Starting phenix.real_space_refine on Thu Mar 5 02:25:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sye_25523/03_2026/7sye_25523.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sye_25523/03_2026/7sye_25523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sye_25523/03_2026/7sye_25523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sye_25523/03_2026/7sye_25523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sye_25523/03_2026/7sye_25523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sye_25523/03_2026/7sye_25523.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10192 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 6316 2.51 5 N 1810 2.21 5 O 1956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10216 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4723 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 30, 'TRANS': 583} Chain: "B" Number of atoms: 4723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4723 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 30, 'TRANS': 583} Chain: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Time building chain proxies: 2.23, per 1000 atoms: 0.22 Number of scatterers: 10216 At special positions: 0 Unit cell: (71.2404, 141.401, 126.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 134 16.00 O 1956 8.00 N 1810 7.00 C 6316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 34 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.02 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 224 " distance=2.02 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 302 " distance=2.04 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 499 " distance=2.02 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 511 " distance=2.02 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 555 " distance=2.04 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 593 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 612 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 227 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 267 " distance=2.03 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 283 " distance=2.02 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 309 " distance=2.04 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 475 " distance=2.04 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 499 " distance=2.07 Simple disulfide: pdb=" SG CYS B 502 " - pdb=" SG CYS B 511 " distance=2.02 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 547 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 555 " distance=2.05 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 567 " distance=2.06 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 593 " distance=2.06 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 612 " distance=2.04 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 42 " distance=2.02 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 20 " distance=2.04 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 31 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 42 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 580.7 milliseconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 29 sheets defined 12.3% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.960A pdb=" N THR A 57 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.778A pdb=" N ASN A 91 " --> pdb=" O TYR A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 147 through 151 removed outlier: 4.007A pdb=" N SER A 150 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 151 " --> pdb=" O PHE A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 151' Processing helix chain 'A' and resid 170 through 174 removed outlier: 4.071A pdb=" N GLY A 173 " --> pdb=" O CYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.710A pdb=" N ASP A 206 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N CYS A 207 " --> pdb=" O PRO A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 207' Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 348 through 354 removed outlier: 4.098A pdb=" N PHE A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.654A pdb=" N ASP A 369 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 407 through 410 removed outlier: 3.649A pdb=" N GLY A 410 " --> pdb=" O LYS A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'B' and resid 19 through 31 Processing helix chain 'B' and resid 139 through 144 removed outlier: 4.242A pdb=" N ILE B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 144 " --> pdb=" O TRP B 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 139 through 144' Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.618A pdb=" N ILE B 332 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 333 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 removed outlier: 3.599A pdb=" N ARG B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.528A pdb=" N ASP B 369 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 373 