Starting phenix.real_space_refine on Tue Jun 10 11:21:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sz7_25563/06_2025/7sz7_25563.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sz7_25563/06_2025/7sz7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sz7_25563/06_2025/7sz7_25563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sz7_25563/06_2025/7sz7_25563.map" model { file = "/net/cci-nas-00/data/ceres_data/7sz7_25563/06_2025/7sz7_25563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sz7_25563/06_2025/7sz7_25563.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.17, per 1000 atoms: 0.70 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: 2.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.20 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: 3.02 Time building geometry restraints manager: 2.80 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: 0.00 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: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.580 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.200 ------------------------------------------------------------------------------- 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 : 9.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.001 TRP A 492 HIS 0.005 0.001 HIS A 409 PHE 0.010 0.001 PHE C 15 TYR 0.010 0.001 TYR B 45 ARG 0.003 0.000 ARG B 427 Details of bonding type rmsd hydrogen bonds : bond 0.31001 ( 135) hydrogen bonds : angle 10.16960 ( 261) SS BOND : bond 0.00572 ( 56) SS BOND : angle 2.10014 ( 112) covalent geometry : bond 0.00514 (10424) covalent geometry : angle 0.79404 (14104) *********************** 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 : 1.109 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: 0.2703 time to fit residues: 33.0077 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 : 1.230 ------------------------------------------------------------------------------- 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 111 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 139 GLN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN A 462 GLN A 469 ASN A 473 ASN A 480 GLN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN A 599 ASN B 23 HIS B 70 ASN B 100 ASN B 134 ASN B 209 HIS B 252 GLN ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** D 18 HIS ** D 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.051116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.033545 restraints weight = 54285.445| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 5.71 r_work: 0.2529 rms_B_bonded: 5.46 restraints_weight: 2.0000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10480 Z= 0.286 Angle : 0.722 7.798 14216 Z= 0.379 Chirality : 0.047 0.169 1544 Planarity : 0.005 0.063 1872 Dihedral : 6.451 56.452 1431 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.38 % Favored : 89.55 % Rotamer: Outliers : 1.38 % Allowed : 11.92 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.21), residues: 1320 helix: -2.94 (0.51), residues: 81 sheet: -2.77 (0.37), residues: 162 loop : -2.47 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 584 HIS 0.007 0.001 HIS B 209 PHE 0.015 0.002 PHE A 380 TYR 0.015 0.002 TYR B 561 ARG 0.005 0.001 ARG B 427 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 135) hydrogen bonds : angle 6.56450 ( 261) SS BOND : bond 0.00473 ( 56) SS BOND : angle 1.29407 ( 112) covalent geometry : bond 0.00625 (10424) covalent geometry : angle 0.71548 (14104) *********************** 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: 16 poor density : 49 time to evaluate : 1.071 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: 0.9652 (tpp) cc_final: 0.9291 (tpt) REVERT: A 128 ASN cc_start: 0.9259 (OUTLIER) cc_final: 0.8338 (t0) REVERT: A 550 ARG cc_start: 0.9380 (mtm-85) cc_final: 0.7844 (tpt90) REVERT: B 82 ILE cc_start: 0.9714 (pt) cc_final: 0.9451 (mp) REVERT: B 523 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8524 (mmt90) outliers start: 16 outliers final: 7 residues processed: 62 average time/residue: 0.2239 time to fit residues: 20.5986 Evaluate side-chains 52 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 491 CYS 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 84 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN B 134 ASN B 394 HIS ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.051537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.033785 restraints weight = 54826.195| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 5.83 r_work: 0.2550 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10480 Z= 0.174 Angle : 0.613 8.886 14216 Z= 0.325 Chirality : 0.045 0.146 1544 Planarity : 