " pdb=" C LLP A 119 " pdb=" N ASP A 120 " ideal model delta sigma weight residual 123.00 86.08 36.92 1.60e+00 3.91e-01 5.33e+02 angle pdb=" O LLP D 119 " pdb=" C LLP D 119 " pdb=" N ASP D 120 " ideal model delta sigma weight residual 123.00 87.69 35.31 1.60e+00 3.91e-01 4.87e+02 angle pdb=" OP1 LLP A 119 " pdb=" P LLP A 119 " pdb=" OP4 LLP A 119 " ideal model delta sigma weight residual 100.47 110.60 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" OP1 LLP D 119 " pdb=" P LLP D 119 " pdb=" OP4 LLP D 119 " ideal model delta sigma weight residual 100.47 110.28 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C LYS B 384 " pdb=" CA LYS B 384 " pdb=" CB LYS B 384 " ideal model delta sigma weight residual 110.42 115.84 -5.42 1.99e+00 2.53e-01 7.41e+00 ... (remaining 50015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 12328 35.03 - 70.05: 415 70.05 - 105.08: 41 105.08 - 140.10: 2 140.10 - 175.13: 1 Dihedral angle restraints: 12787 sinusoidal: 7201 harmonic: 5586 Sorted by residual: dihedral pdb=" C5A PLP C 602 " pdb=" O4P PLP C 602 " pdb=" P PLP C 602 " pdb=" O1P PLP C 602 " ideal model delta sinusoidal sigma weight residual 76.43 -98.70 175.13 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5 PLP B 602 " pdb=" C4 PLP B 602 " pdb=" C4A PLP B 602 " pdb=" O4A PLP B 602 " ideal model delta sinusoidal sigma weight residual 0.00 -137.31 137.31 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" C5A PLP B 602 " pdb=" O4P PLP B 602 " pdb=" P PLP B 602 " pdb=" O1P PLP B 602 " ideal model delta sinusoidal sigma weight residual 76.43 -58.43 134.86 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 12784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1405 0.036 - 0.073: 519 0.073 - 0.109: 131 0.109 - 0.146: 53 0.146 - 0.182: 4 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CA PRO A 375 " pdb=" N PRO A 375 " pdb=" C PRO A 375 " pdb=" CB PRO A 375 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CA PRO B 375 " pdb=" N PRO B 375 " pdb=" C PRO B 375 " pdb=" CB PRO B 375 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA PRO C 375 " pdb=" N PRO C 375 " pdb=" C PRO C 375 " pdb=" CB PRO C 375 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 2109 not shown) Planarity restraints: 4077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LLP A 119 " 0.137 2.00e-02 2.50e+03 2.22e-01 4.92e+02 pdb=" C LLP A 119 " -0.384 2.00e-02 2.50e+03 pdb=" O LLP A 119 " 0.135 2.00e-02 2.50e+03 pdb=" N ASP A 120 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP D 119 " -0.132 2.00e-02 2.50e+03 2.16e-01 4.66e+02 pdb=" C LLP D 119 " 0.374 2.00e-02 2.50e+03 pdb=" O LLP D 119 " -0.131 2.00e-02 2.50e+03 pdb=" N ASP D 120 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 374 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.12e+00 pdb=" N PRO A 375 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.025 5.00e-02 4.00e+02 ... (remaining 4074 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 914 2.14 - 2.75: 52195 2.75 - 3.37: 78159 3.37 - 3.98: 98302 3.98 - 4.60: 156215 Nonbonded interactions: 385785 Sorted by model distance: nonbonded pdb=" OD2 ASP C 249 " pdb=" H ARG C 369 " model vdw 1.525 2.450 nonbonded pdb=" OD2 ASP B 249 " pdb=" H ARG B 369 " model vdw 1.536 2.450 nonbonded pdb=" OE1 GLU D 201 " pdb=" H GLU D 201 " model vdw 1.546 2.450 nonbonded pdb=" OE1 GLU B 399 " pdb=" H GLU B 399 " model vdw 1.546 2.450 nonbonded pdb=" OE1 GLU A 201 " pdb=" H GLU A 201 " model vdw 1.550 2.450 ... (remaining 385780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 42 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 120 through 548 or resid 601 through 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.650 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: 0.440 Extract box with map and model: 0.920 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 62.010 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 13973 Z= 0.259 Angle : 0.782 36.925 18972 Z= 0.430 Chirality : 0.043 0.182 2112 Planarity : 0.007 0.222 2432 Dihedral : 15.676 175.125 5214 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.56 % Favored : 94.21 % Rotamer: Outliers : 0.14 % Allowed : 12.70 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP B 323 HIS 0.005 0.001 HIS D 203 PHE 0.012 0.002 PHE A 324 TYR 0.015 0.002 TYR D 233 ARG 0.005 0.001 ARG D 209 Details of bonding type rmsd hydrogen bonds : bond 0.18502 ( 541) hydrogen bonds : angle 6.69739 ( 1479) covalent geometry : bond 0.00583 (13968) covalent geometry : angle 0.78182 (18972) Misc. bond : bond 0.07693 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 2.291 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: 0.5382 time to fit residues: 97.6527 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 : 2.275 ------------------------------------------------------------------------------- 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 145 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 HIS D 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.106380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.089201 restraints weight = 85102.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.093241 restraints weight = 41118.