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.870A pdb=" N GLY B 410 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.750A pdb=" N GLY B 479 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 555 removed outlier: 3.819A pdb=" N CYS B 555 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.946A pdb=" N ASN B 580 " --> pdb=" O GLY B 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.685A pdb=" N ASP C 11 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 50 removed outlier: 3.631A pdb=" N TRP C 50 " --> pdb=" O LEU C 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 50' Processing helix chain 'D' and resid 7 through 11 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.871A pdb=" N ALA A 123 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 95 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.742A pdb=" N GLN A 252 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 277 Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 removed outlier: 3.676A pdb=" N LYS A 301 " --> pdb=" O MET A 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.372A pdb=" N CYS A 313 " --> pdb=" O SER A 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 347 removed outlier: 4.849A pdb=" N PHE A 412 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE A 438 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 414 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER A 440 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 416 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 437 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 467 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 439 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 401 through 402 Processing sheet with id=AB2, first strand: chain 'A' and resid 505 through 507 removed outlier: 3.538A pdb=" N GLU A 510 " --> pdb=" O ARG A 507 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 573 through 575 removed outlier: 5.538A pdb=" N VAL A 583 " --> pdb=" O GLY A 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.321A pdb=" N VAL B 65 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 98 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B 67 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR B 93 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ARG B 125 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 95 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER B 127 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 97 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AB7, first strand: chain 'B' and resid 244 through 247 removed outlier: 3.641A pdb=" N ASN B 247 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 252 " --> pdb=" O ASN B 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AB9, first strand: chain 'B' and resid 276 through 277 Processing sheet with id=AC1, first strand: chain 'B' and resid 291 through 293 Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 314 removed outlier: 3.503A pdb=" N CYS B 313 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 342 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 341 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 345 through 347 removed outlier: 6.232A pdb=" N LEU B 345 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 437 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE B 467 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 439 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 505 through 506 removed outlier: 4.141A pdb=" N VAL B 505 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 524 through 527 removed outlier: 3.531A pdb=" N GLU B 527 " --> pdb=" O GLU B 530 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 561 through 563 Processing sheet with id=AC7, first strand: chain 'B' and resid 585 through 587 Processing sheet with id=AC8, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.641A pdb=" N ALA C 30 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 28 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AD1, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.544A pdb=" N LYS D 28 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 37 through 38 131 hydrogen bonds defined for protein. 249 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3391 1.34 - 1.46: 2076 1.46 - 1.58: 4799 1.58 - 1.70: 0 1.70 - 1.83: 156 Bond restraints: 10422 Sorted by residual: bond pdb=" N VAL B 500 " pdb=" CA VAL B 500 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.19e-02 7.06e+03 1.68e+01 bond pdb=" N CYS B 170 " pdb=" CA CYS B 170 " ideal model delta sigma weight residual 1.456 1.495 -0.038 9.40e-03 1.13e+04 1.65e+01 bond pdb=" N CYS A 538 " pdb=" CA CYS A 538 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" N ARG B 503 " pdb=" CA ARG B 503 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.22e+01 bond pdb=" N CYS A 482 " pdb=" CA CYS A 482 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.22e+01 ... (remaining 10417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 