0.004 0.055 1872 Dihedral : 5.619 48.967 1422 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.39 % Favored : 90.53 % Rotamer: Outliers : 1.12 % Allowed : 14.08 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.22), residues: 1320 helix: -2.57 (0.56), residues: 80 sheet: -2.49 (0.40), residues: 162 loop : -2.05 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 584 HIS 0.008 0.001 HIS B 591 PHE 0.011 0.001 PHE A 380 TYR 0.009 0.001 TYR B 45 ARG 0.003 0.000 ARG B 427 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 135) hydrogen bonds : angle 6.04690 ( 261) SS BOND : bond 0.00293 ( 56) SS BOND : angle 0.97483 ( 112) covalent geometry : bond 0.00388 (10424) covalent geometry : angle 0.60958 (14104) *********************** 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 65 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9629 (tpp) cc_final: 0.9297 (tpt) REVERT: B 82 ILE cc_start: 0.9684 (pt) cc_final: 0.9434 (mp) REVERT: B 400 GLU cc_start: 0.9173 (tp30) cc_final: 0.8894 (tp30) REVERT: D 29 LYS cc_start: 0.9591 (mmmm) cc_final: 0.9314 (mmmm) outliers start: 13 outliers final: 7 residues processed: 62 average time/residue: 0.2511 time to fit residues: 22.5178 Evaluate side-chains 52 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 280 HIS 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 Chi-restraints excluded: chain B residue 523 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 124 optimal weight: 6.9990 chunk 20 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3303 r_free = 0.3303 target = 0.052099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.034552 restraints weight = 53325.719| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 5.76 r_work: 0.2580 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2244 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= 0.107 Angle : 0.567 8.541 14216 Z= 0.300 Chirality : 0.045 0.162 1544 Planarity : 0.004 0.044 1872 Dihedral : 5.310 49.235 1422 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.64 % Favored : 91.29 % Rotamer: Outliers : 1.73 % Allowed : 14.77 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.22), residues: 1320 helix: -2.42 (0.56), residues: 80 sheet: -2.23 (0.41), residues: 162 loop : -1.80 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 584 HIS 0.006 0.001 HIS B 591 PHE 0.010 0.001 PHE A 380 TYR 0.009 0.001 TYR A 251 ARG 0.002 0.000 ARG B 427 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 135) hydrogen bonds : angle 5.74441 ( 261) SS BOND : bond 0.00207 ( 56) SS BOND : angle 0.77333 ( 112) covalent geometry : bond 0.00242 (10424) covalent geometry : angle 0.56516 (14104) *********************** 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 71 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 1.122 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: 0.9617 (tpp) cc_final: 0.9355 (tpt) REVERT: A 71 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.9110 (p) REVERT: A 128 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8063 (t0) REVERT: A 509 ARG cc_start: 0.8111 (tpt170) cc_final: 0.7810 (ttp80) REVERT: C 26 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8690 (mt0) REVERT: B 82 ILE cc_start: 0.9672 (pt) cc_final: 0.9409 (mp) REVERT: B 400 GLU cc_start: 0.9160 (tp30) cc_final: 0.8848 (tp30) REVERT: D 29 LYS cc_start: 0.9615 (mmmm) cc_final: 0.9344 (mmmm) outliers start: 20 outliers final: 10 residues processed: 69 average time/residue: 0.2224 time to fit residues: 22.5717 Evaluate side-chains 58 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 163 CYS Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 0.0270 chunk 95 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 112 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 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** ** D 4 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 = 0.3296 r_free = 0.3296 target = 0.052466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.034712 restraints weight = 54006.984| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 5.71 r_work: 0.2570 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2445 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= 0.139 Angle : 0.566 8.753 14216 Z= 0.299 Chirality : 0.045 0.139 1544 Planarity : 0.004 0.046 1872 Dihedral : 5.187 48.852 1422 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.33 % Allowed : 14.34 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.22), residues: 1320 helix: -2.28 (0.58), residues: 80 sheet: -2.12 (0.40), residues: 164 loop : -1.65 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 584 HIS 0.006 0.001 HIS B 591 PHE 0.010 0.001 PHE A 380 TYR 0.009 0.001 TYR