Starting phenix.real_space_refine on Thu Jul 2 08:01:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kzc_62659/07_2026/9kzc_62659.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kzc_62659/07_2026/9kzc_62659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kzc_62659/07_2026/9kzc_62659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kzc_62659/07_2026/9kzc_62659.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kzc_62659/07_2026/9kzc_62659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kzc_62659/07_2026/9kzc_62659.map" } resolution = 2.78 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= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 66 5.16 5 C 4953 2.51 5 N 1326 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7846 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3696 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 13, 'TRANS': 468} Chain breaks: 1 Chain: "B" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2718 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 11, 'TRANS': 318} Chain: "D" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1428 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 1.39, per 1000 atoms: 0.18 Number of scatterers: 7846 At special positions: 0 Unit cell: (69.936, 102.272, 115.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 66 16.00 O 1497 8.00 N 1326 7.00 C 4953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 401 " distance=2.03 Simple disulfide: pdb=" SG CYS A 447 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 460 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 494 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 554 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 569 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 583 " - pdb=" SG CYS A 593 " distance=2.03 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 663 " distance=2.03 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 688 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 702 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 286 " distance=2.04 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS D 177 " - pdb=" SG CYS D 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 221 " 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: 0.44 Conformation dependent library (CDL) restraints added in 347.4 milliseconds 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 18 sheets defined 14.7% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 248 through 255 removed outlier: 3.570A pdb=" N HIS A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 281 removed outlier: 3.691A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 319 Processing helix chain 'A' and resid 362 through 378 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 415 through 428 Processing helix chain 'A' and resid 431 through 436 removed outlier: 4.202A pdb=" N PHE A 435 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN A 436 " --> pdb=" O CYS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.764A pdb=" N VAL A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 558 removed outlier: 3.658A pdb=" N GLN A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 removed outlier: 3.716A pdb=" N TYR A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.636A pdb=" N VAL D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 207 removed outlier: 3.966A pdb=" N LYS D 207 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 214 Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 292 removed outlier: 7.763A pdb=" N ILE A 245 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET A 290 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASN A 247 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR A 292 " --> pdb=" O ASN A 247 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ALA A 326 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU A 242 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N HIS A 328 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N MET A 244 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE A 330 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 246 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AA3, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA4, first strand: chain 'A' and resid 502 through 504 removed outlier: 3.628A pdb=" N ARG A 504 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 535 removed outlier: 3.900A pdb=" N GLY A 540 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 564 Processing sheet with id=AA7, first strand: chain 'A' and resid 622 through 624 Processing sheet with id=AA8, first strand: chain 'A' and resid 656 through 658 removed outlier: 5.965A pdb=" N CYS A 663 " --> pdb=" O PRO A 656 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AB1, first strand: chain 'B' and resid 226 through 232 removed outlier: 6.628A pdb=" N ILE B 547 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP B 231 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR B 545 