13667 2.24 - 4.49: 392 4.49 - 6.73: 35 6.73 - 8.97: 4 8.97 - 11.21: 2 Bond angle restraints: 14100 Sorted by residual: angle pdb=" N ASN B 504 " pdb=" CA ASN B 504 " pdb=" C ASN B 504 " ideal model delta sigma weight residual 113.28 102.07 11.21 1.22e+00 6.72e-01 8.45e+01 angle pdb=" C CYS B 571 " pdb=" N PRO B 572 " pdb=" CA PRO B 572 " ideal model delta sigma weight residual 119.90 125.34 -5.44 1.02e+00 9.61e-01 2.85e+01 angle pdb=" N VAL B 500 " pdb=" CA VAL B 500 " pdb=" CB VAL B 500 " ideal model delta sigma weight residual 110.13 117.72 -7.59 1.68e+00 3.54e-01 2.04e+01 angle pdb=" C CYS B 170 " pdb=" N PRO B 171 " pdb=" CA PRO B 171 " ideal model delta sigma weight residual 119.84 125.39 -5.55 1.25e+00 6.40e-01 1.97e+01 angle pdb=" N VAL B 526 " pdb=" CA VAL B 526 " pdb=" C VAL B 526 " ideal model delta sigma weight residual 107.75 114.11 -6.36 1.46e+00 4.69e-01 1.90e+01 ... (remaining 14095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 5769 17.42 - 34.85: 547 34.85 - 52.27: 116 52.27 - 69.69: 28 69.69 - 87.11: 20 Dihedral angle restraints: 6480 sinusoidal: 2692 harmonic: 3788 Sorted by residual: dihedral pdb=" CB CYS B 195 " pdb=" SG CYS B 195 " pdb=" SG CYS B 207 " pdb=" CB CYS B 207 " ideal model delta sinusoidal sigma weight residual 93.00 -179.89 -87.11 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 163 " pdb=" CB CYS A 163 " ideal model delta sinusoidal sigma weight residual 93.00 176.89 -83.89 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS A 515 " pdb=" SG CYS A 515 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual 93.00 166.48 -73.48 1 1.00e+01 1.00e-02 6.87e+01 ... (remaining 6477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1216 0.061 - 0.122: 284 0.122 - 0.183: 26 0.183 - 0.244: 5 0.244 - 0.305: 3 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CA CYS B 596 " pdb=" N CYS B 596 " pdb=" C CYS B 596 " pdb=" CB CYS B 596 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.30 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA CYS A 538 " pdb=" N CYS A 538 " pdb=" C CYS A 538 " pdb=" CB CYS A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA VAL A 481 " pdb=" N VAL A 481 " pdb=" C VAL A 481 " pdb=" CB VAL A 481 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1531 not shown) Planarity restraints: 1864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 503 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C ARG B 503 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG B 503 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN B 504 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 169 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C SER A 169 " -0.031 2.00e-02 2.50e+03 pdb=" O SER A 169 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS A 170 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 501 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C SER B 501 " -0.031 2.00e-02 2.50e+03 pdb=" O SER B 501 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS B 502 " 0.010 2.00e-02 2.50e+03 ... (remaining 1861 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 130 2.63 - 3.20: 9474 3.20 - 3.76: 14330 3.76 - 4.33: 21089 4.33 - 4.90: 34765 Nonbonded interactions: 79788 Sorted by model distance: nonbonded pdb=" OG1 THR B 391 " pdb=" OG1 THR B 422 " model vdw 2.060 3.040 nonbonded pdb=" O GLU A 397 " pdb=" OG SER A 428 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR B 10 " pdb=" OE1 GLU B 42 " model vdw 2.155 3.040 nonbonded pdb=" OG1 THR A 10 " pdb=" OE1 GLU A 42 " model vdw 2.158 3.040 nonbonded pdb=" OG SER B 413 " pdb=" O ASP B 434 " model vdw 2.183 3.040 ... (remaining 79783 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.610 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 10478 Z= 0.355 Angle : 0.878 11.213 14212 Z= 0.540 Chirality : 0.052 0.305 1534 Planarity : 0.004 0.042 1864 Dihedral : 14.404 86.804 3884 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.84 % Favored : 84.86 % Rotamer: Outliers : 1.65 % Allowed : 8.06 % Favored : 90.29 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.43 (0.19), residues: 1314 helix: -4.23 (0.32), residues: 86 sheet: -2.51 (0.54), residues: 87 loop : -3.22 (0.15), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.011 0.002 TYR B 246 PHE 0.010 0.001 PHE A 156 TRP 0.008 0.001 TRP B 140 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00655 (10422) covalent geometry : angle 0.85708 (14100) SS BOND : bond 0.01028 ( 56) SS BOND : angle 2.32842 ( 112) hydrogen bonds : bond 0.28727 ( 131) hydrogen bonds : angle 10.50116 ( 249) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.7645 (tmm) cc_final: 0.7321 (tmm) outliers start: 19 outliers final: 5 residues processed: 88 average time/residue: 0.1060 time to fit residues: 13.4869 Evaluate side-chains 51 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain B residue 515 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN A 384 GLN A 452 