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095910 restraints weight = 25261.855| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 13973 Z= 0.234 Angle : 0.625 6.764 18972 Z= 0.317 Chirality : 0.044 0.159 2112 Planarity : 0.004 0.035 2432 Dihedral : 9.722 132.403 1916 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.92 % Favored : 95.02 % Rotamer: Outliers : 1.02 % Allowed : 12.91 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1726 helix: 0.12 (0.20), residues: 654 sheet: -1.16 (0.29), residues: 268 loop : 0.03 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 323 HIS 0.005 0.001 HIS A 203 PHE 0.011 0.001 PHE D 310 TYR 0.011 0.002 TYR D 233 ARG 0.004 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 541) hydrogen bonds : angle 5.31132 ( 1479) covalent geometry : bond 0.00558 (13968) covalent geometry : angle 0.62470 (18972) Misc. bond : bond 0.09819 ( 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 130 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 2.119 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: 0.7963 (OUTLIER) cc_final: 0.7723 (t0) outliers start: 15 outliers final: 11 residues processed: 123 average time/residue: 0.5374 time to fit residues: 102.7368 Evaluate side-chains 123 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 66 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 55 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.105882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.088583 restraints weight = 85133.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.092613 restraints weight = 41496.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095300 restraints weight = 25592.499| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 13973 Z= 0.222 Angle : 0.600 6.762 18972 Z= 0.304 Chirality : 0.043 0.164 2112 Planarity : 0.004 0.038 2432 Dihedral : 9.319 121.022 1915 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.74 % Favored : 94.15 % Rotamer: Outliers : 1.43 % Allowed : 13.52 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1726 helix: 0.33 (0.21), residues: 634 sheet: -1.26 (0.29), residues: 264 loop : -0.20 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 323 HIS 0.005 0.001 HIS A 203 PHE 0.011 0.001 PHE A 324 TYR 0.011 0.002 TYR D 233 ARG 0.004 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 541) hydrogen bonds : angle 5.08086 ( 1479) covalent geometry : bond 0.00531 (13968) covalent geometry : angle 0.59978 (18972) Misc. bond : bond 0.10927 ( 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 144 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 2.333 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: A 184 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8975 (mp) REVERT: C 387 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8488 (p) REVERT: D 184 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8729 (mp) outliers start: 21 outliers final: 14 residues processed: 137 average time/residue: 0.4970 time to fit residues: 105.6246 Evaluate side-chains 131 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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 C residue 311 ILE Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 316 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 115 optimal weight: 1.9990 chunk 154 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.108113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.090706 restraints weight = 85429.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094887 restraints weight = 41157.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097658 restraints weight = 25170.421| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 13973 Z= 0.120 Angle : 0.533 6.555 18972 Z= 0.264 Chirality : 0.041 0.157 2112 Planarity : 0.004 0.032 2432 Dihedral : 8.853 110.669 1914 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.40 % Favored : 95.54 % Rotamer: Outliers : 1.30 % Allowed : 14.14 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1726 helix: 0.60 (0.21), residues: 638 sheet: -1.06 (0.29), residues: 264 loop : -0.04 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 323 HIS 0.004 0.001 HIS D 203 PHE 0.009 0.001 PHE C 443 TYR 0.007 0.001 TYR D 163 ARG 0.002 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 541) hydrogen bonds : angle 4.72027 ( 1479) covalent geometry : bond 0.00293 (13968) covalent geometry : angle 0.53288 (18972) Misc. bond : bond 0.06628 ( 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 150 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 2.903 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: symmetry clash REVERT: B 376 ASP cc_start: 0.8162 (p0) cc_final: 0.7937 (p0) REVERT: C 387 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8622 (p) outliers start: 19 outliers final: 14 residues processed: 144 average time/residue: 0.5017 time to fit residues: 112.8465 Evaluate side-chains 131 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 2.090 ------------------------------------------------------------------------------- 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 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 501 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 314 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 184 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 129 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.088817 restraints weight = 85007.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092864 restraints weight = 41008.