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN B 534 " --> pdb=" O HIS B 550 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER B 524 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 239 through 243 removed outlier: 7.497A pdb=" N GLU B 248 " --> pdb=" O TRP B 265 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP B 265 " --> pdb=" O GLU B 248 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS B 260 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN B 277 " --> pdb=" O CYS B 260 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE B 262 " --> pdb=" O TYR B 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 283 through 290 removed outlier: 3.590A pdb=" N VAL B 285 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU B 295 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 308 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 332 through 339 removed outlier: 3.706A pdb=" N ASP B 334 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TRP B 344 " --> pdb=" O TRP B 362 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B 359 " --> pdb=" O HIS B 370 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 379 through 387 removed outlier: 6.641A pdb=" N SER B 402 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL B 382 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 400 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR B 384 " --> pdb=" O HIS B 398 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS B 398 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU B 386 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N THR B 396 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 410 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN B 423 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 434 through 440 removed outlier: 3.700A pdb=" N ALA B 434 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL B 444 " --> pdb=" O TRP B 460 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY B 453 " --> pdb=" O PRO B 472 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER B 455 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA B 470 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 457 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 479 through 484 removed outlier: 5.847A pdb=" N GLN B 488 " --> pdb=" O TRP B 504 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR B 499 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU B 516 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 501 " --> pdb=" O PHE B 514 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.542A pdb=" N LEU D 72 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N THR D 99 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE D 74 " --> pdb=" O THR D 99 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU D 120 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 102 through 106 removed outlier: 9.033A pdb=" N PHE D 103 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE D 130 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N VAL D 105 " --> pdb=" O ILE D 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 220 hydrogen bonds defined for protein. 588 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: 1.03 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2555 1.34 - 1.46: 1860 1.46 - 1.58: 3515 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 8011 Sorted by residual: bond pdb=" CA ASN B 531 " pdb=" CB ASN B 531 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.70e-02 3.46e+03 1.13e+00 bond pdb=" CB ASN B 531 " pdb=" CG ASN B 531 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CG LEU A 410 " pdb=" CD1 LEU A 410 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.47e-01 bond pdb=" N LYS B 532 " pdb=" CA LYS B 532 " ideal model delta sigma weight residual 1.460 1.473 -0.013 1.95e-02 2.63e+03 4.63e-01 bond pdb=" CB CYS A 569 " pdb=" SG CYS A 569 " ideal model delta sigma weight residual 1.808 1.787 0.021 3.30e-02 9.18e+02 4.17e-01 ... (remaining 8006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 10584 1.36 - 2.73: 208 2.73 - 4.09: 29 4.09 - 5.46: 3 5.46 - 6.82: 2 Bond angle restraints: 10826 Sorted by residual: angle pdb=" C ARG B 389 " pdb=" N THR B 390 " pdb=" CA THR B 390 " ideal model delta sigma weight residual 121.80 115.44 6.36 2.44e+00 1.68e-01 6.79e+00 angle pdb=" N VAL B 284 " pdb=" CA VAL B 284 " pdb=" C VAL B 284 " ideal model delta sigma weight residual 111.81 109.76 2.05 8.60e-01 1.35e+00 5.70e+00 angle pdb=" N ILE D 142 " pdb=" CA ILE D 142 " pdb=" C ILE D 142 " ideal model delta sigma weight residual 113.39 110.05 3.34 1.47e+00 4.63e-01 5.16e+00 angle pdb=" N THR B 390 " pdb=" CA THR B 390 " pdb=" C THR B 390 " ideal model delta sigma weight residual 109.81 114.81 -5.00 2.21e+00 2.05e-01 5.12e+00 angle pdb=" CA ASN B 531 " pdb=" CB ASN B 531 " pdb=" CG ASN B 531 " ideal model delta sigma weight residual 112.60 114.72 -2.12 1.00e+00 1.00e+00 4.49e+00 ... (remaining 10821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4393 17.95 - 35.90: 385 35.90 - 53.85: 