ASN A 473 ASN A 483 HIS A 560 HIS A 599 ASN B 23 HIS B 79 ASN B 115 ASN B 128 ASN B 134 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 389 ASN B 408 GLN B 420 ASN B 444 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.081046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.054190 restraints weight = 43671.220| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 5.67 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10478 Z= 0.134 Angle : 0.636 8.598 14212 Z= 0.333 Chirality : 0.045 0.174 1534 Planarity : 0.004 0.048 1864 Dihedral : 5.959 47.902 1430 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.49 % Favored : 88.28 % Rotamer: Outliers : 1.21 % Allowed : 12.22 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.21), residues: 1314 helix: -2.39 (0.59), residues: 64 sheet: -2.66 (0.47), residues: 121 loop : -2.43 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 509 TYR 0.011 0.001 TYR B 561 PHE 0.011 0.001 PHE B 380 TRP 0.009 0.001 TRP B 492 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00308 (10422) covalent geometry : angle 0.62833 (14100) SS BOND : bond 0.00323 ( 56) SS BOND : angle 1.25607 ( 112) hydrogen bonds : bond 0.03788 ( 131) hydrogen bonds : angle 6.28761 ( 249) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 253 MET cc_start: 0.8570 (mtp) cc_final: 0.8192 (mmm) REVERT: A 294 MET cc_start: 0.8541 (tmm) cc_final: 0.7837 (tmm) REVERT: A 543 MET cc_start: 0.8212 (tmm) cc_final: 0.7746 (tpt) REVERT: B 134 ASN cc_start: 0.7202 (OUTLIER) cc_final: 0.6471 (t0) REVERT: B 253 MET cc_start: 0.9625 (mmm) cc_final: 0.9340 (mmm) REVERT: B 294 MET cc_start: 0.7968 (tmm) cc_final: 0.7544 (tmm) REVERT: C 21 MET cc_start: 0.7538 (mtm) cc_final: 0.7197 (ptp) REVERT: D 40 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7589 (tm-30) outliers start: 14 outliers final: 10 residues processed: 66 average time/residue: 0.0902 time to fit residues: 9.2666 Evaluate side-chains 59 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 99 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 47 GLN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS B 8 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN B 444 ASN B 462 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.077887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.051351 restraints weight = 44787.067| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 5.59 r_work: 0.2762 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10478 Z= 0.278 Angle : 0.694 6.166 14212 Z= 0.361 Chirality : 0.046 0.162 1534 Planarity : 0.004 0.042 1864 Dihedral : 6.107 50.713 1429 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.95 % Favored : 87.82 % Rotamer: Outliers : 2.51 % Allowed : 13.78 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.22), residues: 1314 helix: -2.83 (0.46), residues: 100 sheet: -2.01 (0.53), residues: 109 loop : -2.23 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 509 TYR 0.011 0.001 TYR C 44 PHE 0.007 0.001 PHE A 335 TRP 0.021 0.002 TRP A 584 HIS 0.006 0.001 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00628 (10422) covalent geometry : angle 0.68700 (14100) SS BOND : bond 0.00462 ( 56) SS BOND : angle 1.33118 ( 112) hydrogen bonds : bond 0.03991 ( 131) hydrogen bonds : angle 5.95544 ( 249) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 253 MET cc_start: 0.9011 (mtp) cc_final: 0.8417 (mmm) REVERT: A 294 MET cc_start: 0.8755 (tmm) cc_final: 0.8075 (tmm) REVERT: B 253 MET cc_start: 0.9561 (mmm) cc_final: 0.9207 (mmm) REVERT: B 294 MET cc_start: 0.8224 (tmm) cc_final: 0.7345 (tmm) REVERT: B 296 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.8948 (pm20) REVERT: C 21 MET cc_start: 0.7880 (mtm) cc_final: 0.7624 (ptp) REVERT: D 40 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8406 (tm-30) outliers start: 29 outliers final: 16 residues processed: 75 average time/residue: 0.0947 time to fit residues: 10.6808 Evaluate side-chains 67 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 17 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 16 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.079417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.052965 restraints weight = 44234.702| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 5.61 r_work: 0.2816 rms_B_bonded: 5.61 restraints_weight: 2.0000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10478 Z= 0.113 Angle : 0.580 10.084 14212 Z= 0.301 Chirality : 0.044 0.144 1534 Planarity : 0.004 0.056 1864 Dihedral : 5.446 44.465 1427 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.58 % Favored : 89.35 % Rotamer: Outliers : 1.73 % Allowed : 14.82 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.23), residues: 1314 helix: -1.44 (0.64), residues: 70 sheet: -1.78 (0.52), residues: 116 loop : -1.86 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 509 TYR 0.006 0.001 TYR D 37 PHE 0.009 0.001 PHE B 380 TRP 0.028 0.001 TRP A 584 HIS 0.004 0.000 