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095559 restraints weight = 25263.124| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 13973 Z= 0.200 Angle : 0.575 7.566 18972 Z= 0.288 Chirality : 0.042 0.165 2112 Planarity : 0.004 0.036 2432 Dihedral : 8.837 104.420 1914 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.50 % Rotamer: Outliers : 1.71 % Allowed : 14.55 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1726 helix: 0.43 (0.21), residues: 652 sheet: -1.21 (0.29), residues: 268 loop : -0.29 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 323 HIS 0.005 0.001 HIS D 203 PHE 0.011 0.001 PHE A 324 TYR 0.012 0.001 TYR D 163 ARG 0.004 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 541) hydrogen bonds : angle 4.78303 ( 1479) covalent geometry : bond 0.00480 (13968) covalent geometry : angle 0.57476 (18972) Misc. bond : bond 0.10374 ( 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 147 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 2.154 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: A 184 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8961 (mp) REVERT: C 387 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8608 (p) REVERT: D 184 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8724 (mp) outliers start: 25 outliers final: 17 residues processed: 137 average time/residue: 0.5075 time to fit residues: 107.5559 Evaluate side-chains 136 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 2.181 ------------------------------------------------------------------------------- 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 301 TYR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 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 387 SER Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 316 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 146 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.105770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.088294 restraints weight = 85558.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.092369 restraints weight = 41665.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095064 restraints weight = 25728.466| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 13973 Z= 0.207 Angle : 0.576 7.234 18972 Z= 0.290 Chirality : 0.043 0.169 2112 Planarity : 0.004 0.037 2432 Dihedral : 8.831 103.820 1914 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.74 % Favored : 94.15 % Rotamer: Outliers : 1.91 % Allowed : 15.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1726 helix: 0.50 (0.21), residues: 640 sheet: -1.30 (0.29), residues: 268 loop : -0.30 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 408 HIS 0.005 0.001 HIS D 203 PHE 0.010 0.001 PHE A 324 TYR 0.012 0.001 TYR D 163 ARG 0.004 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 541) hydrogen bonds : angle 4.77494 ( 1479) covalent geometry : bond 0.00491 (13968) covalent geometry : angle 0.57602 (18972) Misc. bond : bond 0.11023 ( 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 146 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 2.443 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: 0.9167 (OUTLIER) cc_final: 0.8964 (mp) REVERT: C 387 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8620 (p) REVERT: D 184 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8727 (mp) outliers start: 28 outliers final: 20 residues processed: 138 average time/residue: 0.6336 time to fit residues: 136.3586 Evaluate side-chains 136 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 60 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 167 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.105212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.087125 restraints weight = 87329.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.091211 restraints weight = 42472.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.093992 restraints weight = 26451.185| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 13973 Z= 0.136 Angle : 0.534 6.886 18972 Z= 0.263 Chirality : 0.042 0.163 2112 Planarity : 0.004 0.033 2432 Dihedral : 8.564 101.379 1914 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.64 % Allowed : 15.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1726 helix: 0.67 (0.21), residues: 640 sheet: -1.20 (0.29), residues: 264 loop : -0.15 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 408 HIS 0.005 0.001 HIS A 203 PHE 0.006 0.001 PHE C 443 TYR 0.009 0.001 TYR D 163 ARG 0.002 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03148 ( 541) hydrogen bonds : angle 4.58178 ( 1479) covalent geometry : bond 0.00329 (13968) covalent geometry : angle 0.53409 (18972) Misc. bond : bond 0.08036 ( 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 146 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 2.623 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: 0.9186 (OUTLIER) cc_final: 0.8974 (mp) REVERT: C 387 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8505 (p) REVERT: D 184 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8739 (mp) outliers start: 24 outliers final: 20 residues processed: 139 average time/residue: 0.7190 time to fit residues: 157.1349 Evaluate side-chains 138 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 2.790 ------------------------------------------------------------------------------- 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 365 GLN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 387 SER 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 7 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.086694 restraints weight = 87437.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090711 restraints weight = 42754.