Starting phenix.real_space_refine on Wed Mar 4 06:38:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sz7_25563/03_2026/7sz7_25563.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sz7_25563/03_2026/7sz7_25563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sz7_25563/03_2026/7sz7_25563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sz7_25563/03_2026/7sz7_25563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sz7_25563/03_2026/7sz7_25563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sz7_25563/03_2026/7sz7_25563.map" } resolution = 3.4 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= 0.027 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 1694 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 132 5.16 5 C 6306 2.51 5 N 1824 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 28 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: 10218 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: "C" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 386 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: "D" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 386 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Time building chain proxies: 2.21, per 1000 atoms: 0.22 Number of scatterers: 10218 At special positions: 0 Unit cell: (80.955, 144.64, 130.607, 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 132 16.00 O 1956 8.00 N 1824 7.00 C 6306 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 224 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 511 " distance=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 612 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 21 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 32 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 43 " 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=2.02 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=2.03 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=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 502 " - pdb=" SG CYS B 511 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 593 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 612 " distance=2.04 Simple disulfide: pdb=" SG CYS D 8 " - pdb=" SG CYS D 21 " distance=2.04 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 32 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 43 " 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: 0.72 Conformation dependent library (CDL) restraints added in 391.1 milliseconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 26 sheets defined 13.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 removed outlier: 4.424A pdb=" N LEU A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.685A pdb=" N LEU A 55 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR A 57 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.600A 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 170 through 174 removed outlier: 3.799A pdb=" N GLY A 173 " --> pdb=" O CYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 removed outlier: 4.016A pdb=" N ASP A 206 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.954A 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: 4.269A pdb=" N PHE A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.577A pdb=" N LEU A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.613A pdb=" N PHE A 396 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 410 removed outlier: 3.824A 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 476 Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.655A pdb=" N CYS A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 608 through 612 removed outlier: 4.050A pdb=" N GLY A 611 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N CYS A 612 " --> pdb=" O LEU A 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 612' Processing helix chain 'B' and resid 19 through 32 removed outlier: 3.815A pdb=" N MET B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.659A pdb=" N SER B 137 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 138 " --> pdb=" O VAL B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 134 through 138' Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.654A pdb=" N GLY B 173 " --> pdb=" O CYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.781A pdb=" N LYS B 333 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 369 through 373 removed outlier: 3.936A pdb=" N THR B 373 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.608A pdb=" N GLY B 410 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.507A pdb=" N PHE B 457 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 495 through 499 removed outlier: 3.544A pdb=" N CYS B 499 " --> pdb=" O PRO B 496 " (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: 3.947A pdb=" N ASN B 580 " --> pdb=" O GLY B 577 " (cutoff:3.500A) 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 43 removed outlier: 5.338A pdb=" N ALA A 123 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 95 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 247 removed outlier: 3.721A pdb=" N GLN A 252 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 277 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 295 Processing sheet with id=AA7, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.290A pdb=" N CYS A 313 " --> pdb=" O SER A 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 347 removed outlier: 5.423A pdb=" N PHE A 412 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE A 438 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 414 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N SER A 440 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 416 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 437 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 506 Processing sheet with id=AB2, first strand: chain 'A' and resid 562 through 563 Processing sheet with id=AB3, first strand: chain 'A' and resid 573 through 576 removed outlier: 5.364A pdb=" N ALA A 573 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LYS A 585 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 23 through 24 removed outlier: 3.762A pdb=" N LEU C 24 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 29 " --> pdb=" O LEU C 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AB6, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.547A pdb=" N LEU B 41 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ALA B 68 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 43 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL B 65 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU B 98 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE B 67 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ALA B 123 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 95 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL B 124 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 244 through 246 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 296 Processing sheet with id=AC2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.189A pdb=" N CYS B 313 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 346 through 347 removed outlier: 6.342A pdb=" N LEU B 414 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N SER B 440 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B 416 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 467 " --> pdb=" O ILE B 439 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 524 through 527 removed outlier: 3.683A pdb=" N PHE B 525 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 532 " --> pdb=" O PHE B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 561 through 563 Processing sheet with id=AC6, first strand: chain 'B' and resid 585 through 587 Processing sheet with id=AC7, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.722A pdb=" N LEU D 24 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 29 " --> pdb=" O LEU D 24 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.691A pdb=" N THR D 20 " --> pdb=" O VAL D 33 " (cutoff:3.500A) 135 hydrogen bonds defined for protein. 261 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: 1.38 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1769 1.32 - 1.44: 2647 1.44 - 1.57: 5856 1.57 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 10424 Sorted by residual: bond pdb=" N CYS B 571 " pdb=" CA CYS B 571 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" C ASN B 128 " pdb=" O ASN B 128 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.28e-02 6.10e+03 1.18e+01 bond pdb=" N ARG B 503 " pdb=" CA ARG B 503 " ideal model delta sigma weight residual 1.454 1.494 -0.039 1.16e-02 7.43e+03 1.15e+01 bond pdb=" N VAL D 2 " pdb=" CA VAL D 2 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.06e+01 bond pdb=" N LEU B 595 " pdb=" CA LEU B 595 " ideal model delta sigma weight residual 1.454 1.497 -0.044 1.34e-02 5.57e+03 1.06e+01 ... (remaining 10419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 13693 2.11 - 4.22: 364 4.22 - 6.33: 36 6.33 - 8.44: 9 8.44 - 10.55: 2 Bond angle restraints: 14104 Sorted by residual: angle pdb=" N SER A 169 " pdb=" CA SER A 169 " pdb=" C SER A 169 " ideal model delta sigma weight residual 113.30 105.00 8.30 1.34e+00 5.57e-01 3.83e+01 angle pdb=" CA SER C 3 " pdb=" C SER C 3 " pdb=" O SER C 3 " ideal model delta sigma weight residual 120.55 114.15 6.40 1.06e+00 8.90e-01 3.65e+01 angle pdb=" CA HIS B 560 " pdb=" C HIS B 560 " pdb=" N TYR B 561 " ideal model delta sigma weight residual 119.56 116.13 3.43 5.80e-01 2.97e+00 3.49e+01 angle pdb=" N HIS D 4 " pdb=" CA HIS D 4 " pdb=" C HIS D 4 " ideal model delta sigma weight residual 113.61 105.11 8.50 1.50e+00 4.44e-01 3.21e+01 angle pdb=" CA ASN B 128 " pdb=" C ASN B 128 " pdb=" O ASN B 128 " ideal model delta sigma weight residual 121.84 115.48 6.36 1.16e+00 7.43e-01 3.00e+01 ... (remaining 14099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5742 17.70 - 35.40: 575 35.40 - 53.10: 117 53.10 - 70.80: 36 70.80 - 88.49: 14 Dihedral angle restraints: 6484 sinusoidal: 2682 harmonic: 3802 Sorted by residual: 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 93.00 179.87 -86.87 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 604 " pdb=" CB CYS A 604 " ideal model delta sinusoidal sigma weight residual -86.00 -166.71 80.71 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS B 287 " pdb=" SG CYS B 287 " pdb=" SG CYS B 302 " pdb=" CB CYS B 302 " ideal model delta sinusoidal sigma weight residual 93.00 158.56 -65.56 1 1.00e+01 1.00e-02 5.63e+01 ... (remaining 6481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1205 0.059 - 0.118: 285 0.118 - 0.177: 48 0.177 - 0.235: 4 0.235 - 0.294: 2 Chirality restraints: 1544 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 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB VAL B 505 " pdb=" CA VAL B 505 " pdb=" CG1 VAL B 505 " pdb=" CG2 VAL B 505 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA CYS B 534 " pdb=" N CYS B 534 " pdb=" C CYS B 534 " pdb=" CB CYS B 534 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1541 not shown) Planarity restraints: 1872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 128 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C ASN B 128 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN B 128 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN B 129 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 513 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ASP B 513 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP B 513 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS B 514 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 505 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C VAL B 505 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL B 505 " -0.013 2.00e-02 2.50e+03 pdb=" N SER B 506 " -0.012 2.00e-02 2.50e+03 ... (remaining 1869 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 23 2.35 - 2.98: 5458 2.98 - 3.62: 13721 3.62 - 4.26: 21850 4.26 - 4.90: 37458 Nonbonded interactions: 78510 Sorted by model distance: nonbonded pdb=" O VAL B 505 " pdb=" CG2 VAL B 512 " model vdw 1.707 3.460 nonbonded pdb=" OH TYR A 447 " pdb=" O GLN A 480 " model vdw 2.002 3.040 nonbonded pdb=" OE1 GLU B 397 " pdb=" NH1 ARG B 427 " model vdw 2.226 3.120 nonbonded pdb=" CE1 TYR A 602 " pdb=" SG CYS A 612 " model vdw 2.235 3.700 nonbonded pdb=" NE2 GLN A 252 " pdb=" O ALA B 286 " model vdw 2.236 3.120 ... (remaining 78505 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.760 Find NCS groups from input model: 0.110 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.005 0.044 10480 Z= 0.306 Angle : 0.813 10.555 14216 Z= 0.513 Chirality : 0.052 0.294 1544 Planarity : 0.004 0.042 1872 Dihedral : 14.425 88.495 3872 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.98 % Favored : 88.64 % Rotamer: Outliers : 1.81 % Allowed : 6.04 % Favored : 92.14 % 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: -4.49 (0.19), residues: 1320 helix: -4.31 (0.32), residues: 73 sheet: -3.11 (0.39), residues: 145 loop : -3.19 (0.16), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 427 TYR 0.010 0.001 TYR B 45 PHE 0.010 0.001 PHE C 15 TRP 0.006 0.001 TRP A 492 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00514 (10424) covalent geometry : angle 0.79404 (14104) SS BOND : bond 0.00572 ( 56) SS BOND : angle 2.10014 ( 112) hydrogen bonds : bond 0.31001 ( 135) hydrogen bonds : angle 10.16960 ( 261) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8544 (mmt) cc_final: 0.8304 (mmm) REVERT: B 560 HIS cc_start: 0.7672 (m90) cc_final: 0.7459 (m90) REVERT: B 561 TYR cc_start: 0.8690 (m-80) cc_final: 0.8218 (m-80) REVERT: D 10 ASP cc_start: 0.7561 (t0) cc_final: 0.7340 (t0) outliers start: 21 outliers final: 8 residues processed: 88 average time/residue: 0.1114 time to fit residues: 13.6017 Evaluate side-chains 53 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 514 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 12 ASN A 40 ASN A 100 ASN A 128 ASN A 158 ASN A 462 GLN A 469 ASN A 473 ASN A 480 GLN A 580 ASN B 23 HIS B 70 ASN B 100 ASN B 209 HIS B 252 