59 53.85 - 71.80: 16 71.80 - 89.76: 6 Dihedral angle restraints: 4859 sinusoidal: 1985 harmonic: 2874 Sorted by residual: dihedral pdb=" CB CYS A 569 " pdb=" SG CYS A 569 " pdb=" SG CYS A 635 " pdb=" CB CYS A 635 " ideal model delta sinusoidal sigma weight residual 93.00 159.62 -66.62 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CA THR B 390 " pdb=" C THR B 390 " pdb=" N PRO B 391 " pdb=" CA PRO B 391 " ideal model delta harmonic sigma weight residual 180.00 142.32 37.68 0 5.00e+00 4.00e-02 5.68e+01 dihedral pdb=" CB CYS A 503 " pdb=" SG CYS A 503 " pdb=" SG CYS A 523 " pdb=" CB CYS A 523 " ideal model delta sinusoidal sigma weight residual 93.00 48.61 44.39 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 4856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 715 0.031 - 0.062: 311 0.062 - 0.092: 91 0.092 - 0.123: 63 0.123 - 0.154: 7 Chirality restraints: 1187 Sorted by residual: chirality pdb=" CA ASN B 531 " pdb=" N ASN B 531 " pdb=" C ASN B 531 " pdb=" CB ASN B 531 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE B 298 " pdb=" N ILE B 298 " pdb=" C ILE B 298 " pdb=" CB ILE B 298 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CB VAL A 538 " pdb=" CA VAL A 538 " pdb=" CG1 VAL A 538 " pdb=" CG2 VAL A 538 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1184 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 390 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO B 391 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 391 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 391 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 254 " -0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO B 255 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 255 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 255 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 374 " 0.011 2.00e-02 2.50e+03 1.15e-02 1.98e+00 pdb=" CG HIS B 374 " -0.025 2.00e-02 2.50e+03 pdb=" ND1 HIS B 374 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS B 374 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 374 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 374 " 0.003 2.00e-02 2.50e+03 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1126 2.77 - 3.30: 7136 3.30 - 3.83: 13116 3.83 - 4.37: 16210 4.37 - 4.90: 27376 Nonbonded interactions: 64964 Sorted by model distance: nonbonded pdb=" O CYS D 179 " pdb=" NZ LYS D 182 " model vdw 2.232 3.120 nonbonded pdb=" NE2 GLN B 322 " pdb=" O PHE B 367 " model vdw 2.232 3.120 nonbonded pdb=" O GLN B 520 " pdb=" OG SER B 540 " model vdw 2.300 3.040 nonbonded pdb=" OE1 GLN B 546 " pdb=" OH TYR B 548 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR A 277 " pdb=" O ALA A 371 " model vdw 2.307 3.040 ... (remaining 64959 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 : 0.002 0.027 8036 Z= 0.105 Angle : 0.477 6.821 10876 Z= 0.264 Chirality : 0.043 0.154 1187 Planarity : 0.003 0.064 1394 Dihedral : 13.423 89.756 2936 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.25), residues: 985 helix: 1.40 (0.47), residues: 116 sheet: -0.20 (0.32), residues: 258 loop : -1.23 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 273 TYR 0.012 0.001 TYR B 345 PHE 0.015 0.001 PHE B 346 TRP 0.010 0.001 TRP D 183 HIS 0.012 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 8011) covalent geometry : angle 0.47438 / 0.26 (10826) SS BOND : bond 0.00183 / 0.09 ( 25) SS BOND : angle 0.88213 / 0.53 ( 50) hydrogen bonds : bond 0.20098 / 13.51 ( 220) hydrogen bonds : angle 7.92877 / 5.60 ( 588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.183 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.4362 time to fit residues: 45.4187 Evaluate side-chains 76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 301 GLN B 414 ASN B 469 GLN D 94 GLN D 176 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.195358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.122120 restraints weight = 7270.505| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.02 r_work: 0.3106 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8036 Z= 0.130 Angle : 0.496 8.407 10876 Z= 0.272 Chirality : 0.044 0.147 1187 Planarity : 0.004 0.063 1394 Dihedral : 4.428 37.548 1061 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.81 % Allowed : 7.58 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.01 (0.25), residues: 985 helix: 1.17 (0.46), residues: 124 sheet: -0.22 (0.32), residues: 256 loop : -1.32 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 631 TYR 0.014 0.001 TYR B 345 PHE 0.017 0.001 PHE B 346 TRP 0.007 0.001 TRP D 183 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8011) covalent geometry : angle 0.49525 / 0.27 (10826) SS BOND : bond 0.00221 / 0.11 ( 25) SS BOND : angle 0.67580 / 0.45 ( 50) hydrogen bonds : bond 0.04375 / 2.87 ( 220) hydrogen bonds : angle 5.90268 / 4.09 ( 588) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.296 Fit side-chains REVERT: A 405 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6855 (m-30) REVERT: A 661 MET cc_start: 0.6874 (tpp) cc_final: 0.6582 (tpp) REVERT: D 123 GLU cc_start: 0.8232 (pt0) cc_final: 0.7979 (pt0) outliers start: 16 outliers final: 6 residues processed: 89 average time/residue: 0.4343 time to fit residues: 41.2505 Evaluate side-chains 80 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain D residue 112 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 38 optimal weight: 10.0000 chunk 26 optimal weight: 0.0570 chunk 17 optimal weight: 0.0050 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.196726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123504 restraints weight = 7324.700| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.79 r_work: 0.3180 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8036 Z= 0.096 Angle : 0.457 7.712 10876 Z= 0.249 Chirality : 0.043 0.146 1187 Planarity : 0.003 0.064 1394 Dihedral : 4.213 36.142 1061 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.24 % Allowed : 10.86 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.25), residues: 985 helix: 1.32 (0.46), residues: 125 sheet: -0.27 (0.32), residues: 254 loop : -1.24 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 533 TYR 0.011 0.001 TYR B 345 PHE 0.015 0.001 PHE B 346 TRP 0.006 0.001 TRP D 183 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 8011) covalent geometry : angle 0.45673 / 0.25 (10826) SS BOND : bond 0.00147 / 0.07 ( 25) SS BOND : angle 0.54751 / 0.37 ( 50) hydrogen bonds : bond 0.03513 / 2.31 ( 220) hydrogen bonds : angle 5.46058 / 3.78 ( 588) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.295 Fit side-chains REVERT: A 336 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7864 (mm-30) REVERT: A 405 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6732 (m-30) REVERT: A 661 MET cc_start: 0.6834 (tpp) cc_final: 0.6389 (tpp) REVERT: B 225 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.6997 (pp20) outliers start: 11 outliers final: 5 residues processed: 83 average time/residue: 0.4065 time to fit residues: 36.1727 Evaluate side-chains 81 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain D residue 112 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 77 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 0.1980 chunk 9 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.191973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.116330 restraints weight = 7381.047| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.88 r_work: 0.3060 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8036 Z= 0.239 Angle : 0.586 10.934 10876 Z= 0.312 Chirality : 0.048 0.157 1187 Planarity : 0.004 0.065 1394 Dihedral : 4.822 40.457 1061 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.60 % Allowed : 11.99 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.11 (0.25), residues: 985 helix: 1.10 (0.46), residues: 125 sheet: -0.42 (0.31), residues: 255 loop : -1.32 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 395 TYR 0.016 0.002 TYR A 602 PHE 0.020 0.002 PHE B 346 TRP 0.010 0.002 TRP B 413 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 ( 8011) covalent geometry : angle 0.58309 / 0.31 (10826) SS BOND : bond 0.00312 / 0.16 ( 25) SS BOND : angle 0.99558 / 0.67 ( 50) hydrogen bonds : bond 0.04659 / 3.04 ( 220) hydrogen bonds : angle 5.79740 / 4.02 ( 588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.217 Fit side-chains REVERT: A 405 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: A 661 MET cc_start: 0.6848 (tpp) cc_final: 0.6471 (tpp) REVERT: B 254 GLN cc_start: 0.8177 (tt0) cc_final: 0.7968 (tt0) outliers start: 23 outliers final: 15 residues processed: 89 average time/residue: 0.4094 time to fit residues: 38.8151 Evaluate side-chains 84 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 156 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 40.0000 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.194665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.127058 restraints weight = 7390.229| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.00 r_work: 0.3103 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8036 Z= 0.207 Angle : 0.557 11.330 10876 Z= 0.297 Chirality : 0.046 0.159 1187 Planarity : 0.004 0.069 1394 Dihedral : 4.786 40.113 1061 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.26 % Allowed : 13.57 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.16 (0.25), residues: 985 helix: 1.01 (0.46), residues: 126 sheet: -0.50 (0.31), residues: 255 loop : -1.31 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 613 TYR 0.015 0.002 TYR B 345 PHE 0.019 0.002 PHE B 346 TRP 0.008 0.001 TRP B 413 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 ( 8011) covalent geometry : angle 0.55553 / 0.30 (10826) SS BOND : bond 0.00277 / 0.14 ( 25) SS BOND : angle 0.81097 / 0.57 ( 50) hydrogen bonds : bond 0.04255 / 2.78 ( 220) hydrogen bonds : angle 5.66951 / 3.93 ( 588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.283 Fit side-chains REVERT: A 366 MET cc_start: 0.8754 (ttt) cc_final: 0.8532 (ttt) REVERT: A 405 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7109 (m-30) REVERT: B 254 GLN cc_start: 0.8302 (tt0) cc_final: 0.8032 (tt0) REVERT: B 319 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8506 (pt) outliers start: 20 outliers final: 15 residues processed: 86 average time/residue: 0.3941 time to fit residues: 36.5184 Evaluate side-chains 86 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 129 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 0.0050 overall best weight: 0.7734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.197281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124846 restraints weight = 7393.525| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.29 r_work: 0.3161 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8036 Z= 0.105 Angle : 0.478 8.728 10876 Z= 0.258 Chirality : 0.043 0.157 1187 Planarity : 0.003 0.067 1394 Dihedral : 4.427 38.203 1061 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.92 % Allowed : 14.82 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.04 (0.25), residues: 985 helix: 1.22 (0.46), residues: 126 sheet: -0.45 (0.32), residues: 251 loop : -1.25 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 171 TYR 0.012 0.001 TYR B 345 PHE 0.015 0.001 PHE B 346 TRP 0.008 0.001 TRP D 183 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 8011) covalent geometry : angle 0.47698 / 0.26 (10826) SS BOND : bond 0.00166 / 0.08 ( 25) SS BOND : angle 0.58549 / 0.40 ( 50) hydrogen bonds : bond 0.03346 / 2.19 ( 220) hydrogen bonds : angle 5.34182 / 3.69 ( 588) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.290 Fit side-chains REVERT: A 513 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8223 (ttp80) REVERT: A 661 MET cc_start: 0.6939 (tpp) cc_final: 0.6517 (tpp) REVERT: B 225 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7070 (pp20) REVERT: B 254 GLN cc_start: 0.8073 (tt0) cc_final: 0.7778 (tt0) outliers start: 17 outliers final: 11 residues processed: 86 average time/residue: 0.3812 time to fit residues: 35.2888 Evaluate side-chains 85 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain D residue 112 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 74 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.193349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116764 restraints weight = 7427.777| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.96 r_work: 0.3107 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8036 Z= 0.253 Angle : 0.593 12.411 10876 Z= 0.315 Chirality : 0.048 0.167 1187 Planarity : 0.004 0.067 1394 Dihedral : 4.867 41.253 1061 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.94 % Allowed : 14.48 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.16 (0.25), residues: 985 helix: 1.03 (0.46), residues: 126 sheet: -0.58 (0.30), residues: 259 loop : -1.28 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.014 0.002 TYR B 345 PHE 0.022 0.002 PHE B 346 TRP 0.010 0.002 TRP B 413 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.25 ( 8011) covalent geometry : angle 0.58797 / 0.31 (10826) SS BOND : bond 0.00356 / 0.18 ( 25) SS BOND : angle 1.23476 / 0.73 ( 50) hydrogen bonds : bond 0.04487 / 2.92 ( 220) hydrogen bonds : angle 5.64372 / 3.93 ( 588) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.200 Fit side-chains REVERT: A 417 CYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8124 (m) REVERT: A 661 MET cc_start: 0.6896 (tpp) cc_final: 0.6436 (tpp) REVERT: B 319 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8525 (pt) outliers start: 26 outliers final: 19 residues processed: 89 average time/residue: 0.3581 time to fit residues: 34.3513 Evaluate side-chains 88 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 35 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 4 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.195992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121211 restraints weight = 7453.217| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.93 r_work: 0.3176 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8036 Z= 0.114 Angle : 0.487 9.288 10876 Z= 0.264 Chirality : 0.044 0.158 1187 Planarity : 0.003 0.070 1394 Dihedral : 4.501 38.599 1061 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.15 % Allowed : 15.61 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.07 (0.25), residues: 985 helix: 1.26 (0.46), residues: 125 sheet: -0.53 (0.31), residues: 256 loop : -1.25 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 171 TYR 0.013 0.001 TYR B 345 PHE 0.015 0.001 PHE B 346 TRP 0.008 0.001 TRP D 183 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 8011) covalent geometry : angle 0.48501 / 0.26 (10826) SS BOND : bond 0.00178 / 0.09 ( 25) SS BOND : angle 0.83919 / 0.49 ( 50) hydrogen bonds : bond 0.03406 / 2.22 ( 220) hydrogen bonds : angle 5.30661 / 3.67 ( 588) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.248 Fit side-chains REVERT: A 417 CYS cc_start: 0.8235 (OUTLIER) cc_final: 0.8029 (m) REVERT: A 513 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8220 (ttp80) REVERT: A 661 MET