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093422 restraints weight = 26811.204| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 0.137 13973 Z= 0.170 Angle : 0.553 6.975 18972 Z= 0.275 Chirality : 0.042 0.163 2112 Planarity : 0.004 0.035 2432 Dihedral : 8.556 99.777 1914 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.78 % Allowed : 15.57 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1726 helix: 0.59 (0.21), residues: 652 sheet: -1.25 (0.29), residues: 268 loop : -0.29 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 408 HIS 0.005 0.001 HIS D 203 PHE 0.008 0.001 PHE A 324 TYR 0.016 0.001 TYR B 518 ARG 0.003 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 541) hydrogen bonds : angle 4.63756 ( 1479) covalent geometry : bond 0.00407 (13968) covalent geometry : angle 0.55329 (18972) Misc. bond : bond 0.09571 ( 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 144 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8977 (mp) REVERT: C 387 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8514 (p) REVERT: D 184 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8744 (mp) outliers start: 26 outliers final: 22 residues processed: 136 average time/residue: 0.5074 time to fit residues: 107.8740 Evaluate side-chains 141 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 387 SER 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 18 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 159 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN C 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.107529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.090160 restraints weight = 85387.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094196 restraints weight = 41230.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.096955 restraints weight = 25498.128| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 13973 Z= 0.119 Angle : 0.532 6.746 18972 Z= 0.261 Chirality : 0.041 0.157 2112 Planarity : 0.004 0.036 2432 Dihedral : 8.402 98.678 1914 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.84 % Allowed : 15.78 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1726 helix: 0.66 (0.21), residues: 652 sheet: -1.13 (0.29), residues: 268 loop : -0.19 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 408 HIS 0.008 0.001 HIS C 501 PHE 0.005 0.001 PHE A 332 TYR 0.012 0.001 TYR B 518 ARG 0.002 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 541) hydrogen bonds : angle 4.53390 ( 1479) covalent geometry : bond 0.00292 (13968) covalent geometry : angle 0.53154 (18972) Misc. bond : bond 0.07683 ( 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 153 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 2.623 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: 0.9122 (OUTLIER) cc_final: 0.8912 (mp) REVERT: C 387 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8666 (p) REVERT: D 184 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8722 (mp) outliers start: 27 outliers final: 23 residues processed: 146 average time/residue: 0.5556 time to fit residues: 126.2288 Evaluate side-chains 146 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 387 SER 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 264 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 86 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN C 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.105557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.088084 restraints weight = 86228.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.092050 restraints weight = 41856.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094718 restraints weight = 26064.451| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 13973 Z= 0.224 Angle : 0.591 7.455 18972 Z= 0.297 Chirality : 0.043 0.175 2112 Planarity : 0.004 0.038 2432 Dihedral : 8.545 97.257 1914 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.80 % Rotamer: Outliers : 1.84 % Allowed : 15.71 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1726 helix: 0.54 (0.21), residues: 652 sheet: -1.34 (0.29), residues: 264 loop : -0.33 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 323 HIS 0.010 0.001 HIS C 501 PHE 0.011 0.002 PHE A 324 TYR 0.033 0.002 TYR B 381 ARG 0.004 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 541) hydrogen bonds : angle 4.72402 ( 1479) covalent geometry : bond 0.00532 (13968) covalent geometry : angle 0.59084 (18972) Misc. bond : bond 0.11567 ( 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 145 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7703 (t0) cc_final: 0.7483 (t0) REVERT: A 184 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8961 (mp) REVERT: C 169 MET cc_start: 0.6872 (mtt) cc_final: 0.6305 (ttm) REVERT: C 278 ILE cc_start: 0.9235 (mm) cc_final: 0.8996 (mt) REVERT: C 387 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8590 (p) REVERT: D 184 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8733 (mp) outliers start: 27 outliers final: 22 residues processed: 138 average time/residue: 0.5133 time to fit residues: 110.5461 Evaluate side-chains 142 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 387 SER 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 264 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 20 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN C 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.107036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.089567 restraints weight = 85629.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093628 restraints weight = 41446.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.096333 restraints weight = 25634.810| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 13973 Z= 0.129 Angle : 0.540 7.465 18972 Z= 0.266 Chirality : 0.042 0.161 2112 Planarity : 0.004 0.039 2432 Dihedral : 8.344 96.811 1914 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 1.71 % Allowed : 16.12 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1726 helix: 0.71 (0.21), residues: 640 sheet: -1.20 (0.30), residues: 264 loop : -0.18 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 408 HIS 0.005 0.001 HIS D 203 PHE 0.006 0.001 PHE A 324 TYR 0.026 0.001 TYR B 381 ARG 0.002 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 541) hydrogen bonds : angle 4.56114 ( 1479) covalent geometry : bond 0.00314 (13968) covalent geometry : angle 0.53981 (18972) Misc. bond : bond 0.08660 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7521.06 seconds wall clock time: 131 minutes 53.15 seconds (7913.15 seconds total)