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00261 (10422) covalent geometry : angle 0.57589 (14100) SS BOND : bond 0.00247 ( 56) SS BOND : angle 0.94681 ( 112) hydrogen bonds : bond 0.03007 ( 131) hydrogen bonds : angle 5.38506 ( 249) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.9050 (mtp) cc_final: 0.8360 (mmm) REVERT: A 294 MET cc_start: 0.8852 (tmm) cc_final: 0.8024 (tmm) REVERT: A 467 ILE cc_start: 0.9558 (tt) cc_final: 0.9346 (pt) REVERT: B 253 MET cc_start: 0.9476 (mmm) cc_final: 0.9121 (mmm) REVERT: B 294 MET cc_start: 0.8282 (tmm) cc_final: 0.7581 (tmm) REVERT: D 21 MET cc_start: 0.8376 (ptp) cc_final: 0.8116 (pmm) REVERT: D 40 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8374 (tm-30) outliers start: 20 outliers final: 12 residues processed: 69 average time/residue: 0.0840 time to fit residues: 9.0232 Evaluate side-chains 62 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 90 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 124 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 chunk 44 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.079593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.052726 restraints weight = 43711.815| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 5.78 r_work: 0.2824 rms_B_bonded: 5.73 restraints_weight: 2.0000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10478 Z= 0.098 Angle : 0.554 9.273 14212 Z= 0.287 Chirality : 0.044 0.149 1534 Planarity : 0.003 0.045 1864 Dihedral : 5.011 45.826 1425 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.50 % Favored : 89.42 % Rotamer: Outliers : 2.08 % Allowed : 15.42 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.23), residues: 1314 helix: -1.18 (0.67), residues: 70 sheet: -1.68 (0.52), residues: 116 loop : -1.66 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 509 TYR 0.007 0.001 TYR B 447 PHE 0.006 0.001 PHE B 525 TRP 0.021 0.001 TRP B 492 HIS 0.003 0.000 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00228 (10422) covalent geometry : angle 0.55122 (14100) SS BOND : bond 0.00201 ( 56) SS BOND : angle 0.85182 ( 112) hydrogen bonds : bond 0.02791 ( 131) hydrogen bonds : angle 5.15281 ( 249) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 116 LEU cc_start: 0.9627 (tp) cc_final: 0.9397 (tt) REVERT: A 253 MET cc_start: 0.9147 (mtp) cc_final: 0.8301 (mmm) REVERT: A 294 MET cc_start: 0.8948 (tmm) cc_final: 0.8154 (tmm) REVERT: B 117 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8585 (mp10) REVERT: B 253 MET cc_start: 0.9482 (mmm) cc_final: 0.9133 (mmm) REVERT: B 294 MET cc_start: 0.8214 (tmm) cc_final: 0.7106 (tmm) REVERT: B 296 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8833 (pm20) REVERT: C 8 LEU cc_start: 0.9412 (mm) cc_final: 0.8997 (tp) REVERT: D 40 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8429 (tm-30) outliers start: 24 outliers final: 16 residues processed: 77 average time/residue: 0.0826 time to fit residues: 9.9934 Evaluate side-chains 67 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 91 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 0.0020 chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 78 optimal weight: 0.0070 chunk 113 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.077486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.050879 restraints weight = 45318.868| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 5.70 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10478 Z= 0.245 Angle : 0.659 10.055 14212 Z= 0.338 Chirality : 0.046 0.161 1534 Planarity : 0.004 0.041 1864 Dihedral : 5.339 43.207 1421 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.80 % Favored : 88.13 % Rotamer: Outliers : 2.60 % Allowed : 16.29 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.23), residues: 1314 helix: -1.50 (0.62), residues: 76 sheet: -1.62 (0.52), residues: 116 loop : -1.68 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 509 TYR 0.009 0.001 TYR D 37 PHE 0.007 0.001 PHE B 396 TRP 0.043 0.002 TRP A 584 HIS 0.004 0.001 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00553 (10422) covalent geometry : angle 0.65360 (14100) SS BOND : bond 0.00455 ( 56) SS BOND : angle 1.16649 ( 112) hydrogen bonds : bond 0.03432 ( 131) hydrogen bonds : angle 5.43902 ( 249) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8888 (mtp) cc_final: 0.8112 (mmm) REVERT: A 294 MET cc_start: 0.8762 (tmm) cc_final: 0.7958 (tmm) REVERT: A 543 MET cc_start: 0.7954 (tpt) cc_final: 0.7680 (pmm) REVERT: B 117 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: B 253 MET cc_start: 0.9450 (mmm) cc_final: 0.9031 (mmm) REVERT: B 294 MET cc_start: 0.8285 (tmm) cc_final: 0.7306 (tmm) REVERT: B 296 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8864 (pm20) REVERT: B 445 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8284 (tm) REVERT: D 40 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8066 (tm-30) outliers start: 30 outliers final: 17 residues processed: 82 average time/residue: 