A 251 ARG 0.003 0.000 ARG B 523 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 135) hydrogen bonds : angle 5.60684 ( 261) SS BOND : bond 0.00246 ( 56) SS BOND : angle 0.79281 ( 112) covalent geometry : bond 0.00315 (10424) covalent geometry : angle 0.56340 (14104) *********************** 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 75 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 1.068 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: 0.9654 (tpp) cc_final: 0.9421 (tpt) REVERT: A 60 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7986 (tm-30) REVERT: A 71 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.9046 (p) REVERT: A 521 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8463 (tm-30) REVERT: B 82 ILE cc_start: 0.9690 (pt) cc_final: 0.9406 (mp) REVERT: B 400 GLU cc_start: 0.9216 (tp30) cc_final: 0.8991 (tp30) REVERT: D 29 LYS cc_start: 0.9639 (mmmm) cc_final: 0.9361 (mmmm) outliers start: 27 outliers final: 16 residues processed: 74 average time/residue: 0.2031 time to fit residues: 22.6292 Evaluate side-chains 63 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 24 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 3.9990 chunk 115 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 0.0970 chunk 118 optimal weight: 0.5980 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** D 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.052266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.034821 restraints weight = 54938.374| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 5.72 r_work: 0.2575 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2617 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= 0.123 Angle : 0.571 11.667 14216 Z= 0.298 Chirality : 0.045 0.177 1544 Planarity : 0.004 0.040 1872 Dihedral : 5.071 48.450 1422 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.25 % Allowed : 15.03 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.22), residues: 1320 helix: -2.28 (0.55), residues: 86 sheet: -1.94 (0.40), residues: 164 loop : -1.57 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 584 HIS 0.005 0.001 HIS B 591 PHE 0.010 0.001 PHE C 15 TYR 0.010 0.001 TYR B 292 ARG 0.002 0.000 ARG B 523 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 135) hydrogen bonds : angle 5.44463 ( 261) SS BOND : bond 0.00227 ( 56) SS BOND : angle 0.85098 ( 112) covalent geometry : bond 0.00278 (10424) covalent geometry : angle 0.56796 (14104) *********************** 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: 26 poor density : 47 time to evaluate : 1.231 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: 0.9645 (tpp) cc_final: 0.9427 (tpt) REVERT: A 60 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8021 (tm-30) REVERT: A 71 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9046 (p) REVERT: A 87 MET cc_start: 0.9254 (ttp) cc_final: 0.8863 (ptm) REVERT: A 521 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8466 (tm-30) REVERT: C 26 GLN cc_start: 0.9272 (mm-40) cc_final: 0.8849 (mt0) REVERT: B 30 MET cc_start: 0.9405 (ttt) cc_final: 0.8990 (tmm) REVERT: B 82 ILE cc_start: 0.9698 (pt) cc_final: 0.9402 (mp) REVERT: B 400 GLU cc_start: 0.9224 (tp30) cc_final: 0.8987 (tp30) REVERT: D 29 LYS cc_start: 0.9669 (mmmm) cc_final: 0.9382 (mmmm) outliers start: 26 outliers final: 17 residues processed: 71 average time/residue: 0.2281 time to fit residues: 24.1175 Evaluate side-chains 64 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 D residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 43 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.0770 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 97 optimal weight: 0.0980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.052461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.034858 restraints weight = 53988.997| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 5.76 r_work: 0.2589 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2833 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= 0.106 Angle : 0.566 12.452 14216 Z= 0.294 Chirality : 0.044 0.138 1544 Planarity : 0.003 0.038 1872 Dihedral : 4.893 47.906 1422 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.07 % Allowed : 15.72 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.23), residues: 1320 helix: -1.74 (0.58), residues: 86 sheet: -2.00 (0.38), residues: 180 loop : -1.48 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 584 HIS 0.004 0.001 HIS B 591 PHE 0.010 0.001 PHE C 15 TYR 0.010 0.001 TYR B 292 ARG 0.002 0.000 ARG B 523 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 135) hydrogen bonds : angle 5.46479 ( 261) SS BOND : bond 0.00189 ( 56) SS BOND : angle 