GLN B 394 HIS B 469 ASN B 473 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 HIS ** D 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.051750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.033794 restraints weight = 54284.914| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 5.87 r_work: 0.2546 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10480 Z= 0.232 Angle : 0.680 8.772 14216 Z= 0.359 Chirality : 0.046 0.185 1544 Planarity : 0.004 0.058 1872 Dihedral : 6.348 56.667 1431 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.23 % Favored : 89.70 % Rotamer: Outliers : 1.30 % Allowed : 11.83 % Favored : 86.87 % 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: -3.52 (0.21), residues: 1320 helix: -3.14 (0.49), residues: 80 sheet: -2.71 (0.40), residues: 152 loop : -2.45 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 427 TYR 0.011 0.001 TYR B 45 PHE 0.013 0.001 PHE A 380 TRP 0.019 0.001 TRP A 584 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00511 (10424) covalent geometry : angle 0.67475 (14104) SS BOND : bond 0.00396 ( 56) SS BOND : angle 1.16402 ( 112) hydrogen bonds : bond 0.04356 ( 135) hydrogen bonds : angle 6.66838 ( 261) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9645 (tpp) cc_final: 0.9285 (tpt) REVERT: A 128 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.8302 (t0) REVERT: A 550 ARG cc_start: 0.9354 (mtm-85) cc_final: 0.7847 (tpt90) REVERT: B 82 ILE cc_start: 0.9684 (pt) cc_final: 0.9454 (mp) outliers start: 15 outliers final: 7 residues processed: 62 average time/residue: 0.1074 time to fit residues: 9.6322 Evaluate side-chains 51 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 523 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 120 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 4 optimal weight: 0.0170 chunk 106 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.052433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.034746 restraints weight = 53476.511| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 5.70 r_work: 0.2589 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10480 Z= 0.117 Angle : 0.584 9.810 14216 Z= 0.311 Chirality : 0.045 0.220 1544 Planarity : 0.004 0.051 1872 Dihedral : 5.445 49.506 1422 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.18 % Favored : 91.74 % Rotamer: Outliers : 1.38 % Allowed : 13.47 % Favored : 85.15 % 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: -2.99 (0.22), residues: 1320 helix: -2.72 (0.53), residues: 80 sheet: -2.49 (0.39), residues: 169 loop : -2.01 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 427 TYR 0.008 0.001 TYR A 251 PHE 0.011 0.001 PHE A 380 TRP 0.032 0.001 TRP A 584 HIS 0.007 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00265 (10424) covalent geometry : angle 0.58124 (14104) SS BOND : bond 0.00215 ( 56) SS BOND : angle 0.89596 ( 112) hydrogen bonds : bond 0.03740 ( 135) hydrogen bonds : angle 6.12472 ( 261) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9602 (tpp) cc_final: 0.9283 (tpt) REVERT: A 60 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7969 (tm-30) REVERT: A 550 ARG cc_start: 0.9298 (mtm-85) cc_final: 0.7810 (tpt90) REVERT: B 82 ILE cc_start: 0.9661 (pt) cc_final: 0.9451 (mp) REVERT: B 400 GLU cc_start: 0.9153 (tp30) cc_final: 0.8868 (tp30) outliers start: 16 outliers final: 8 residues processed: 66 average time/residue: 0.0958 time to fit residues: 9.2176 Evaluate side-chains 51 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 64 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 139 GLN A 172 ASN B 134 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.052299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.034690 restraints weight = 54478.017| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 5.68 r_work: 0.2584 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10480 Z= 0.129 Angle : 0.563 8.382 14216 Z= 0.299 Chirality : 0.045 0.181 1544 Planarity : 0.004 0.040 1872 Dihedral : 5.253 50.056 1422 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.71 % Favored : 91.21 % Rotamer: Outliers : 1.64 % Allowed : 14.08 % Favored : 84.28 % 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: -2.68 (0.22), residues: 1320 helix: -2.45 (0.56), residues: 80 sheet: -2.33 (0.41), residues: 161 loop : -1.78 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 523 TYR 0.008 0.001 TYR A 251 PHE 0.010 0.001 PHE A 380 TRP 0.019 0.001 TRP A 584 HIS 0.006 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00289 (10424) covalent geometry : angle 0.56029 (14104) SS BOND : bond 0.00278 ( 56) SS BOND : angle 0.80717 ( 112) hydrogen bonds : bond 0.03397 ( 135) hydrogen bonds : angle 5.85984 ( 261) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9636 (tpp) cc_final: 0.9351 (tpt) REVERT: A 71 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9073 (p) REVERT: A 128 ASN cc_start: 0.9257 (OUTLIER) cc_final: 0.8191 (t0) REVERT: A 550 ARG cc_start: 0.9377 (mtm-85) cc_final: 0.7847 (tpt90) REVERT: C 26 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8732 (mt0) REVERT: B 82 ILE cc_start: 0.9672 (pt) cc_final: 0.9434 (mp) REVERT: B 294 MET cc_start: 0.8464 (ptt) cc_final: 0.8161 (pmm) REVERT: B 400 GLU cc_start: 0.9181 (tp30) cc_final: 0.8969 (tp30) REVERT: D 29 LYS cc_start: 0.9590 (mmmm) cc_final: 0.9301 (mmmm) outliers start: 19 outliers final: 9 residues processed: 66 average time/residue: 0.0933 time to fit residues: 9.2399 Evaluate side-chains 54 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain D residue 24 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 120 optimal weight: 0.0470 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.052285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.034514 restraints weight = 54602.700| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 5.89 r_work: 0.2566 rms_B_bonded: 5.62 restraints_weight: 2.0000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10480 Z= 0.133 Angle : 0.558 9.564 14216 Z= 0.295 Chirality : 0.045 0.159 1544 Planarity : 0.004 0.038 1872 Dihedral : 5.151 49.536 1422 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.41 % Favored : 91.52 % Rotamer: Outliers : 1.81 % Allowed : 14.42 % Favored : 83.77 % 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: -2.48 (0.22), residues: 1320 helix: -2.24 (0.58), residues: 80 sheet: -2.23 (0.41), residues: 161 loop : -1.64 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 523 TYR 0.009 0.001 TYR A 251 PHE 0.010 0.001 PHE A 380 TRP 0.019 0.001 TRP A 584 HIS 0.007 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00302 (10424) covalent geometry : angle 0.55545 (14104) SS BOND : bond 0.00227 ( 56) SS BOND : angle 0.79643 ( 112) hydrogen bonds : bond 0.03297 ( 135) hydrogen bonds : angle 5.65351 ( 261) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9645 (tpp) cc_final: 0.9396 (tpt) REVERT: A 60 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 71 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.9066 (p) REVERT: A 550 ARG cc_start: 0.9324 (mtm-85) cc_final: 0.7758 (tpt90) REVERT: B 82 ILE cc_start: 0.9685 (pt) cc_final: 0.9420 (mp) REVERT: B 294 MET cc_start: 0.8527 (ptt) cc_final: 0.8042 (ppp) REVERT: B 400 GLU cc_start: 0.9210 (tp30) cc_final: 0.8972 (tp30) REVERT: D 29 LYS cc_start: 0.9634 (mmmm) cc_final: 0.9358 (mmmm) outliers start: 21 outliers final: 16 residues processed: 65 average time/residue: 0.0876 time to fit residues: 8.5830 Evaluate side-chains 61 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 24 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 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 = 0.3287 r_free = 0.3287 target = 0.051867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.034107 restraints weight = 54590.800| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 5.82 r_work: 0.2556 rms_B_bonded: 5.50 restraints_weight: 2.0000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10480 Z= 0.178 Angle : 0.584 11.400 14216 Z= 0.306 Chirality : 0.045 0.140 1544 Planarity : 0.004 0.036 1872 Dihedral : 5.144 48.578 1422 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.50 % Allowed : 13.90 % Favored : 83.59 % 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: -2.35 (0.23), residues: 1320 helix: -2.07 (0.60), residues: 80 sheet: -2.07 (0.42), residues: 154 loop : -1.57 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 523 TYR 0.009 0.001 TYR A 251 PHE 0.009 0.001 PHE A 380 TRP 0.017 0.001 TRP A 584 HIS 0.007 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00395 (10424) covalent geometry : angle 0.58145 (14104) SS BOND : bond 0.00287 ( 56) SS BOND : angle 0.82325 ( 112) hydrogen bonds : bond 0.03429 ( 135) hydrogen bonds : angle 5.54745 ( 261) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 44 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9683 (tpp) cc_final: 0.9433 (tpt) REVERT: A 71 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9063 (p) REVERT: A 521 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: C 26 GLN cc_start: 0.9299 (mm-40) cc_final: 0.8838 (mt0) REVERT: B 82 ILE cc_start: 0.9704 (pt) cc_final: 0.9423 (mp) REVERT: B 294 MET cc_start: 0.8608 (ptt) cc_final: 0.8189 (ppp) REVERT: D 29 LYS cc_start: 0.9648 (mmmm) cc_final: 0.9363 (mmmm) outliers start: 29 outliers final: 18 residues processed: 71 average time/residue: 0.0902 time to fit residues: 9.5965 Evaluate side-chains 61 