0.0808 time to fit residues: 10.2079 Evaluate side-chains 73 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.078169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.051505 restraints weight = 44487.545| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 5.88 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10478 Z= 0.154 Angle : 0.603 10.302 14212 Z= 0.308 Chirality : 0.045 0.150 1534 Planarity : 0.003 0.042 1864 Dihedral : 5.154 43.071 1421 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.11 % Favored : 88.81 % Rotamer: Outliers : 2.69 % Allowed : 16.64 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.23), residues: 1314 helix: -1.13 (0.66), residues: 70 sheet: -1.60 (0.50), residues: 126 loop : -1.55 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 509 TYR 0.009 0.001 TYR D 44 PHE 0.008 0.001 PHE A 412 TRP 0.058 0.002 TRP A 584 HIS 0.004 0.001 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00354 (10422) covalent geometry : angle 0.59893 (14100) SS BOND : bond 0.00277 ( 56) SS BOND : angle 0.98402 ( 112) hydrogen bonds : bond 0.03003 ( 131) hydrogen bonds : angle 5.29156 ( 249) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 253 MET cc_start: 0.8869 (mtp) cc_final: 0.8103 (mmm) REVERT: A 294 MET cc_start: 0.8768 (tmm) cc_final: 0.7959 (tmm) REVERT: A 376 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: A 543 MET cc_start: 0.7752 (tpt) cc_final: 0.7337 (pmm) REVERT: B 117 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8437 (mp10) REVERT: B 253 MET cc_start: 0.9401 (mmm) cc_final: 0.8988 (mmm) REVERT: B 294 MET cc_start: 0.8215 (tmm) cc_final: 0.7363 (tmm) REVERT: B 296 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8781 (pm20) REVERT: D 21 MET cc_start: 0.8277 (ptp) cc_final: 0.7935 (pmm) REVERT: D 40 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8051 (tm-30) outliers start: 31 outliers final: 23 residues processed: 82 average time/residue: 0.0883 time to fit residues: 11.1134 Evaluate side-chains 77 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.078560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051895 restraints weight = 44671.726| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 5.69 r_work: 0.2803 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10478 Z= 0.137 Angle : 0.599 10.094 14212 Z= 0.304 Chirality : 0.044 0.140 1534 Planarity : 0.003 0.041 1864 Dihedral : 5.036 42.543 1421 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.96 % Favored : 88.96 % Rotamer: Outliers : 2.77 % Allowed : 17.07 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.23), residues: 1314 helix: -1.10 (0.67), residues: 70 sheet: -1.65 (0.47), residues: 136 loop : -1.46 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 509 TYR 0.008 0.001 TYR D 44 PHE 0.009 0.001 PHE A 412 TRP 0.063 0.002 TRP A 584 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00317 (10422) covalent geometry : angle 0.59550 (14100) SS BOND : bond 0.00262 ( 56) SS BOND : angle 0.90936 ( 112) hydrogen bonds : bond 0.02937 ( 131) hydrogen bonds : angle 5.12146 ( 249) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 253 MET cc_start: 0.9137 (mtp) cc_final: 0.8234 (mmm) REVERT: A 294 MET cc_start: 0.8970 (tmm) cc_final: 0.8176 (tmm) REVERT: A 376 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8921 (tt0) REVERT: A 543 MET cc_start: 0.8000 (tpt) cc_final: 0.7380 (pmm) REVERT: B 117 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8565 (mp10) REVERT: B 253 MET cc_start: 0.9447 (mmm) cc_final: 0.9038 (mmm) REVERT: B 279 ASP cc_start: 0.9025 (p0) cc_final: 0.8567 (p0) REVERT: B 294 MET cc_start: 0.8303 (tmm) cc_final: 0.7299 (tmm) REVERT: B 296 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8847 (pm20) REVERT: D 21 MET cc_start: 0.8335 (ptp) cc_final: 0.8021 (pmm) REVERT: D 40 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8396 (tm-30) outliers start: 32 outliers final: 25 residues processed: 79 average time/residue: 0.0833 time to fit residues: 10.4002 Evaluate side-chains 77 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 49 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 584 TRP Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 ARG Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 56 optimal weight: 0.0770 chunk 112 optimal weight: 0.0040 chunk 116 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 120 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.079996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.053395 restraints weight = 44616.295| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 5.85 r_work: 0.2857 rms_B_bonded: 5.83 restraints_weight: 2.0000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10478 Z= 0.089 Angle : 0.568 10.305 14212 Z= 0.288 Chirality : 0.044 0.149 1534 Planarity : 0.003 0.044 1864 Dihedral : 4.715 42.884 1421 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.36 % Favored : 90.56 % Rotamer: Outliers : 1.99 % Allowed : 17.42 