0.95613 ( 112) covalent geometry : bond 0.00243 (10424) covalent geometry : angle 0.56219 (14104) *********************** 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: 24 poor density : 45 time to evaluate : 1.177 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: 0.8307 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 71 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.9085 (p) REVERT: A 87 MET cc_start: 0.9189 (ttp) cc_final: 0.8841 (ptm) REVERT: A 521 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8448 (tm-30) REVERT: B 82 ILE cc_start: 0.9685 (pt) cc_final: 0.9394 (mp) REVERT: B 87 MET cc_start: 0.9050 (tpp) cc_final: 0.8770 (tpp) REVERT: B 400 GLU cc_start: 0.9204 (tp30) cc_final: 0.8945 (tp30) REVERT: D 29 LYS cc_start: 0.9690 (mmmm) cc_final: 0.9407 (mmmm) outliers start: 24 outliers final: 17 residues processed: 66 average time/residue: 0.2296 time to fit residues: 22.6288 Evaluate side-chains 63 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 186 LEU 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 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 D residue 4 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 85 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 7 optimal weight: 0.0170 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** 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 = 0.3313 r_free = 0.3313 target = 0.052456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.034809 restraints weight = 54709.447| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 5.77 r_work: 0.2585 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2906 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= 0.115 Angle : 0.577 12.529 14216 Z= 0.297 Chirality : 0.044 0.157 1544 Planarity : 0.003 0.036 1872 Dihedral : 4.892 47.444 1422 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.07 % Allowed : 16.32 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.23), residues: 1320 helix: -1.58 (0.59), residues: 86 sheet: -1.78 (0.43), residues: 153 loop : -1.45 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 584 HIS 0.005 0.001 HIS B 591 PHE 0.011 0.001 PHE C 15 TYR 0.009 0.001 TYR B 292 ARG 0.002 0.000 ARG B 523 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 135) hydrogen bonds : angle 5.40863 ( 261) SS BOND : bond 0.00200 ( 56) SS BOND : angle 1.07579 ( 112) covalent geometry : bond 0.00264 (10424) covalent geometry : angle 0.57079 (14104) *********************** 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: 24 poor density : 44 time to evaluate : 1.276 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: 0.9726 (tpp) cc_final: 0.9481 (tpt) REVERT: A 71 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.9087 (p) REVERT: A 87 MET cc_start: 0.9205 (ttp) cc_final: 0.8772 (ptm) REVERT: A 521 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8432 (tm-30) REVERT: B 30 MET cc_start: 0.9389 (ttt) cc_final: 0.9126 (tmm) REVERT: B 82 ILE cc_start: 0.9691 (pt) cc_final: 0.9395 (mp) REVERT: B 400 GLU cc_start: 0.9216 (tp30) cc_final: 0.8969 (tp30) REVERT: D 29 LYS cc_start: 0.9692 (mmmm) cc_final: 0.9406 (mmmm) outliers start: 24 outliers final: 19 residues processed: 66 average time/residue: 0.2144 time to fit residues: 21.9457 Evaluate side-chains 62 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 438 ILE 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 D residue 24 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 77 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.052111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.034608 restraints weight = 54484.657| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 5.72 r_work: 0.2575 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10480 Z= 0.134 Angle : 0.588 12.456 14216 Z= 0.302 Chirality : 0.044 0.159 1544 Planarity : 0.003 0.036 1872 Dihedral : 4.889 46.219 1422 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 1.90 % Allowed : 16.41 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.23), residues: 1320 helix: -1.49 (0.60), residues: 86 sheet: -1.70 (0.45), residues: 143 loop : -1.39 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 584 HIS 0.005 0.001 HIS B 591 PHE 0.009 0.001 PHE C 15 TYR 0.013 0.001 TYR B 292 ARG 0.003 0.000 ARG A 509 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 135) hydrogen bonds : angle 5.33895 ( 261) SS BOND : bond 0.00225 ( 56) SS BOND : angle 1.04689 ( 112) covalent geometry : bond 0.00304 (10424) covalent geometry : angle 0.58298 (14104) *********************** 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: 22 poor density : 44 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9735 (tpp) cc_final: 0.9504 (tpt) REVERT: A 71 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9098 (p) REVERT: A 87 MET cc_start: 0.9195 (ttp) cc_final: 0.8749 (ptm) REVERT: A 521 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8434 (tm-30) REVERT: C 26 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8919 (mm-40) REVERT: B 30 MET cc_start: 0.9397 (ttt) cc_final: 0.9143 (tmm) REVERT: B 82 ILE cc_start: 0.9695 (pt) cc_final: 0.9402 (mp) REVERT: B 87 MET cc_start: 0.9099 (tpp) cc_final: 0.8829 (tpp) REVERT: B 400 GLU cc_start: 0.9221 (tp30) cc_final: 0.8973 (tp30) REVERT: D 29 LYS cc_start: 0.9690 (mmmm) cc_final: 0.9412 (mmmm) outliers start: 22 outliers final: 17 residues processed: 64 average time/residue: 0.2097 time to fit residues: 20.3871 Evaluate side-chains 59 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 438 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain D residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 118 optimal weight: 0.0970 chunk 129 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 90 optimal weight: 0.0000 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3320 r_free = 0.3320 target = 0.052536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.034932 restraints weight = 53878.465| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 5.72 r_work: 0.2591 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10480 Z= 0.113 Angle : 0.609 12.274 14216 Z= 0.313 Chirality : 0.045 0.158 1544 Planarity : 0.004 0.041 1872 Dihedral : 4.872 45.550 1422 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.73 % Allowed : 16.67 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.23), residues: 1320 helix: -1.46 (0.60), residues: 86 sheet: -1.54 (0.44), residues: 148 loop : -1.40 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 584 HIS 0.005 0.001 HIS B 591 PHE 0.009 0.001 PHE C 15 TYR 0.011 0.001 TYR B 292 ARG 0.002 0.000 ARG A 509 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 135) hydrogen bonds : angle 5.29266 ( 261) SS BOND : bond 0.00250 ( 56) SS BOND : angle 1.30257 ( 112) covalent geometry : bond 0.00269 (10424) covalent geometry : angle 0.60016 (14104) ********************** 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 : 1.157 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: 0.9729 (tpp) cc_final: 0.9519 (tpt) REVERT: A 71 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.9109 (p) REVERT: A 87 MET cc_start: 0.9178 (ttp) cc_final: 0.8754 (ptm) REVERT: A 521 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: A 567 CYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6420 (p) REVERT: B 30 MET cc_start: 0.9366 (ttt) cc_final: 0.9148 (tmm) REVERT: B 82 ILE cc_start: 0.9686 (pt) cc_final: 0.9405 (mp) REVERT: B 87 MET cc_start: 0.9078 (tpp) cc_final: 0.8771 (tpp) REVERT: B 400 GLU cc_start: 0.9214 (tp30) cc_final: 0.8970 (tp30) REVERT: D 29 LYS cc_start: 0.9682 (mmmm) cc_final: 0.9398 (mmmm) outliers start: 20 outliers final: 17 residues processed: 61 average time/residue: 0.2013 time to fit residues: 19.2905 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 : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 438 ILE 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 D residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 123 optimal weight: 40.0000 chunk 81 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 130 optimal weight: 0.0980 chunk 74 optimal weight: 0.4980 chunk 124 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3323 r_free = 0.3323 target = 0.052597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.035037 restraints weight = 53843.957| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 5.67 r_work: 0.2599 rms_B_bonded: 5.46 restraints_weight: 2.0000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10480 Z= 0.110 Angle : 0.590 11.934 14216 Z= 0.303 Chirality : 0.044 0.156 1544 Planarity : 0.003 0.036 1872 Dihedral : 4.773 44.006 1422 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 1.81 % Allowed : 16.93 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.23), residues: 1320 helix: -1.40 (0.61), residues: 86 sheet: -1.48 (0.45), residues: 138 loop : -1.34 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 584 HIS 0.005 0.001 HIS B 591 PHE 0.009 0.001 PHE C 15 TYR 0.010 0.001 TYR B 292 ARG 0.003 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.02798 ( 135) hydrogen bonds : angle 5.25631 ( 261) SS BOND : bond 0.00181 ( 56) SS BOND : angle 1.10045 ( 112) covalent geometry : bond 0.00259 (10424) covalent geometry : angle 0.58390 (14104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5699.50 seconds wall clock time: 98 minutes 14.36 seconds (5894.36 seconds total)