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain D residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.0470 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 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 = 0.3307 r_free = 0.3307 target = 0.052665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.034953 restraints weight = 53633.819| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 5.68 r_work: 0.2579 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10480 Z= 0.109 Angle : 0.569 12.272 14216 Z= 0.297 Chirality : 0.045 0.144 1544 Planarity : 0.003 0.035 1872 Dihedral : 4.976 47.868 1422 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.16 % Allowed : 14.77 % Favored : 83.07 % 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: -2.28 (0.23), residues: 1320 helix: -1.99 (0.55), residues: 92 sheet: -2.00 (0.40), residues: 170 loop : -1.50 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 523 TYR 0.009 0.001 TYR A 251 PHE 0.010 0.001 PHE C 15 TRP 0.014 0.001 TRP A 584 HIS 0.007 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00249 (10424) covalent geometry : angle 0.56546 (14104) SS BOND : bond 0.00203 ( 56) SS BOND : angle 0.87119 ( 112) hydrogen bonds : bond 0.03091 ( 135) hydrogen bonds : angle 5.51639 ( 261) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7978 (tm-30) REVERT: A 71 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9076 (p) REVERT: A 521 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: B 82 ILE cc_start: 0.9692 (pt) cc_final: 0.9408 (mp) REVERT: B 294 MET cc_start: 0.8584 (ptt) cc_final: 0.8138 (ppp) REVERT: B 400 GLU cc_start: 0.9191 (tp30) cc_final: 0.8941 (tp30) REVERT: D 29 LYS cc_start: 0.9652 (mmmm) cc_final: 0.9364 (mmmm) outliers start: 25 outliers final: 18 residues processed: 68 average time/residue: 0.0931 time to fit residues: 9.3511 Evaluate side-chains 63 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain D residue 24 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 HIS D 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.051932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.034161 restraints weight = 54616.040| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 5.75 r_work: 0.2558 rms_B_bonded: 5.58 restraints_weight: 2.0000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10480 Z= 0.159 Angle : 0.598 11.844 14216 Z= 0.309 Chirality : 0.045 0.139 1544 Planarity : 0.004 0.034 1872 Dihedral : 4.994 46.624 1422 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 2.16 % Allowed : 16.06 % Favored : 81.78 % 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: -2.16 (0.23), residues: 1320 helix: -1.79 (0.57), residues: 92 sheet: -1.86 (0.41), residues: 163 loop : -1.43 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 42 TYR 0.010 0.001 TYR A 251 PHE 0.009 0.001 PHE C 15 TRP 0.012 0.001 TRP A 584 HIS 0.007 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00357 (10424) covalent geometry : angle 0.59202 (14104) SS BOND : bond 0.00281 ( 56) SS BOND : angle 1.13654 ( 112) hydrogen bonds : bond 0.03290 ( 135) hydrogen bonds : angle 5.49399 ( 261) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9725 (tpp) cc_final: 0.9474 (tpt) REVERT: A 60 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8012 (tm-30) REVERT: A 71 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.9056 (p) REVERT: A 521 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8503 (tm-30) REVERT: B 82 ILE cc_start: 0.9710 (pt) cc_final: 0.9415 (mp) REVERT: B 294 MET cc_start: 0.8508 (ptt) cc_final: 0.8094 (ppp) REVERT: D 29 LYS cc_start: 0.9679 (mmmm) cc_final: 0.9409 (mmmm) outliers start: 25 outliers final: 19 residues processed: 65 average time/residue: 0.0953 time to fit residues: 9.2896 Evaluate side-chains 64 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 584 TRP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain D residue 24 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 114 optimal weight: 0.0170 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 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 = 0.3279 r_free = 0.3279 target = 0.051490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.033888 restraints weight = 55067.125| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 5.74 r_work: 0.2549 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10480 Z= 0.195 Angle : 0.621 11.783 14216 Z= 0.323 Chirality : 0.045 0.139 1544 Planarity : 0.004 0.033 1872 Dihedral : 5.153 45.409 1422 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 1.99 % Allowed : 15.98 % Favored : 82.04 % 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: -2.11 (0.23), residues: 1320 helix: -1.72 (0.57), residues: 92 sheet: -1.69 (0.45), residues: 138 loop : -1.45 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 509 TYR 0.010 0.001 TYR A 251 PHE 0.011 0.001 PHE C 15 TRP 0.011 0.001 TRP A 140 HIS 0.006 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00432 (10424) covalent geometry : angle 0.61323 (14104) SS BOND : bond 0.00339 ( 56) SS BOND : angle 1.26736 ( 112) hydrogen bonds : bond 0.03369 ( 135) hydrogen bonds : angle 5.40207 ( 261) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9741 (tpp) cc_final: 0.9503 (tpt) REVERT: A 60 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8032 (tm-30) REVERT: A 71 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.9084 (p) REVERT: A 521 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8461 (tm-30) REVERT: B 82 ILE cc_start: 0.9720 (pt) cc_final: 0.9422 (mp) REVERT: B 294 MET cc_start: 0.8486 (ptt) cc_final: 0.8080 (ppp) REVERT: D 29 LYS cc_start: 0.9681 (mmmm) cc_final: 0.9428 (mmmm) outliers start: 23 outliers final: 18 residues processed: 65 average time/residue: 0.0964 time to fit residues: 9.2480 Evaluate side-chains 59 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 584 TRP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 566 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 87 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 77 optimal weight: 0.0980 chunk 69 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 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 = 0.3309 r_free = 0.3309 target = 0.052380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.034773 restraints weight = 53852.892| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 5.75 r_work: 0.2585 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10480 Z= 0.106 Angle : 0.594 12.118 14216 Z= 0.306 Chirality : 0.045 0.148 1544 Planarity : 0.004 0.036 1872 Dihedral : 4.893 44.148 1422 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 1.73 % Allowed : 16.41 % Favored : 81.87 % 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: -1.96 (0.23), residues: 1320 helix: -1.38 (0.61), residues: 86 sheet: -1.63 (0.43), residues: 155 loop : -1.34 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.009 0.001 TYR A 251 PHE 0.010 0.001 PHE C 15 TRP 0.012 0.001 TRP A 584 HIS 0.007 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00246 (10424) covalent geometry : angle 0.58951 (14104) SS BOND : bond 0.00178 ( 56) SS BOND : angle 1.00963 ( 112) hydrogen bonds : bond 0.02853 ( 135) hydrogen bonds : angle 5.38711 ( 261) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9730 (tpp) cc_final: 0.9519 (tpt) REVERT: A 60 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 71 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9080 (p) REVERT: A 521 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8414 (tm-30) REVERT: A 567 CYS cc_start: 0.6740 (OUTLIER) cc_final: 0.6455 (p) REVERT: B 82 ILE cc_start: 0.9693 (pt) cc_final: 0.9418 (mp) REVERT: B 294 MET cc_start: 0.8502 (ptt) cc_final: 0.8084 (ppp) REVERT: B 400 GLU cc_start: 0.9227 (tp30) cc_final: 0.8952 (tp30) REVERT: D 29 LYS cc_start: 0.9650 (mmmm) cc_final: 0.9382 (mmmm) outliers start: 20 outliers final: 15 residues processed: 61 average time/residue: 0.0806 time to fit residues: 7.8201 Evaluate side-chains 60 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 584 TRP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 33 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 26 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 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 = 0.3305 r_free = 0.3305 target = 0.052256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.034866 restraints weight = 54243.256| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 5.70 r_work: 0.2581 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10480 Z= 0.121 Angle : 0.587 10.956 14216 Z= 0.304 Chirality : 0.044 0.153 1544 Planarity : 0.003 0.034 1872 Dihedral : 4.833 43.541 1422 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 1.81 % Allowed : 16.67 % Favored : 81.52 % 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: -1.88 (0.23), residues: 1320 helix: -1.35 (0.61), residues: 86 sheet: -1.56 (0.45), residues: 145 loop : -1.30 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.008 0.001 TYR A 251 PHE 0.009 0.001 PHE C 15 TRP 0.012 0.001 TRP A 584 HIS 0.007 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00278 (10424) covalent geometry : angle 0.58255 (14104) SS BOND : bond 0.00213 ( 56) SS BOND : angle 0.98693 ( 112) hydrogen bonds : bond 0.02904 ( 135) hydrogen bonds : angle 5.32397 ( 261) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2581.34 seconds wall clock time: 44 minutes 50.34 seconds (2690.34 seconds total)