cc_start: 0.6805 (tpp) cc_final: 0.6333 (tpp) REVERT: B 225 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.6996 (pp20) outliers start: 19 outliers final: 13 residues processed: 86 average time/residue: 0.3879 time to fit residues: 36.0322 Evaluate side-chains 86 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain D residue 112 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 0.0370 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.194038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118251 restraints weight = 7395.020| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.92 r_work: 0.3134 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8036 Z= 0.210 Angle : 0.561 11.636 10876 Z= 0.299 Chirality : 0.046 0.170 1187 Planarity : 0.004 0.067 1394 Dihedral : 4.767 40.968 1061 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.04 % Allowed : 16.29 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.12 (0.25), residues: 985 helix: 1.07 (0.46), residues: 126 sheet: -0.55 (0.31), residues: 254 loop : -1.26 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 171 TYR 0.015 0.002 TYR B 345 PHE 0.020 0.002 PHE B 346 TRP 0.009 0.001 TRP B 413 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 ( 8011) covalent geometry : angle 0.55880 / 0.30 (10826) SS BOND : bond 0.00288 / 0.15 ( 25) SS BOND : angle 0.91947 / 0.60 ( 50) hydrogen bonds : bond 0.04179 / 2.73 ( 220) hydrogen bonds : angle 5.50249 / 3.82 ( 588) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 417 CYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8080 (m) REVERT: A 661 MET cc_start: 0.6829 (tpp) cc_final: 0.6338 (tpp) outliers start: 18 outliers final: 16 residues processed: 81 average time/residue: 0.3702 time to fit residues: 32.4157 Evaluate side-chains 85 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 198 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.195945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126958 restraints weight = 7391.410| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.08 r_work: 0.3176 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8036 Z= 0.113 Angle : 0.494 9.585 10876 Z= 0.266 Chirality : 0.044 0.162 1187 Planarity : 0.003 0.069 1394 Dihedral : 4.507 38.877 1061 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.26 % Allowed : 15.84 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.07 (0.25), residues: 985 helix: 1.16 (0.46), residues: 126 sheet: -0.53 (0.31), residues: 256 loop : -1.23 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 171 TYR 0.013 0.001 TYR B 345 PHE 0.016 0.001 PHE B 346 TRP 0.008 0.001 TRP D 183 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 8011) covalent geometry : angle 0.49232 / 0.27 (10826) SS BOND : bond 0.00192 / 0.09 ( 25) SS BOND : angle 0.73745 / 0.46 ( 50) hydrogen bonds : bond 0.03454 / 2.26 ( 220) hydrogen bonds : angle 5.27133 / 3.65 ( 588) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 417 CYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8040 (m) REVERT: A 513 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8287 (ttp80) REVERT: A 661 MET cc_start: 0.6722 (tpp) cc_final: 0.6268 (tpp) REVERT: B 225 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7043 (pp20) REVERT: D 123 GLU cc_start: 0.8333 (pt0) cc_final: 0.8113 (pt0) outliers start: 20 outliers final: 16 residues processed: 84 average time/residue: 0.3561 time to fit residues: 32.2951 Evaluate side-chains 86 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 198 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 8 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 63 optimal weight: 0.0980 chunk 37 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 26 optimal weight: 0.0000 chunk 75 optimal weight: 5.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 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 = 0.4132 r_free = 0.4132 target = 0.196316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124104 restraints weight = 7380.568| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.26 r_work: 0.3154 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8036 Z= 0.116 Angle : 0.485 8.727 10876 Z= 0.262 Chirality : 0.044 0.165 1187 Planarity : 0.003 0.068 1394 Dihedral : 4.391 38.980 1061 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.04 % Allowed : 16.74 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.02 (0.25), residues: 985 helix: 1.20 (0.46), residues: 126 sheet: -0.51 (0.31), residues: 260 loop : -1.19 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 171 TYR 0.013 0.001 TYR B 345 PHE 0.016 0.001 PHE B 346 TRP 0.008 0.001 TRP B 362 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8011) covalent geometry : angle 0.48378 / 0.26 (10826) SS BOND : bond 0.00182 / 0.09 ( 25) SS BOND : angle 0.70903 / 0.45 ( 50) hydrogen bonds : bond 0.03362 / 2.21 ( 220) hydrogen bonds : angle 5.19547 / 3.60 ( 588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2293.05 seconds wall clock time: 39 minutes 49.58 seconds (2389.58 seconds total)