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.23), residues: 1314 helix: -1.17 (0.63), residues: 76 sheet: -1.59 (0.48), residues: 136 loop : -1.36 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 509 TYR 0.010 0.001 TYR B 447 PHE 0.007 0.001 PHE B 525 TRP 0.041 0.002 TRP A 584 HIS 0.003 0.000 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00205 (10422) covalent geometry : angle 0.56603 (14100) SS BOND : bond 0.00197 ( 56) SS BOND : angle 0.77671 ( 112) hydrogen bonds : bond 0.02515 ( 131) hydrogen bonds : angle 4.84784 ( 249) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.419 Fit side-chains REVERT: A 253 MET cc_start: 0.9156 (mtp) cc_final: 0.8212 (mmm) REVERT: A 294 MET cc_start: 0.9011 (tmm) cc_final: 0.8228 (tmm) REVERT: A 543 MET cc_start: 0.7703 (tpt) cc_final: 0.6969 (pmm) REVERT: B 117 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8498 (mp10) REVERT: B 253 MET cc_start: 0.9401 (mmm) cc_final: 0.9006 (mmm) REVERT: B 279 ASP cc_start: 0.8942 (p0) cc_final: 0.8526 (p0) REVERT: B 294 MET cc_start: 0.8201 (tmm) cc_final: 0.6998 (tmm) REVERT: B 296 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8802 (pm20) REVERT: D 21 MET cc_start: 0.8266 (ptp) cc_final: 0.8007 (pmm) REVERT: D 40 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8126 (tm-30) outliers start: 23 outliers final: 18 residues processed: 78 average time/residue: 0.0796 time to fit residues: 9.8622 Evaluate side-chains 72 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 584 TRP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 109 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 75 optimal weight: 0.0470 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.078885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.052171 restraints weight = 44143.584| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 5.91 r_work: 0.2820 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10478 Z= 0.134 Angle : 0.600 11.926 14212 Z= 0.301 Chirality : 0.044 0.245 1534 Planarity : 0.003 0.039 1864 Dihedral : 4.804 43.203 1421 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.05 % Favored : 89.88 % Rotamer: Outliers : 1.99 % Allowed : 17.59 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.23), residues: 1314 helix: -1.17 (0.63), residues: 76 sheet: -1.61 (0.48), residues: 136 loop : -1.30 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 509 TYR 0.024 0.001 TYR C 44 PHE 0.021 0.001 PHE B 380 TRP 0.037 0.002 TRP A 584 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00312 (10422) covalent geometry : angle 0.59737 (14100) SS BOND : bond 0.00242 ( 56) SS BOND : angle 0.85495 ( 112) hydrogen bonds : bond 0.02756 ( 131) hydrogen bonds : angle 4.85349 ( 249) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.377 Fit side-chains REVERT: A 253 MET cc_start: 0.9198 (mtp) cc_final: 0.8228 (mmm) REVERT: A 294 MET cc_start: 0.9013 (tmm) cc_final: 0.8243 (tmm) REVERT: A 543 MET cc_start: 0.7625 (tpt) cc_final: 0.6922 (pmm) REVERT: B 117 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8536 (mp10) REVERT: B 253 MET cc_start: 0.9416 (mmm) cc_final: 0.9016 (mmm) REVERT: B 279 ASP cc_start: 0.8979 (p0) cc_final: 0.8595 (p0) REVERT: B 294 MET cc_start: 0.8261 (tmm) cc_final: 0.7025 (tmm) REVERT: B 296 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8831 (pm20) REVERT: D 21 MET cc_start: 0.8275 (ptp) cc_final: 0.7996 (pmm) REVERT: D 40 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8433 (tm-30) outliers start: 23 outliers final: 19 residues processed: 72 average time/residue: 0.0788 time to fit residues: 9.2127 Evaluate side-chains 73 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 584 TRP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 115 optimal weight: 30.0000 chunk 119 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.078936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.052018 restraints weight = 44746.578| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 5.88 r_work: 0.2818 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10478 Z= 0.124 Angle : 0.590 12.364 14212 Z= 0.296 Chirality : 0.044 0.188 1534 Planarity : 0.003 0.042 1864 Dihedral : 4.802 43.389 1421 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.97 % Favored : 89.95 % Rotamer: Outliers : 1.99 % Allowed : 17.50 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.23), residues: 1314 helix: -1.17 (0.63), residues: 76 sheet: -1.62 (0.47), residues: 136 loop : -1.25 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 509 TYR 0.010 0.001 TYR D 44 PHE 0.018 0.001 PHE B 380 TRP 0.032 0.002 TRP B 492 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00290 (10422) covalent geometry : angle 0.58784 (14100) SS BOND : bond 0.00232 ( 56) SS BOND : angle 0.83006 ( 112) hydrogen bonds : bond 0.02700 ( 131) hydrogen bonds : angle 4.83060 ( 249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3065.82 seconds wall clock time: 53 minutes 5.07 seconds (3185.07 seconds total)