Starting phenix.real_space_refine on Wed Sep 17 09:36:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kzc_62659/09_2025/9kzc_62659.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kzc_62659/09_2025/9kzc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9kzc_62659/09_2025/9kzc_62659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kzc_62659/09_2025/9kzc_62659.map" model { file = "/net/cci-nas-00/data/ceres_data/9kzc_62659/09_2025/9kzc_62659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kzc_62659/09_2025/9kzc_62659.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.68, per 1000 atoms: 0.21 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: 0.59 Conformation dependent library (CDL) restraints added in 424.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.31 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: 1.26 Time building geometry restraints manager: 0.82 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: 1.250 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.380 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:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 aren 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 covalent geometry : bond 0.00233 ( 8011) covalent geometry : angle 0.47438 (10826) SS BOND : bond 0.00183 ( 25) SS BOND : angle 0.88213 ( 50) hydrogen bonds : bond 0.20098 ( 220) hydrogen bonds : angle 7.92877 ( 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 : 0.208 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.5839 time to fit residues: 60.6886 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 : 0.322 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4100 r_free = 0.4100 target = 0.195089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121850 restraints weight = 7270.002| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.03 r_work: 0.3108 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0857 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= 0.129 Angle : 0.498 8.435 10876 Z= 0.273 Chirality : 0.044 0.144 1187 Planarity : 0.004 0.063 1394 Dihedral : 4.418 37.473 1061 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.70 % Allowed : 7.92 % Favored : 90.38 % 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 aren not related in a simple way. whole: -1.00 (0.25), residues: 985 helix: 1.14 (0.46), residues: 124 sheet: -0.23 (0.32), residues: 256 loop : -1.30 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 631 TYR 0.013 0.001 TYR B 345 PHE 0.017 0.001 PHE B 346 TRP 0.008 0.001 TRP D 183 HIS 0.007 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8011) covalent geometry : angle 0.49665 (10826) SS BOND : bond 0.00220 ( 25) SS BOND : angle 0.66542 ( 50) hydrogen bonds : bond 0.04191 ( 220) hydrogen bonds : angle 5.93992 ( 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 97 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.320 Fit side-chains REVERT: A 405 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6860 (m-30) REVERT: A 661 MET cc_start: 0.6851 (tpp) cc_final: 0.6574 (tpp) REVERT: D 123 GLU cc_start: 0.8235 (pt0) cc_final: 0.7987 (pt0) outliers start: 15 outliers final: 6 residues processed: 89 average time/residue: 0.5356 time to fit residues: 50.8311 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 : 0.308 ------------------------------------------------------------------------------- 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: 0.0470 chunk 55 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 26 optimal weight: 0.0000 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 39 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 overall best weight: 0.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.196956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.123825 restraints weight = 7308.509| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.28 r_work: 0.3125 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1113 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= 0.089 Angle : 0.450 7.457 10876 Z= 0.245 Chirality : 0.043 0.149 1187 Planarity : 0.003 0.064 1394 Dihedral : 4.154 35.704 1061 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.36 % Allowed : 10.41 % Favored : 88.24 % 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 aren not related in a simple way. whole: -0.91 (0.26), residues: 985 helix: 1.33 (0.46), residues: 125 sheet: -0.26 (0.32), residues: 261 loop : -1.22 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 513 TYR 0.011 0.001 TYR B 345 PHE 0.014 0.001 PHE B 346 TRP 0.006 0.001 TRP B 362 HIS 0.003 0.000 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 8011) covalent geometry : angle 0.44960 (10826) SS BOND : bond 0.00152 ( 25) SS BOND : angle 0.52594 ( 50) hydrogen bonds : bond 0.03380 ( 220) hydrogen bonds : angle 5.45007 ( 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 90 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.265 Fit side-chains REVERT: A 336 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7895 (mm-30) REVERT: A 405 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6868 (m-30) REVERT: A 661 MET cc_start: 0.6805 (tpp) cc_final: 0.6371 (tpp) outliers start: 12 outliers final: 5 residues processed: 84 average time/residue: 0.5096 time to fit residues: 45.8909 Evaluate side-chains 80 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 9 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.192196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.117094 restraints weight = 7381.178| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.15 r_work: 0.3025 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1256 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= 0.221 Angle : 0.564 10.604 10876 Z= 0.300 Chirality : 0.047 0.160 1187 Planarity : 0.004 0.064 1394 Dihedral : 4.691 39.758 1061 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.15 % Allowed : 12.33 % Favored : 85.52 % 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 aren not related in a simple way. whole: -1.08 (0.25), residues: 985 helix: 1.14 (0.46), residues: 125 sheet: -0.48 (0.31), residues: 259 loop : -1.26 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 395 TYR 0.016 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 covalent geometry : bond 0.00523 ( 8011) covalent geometry : angle 0.56121 (10826) SS BOND : bond 0.00298 ( 25) SS BOND : angle 0.96723 ( 50) hydrogen bonds : bond 0.04425 ( 220) hydrogen bonds : angle 5.71417 ( 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 94 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.298 Fit side-chains REVERT: A 405 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.7067 (m-30) REVERT: A 661 MET cc_start: 0.6823 (tpp) cc_final: 0.6469 (tpp) REVERT: B 225 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7336 (pp20) outliers start: 19 outliers final: 11 residues processed: 87 average time/residue: 0.5119 time to fit residues: 47.6776 Evaluate side-chains 84 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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 545 THR Chi-restraints excluded: chain D residue 112 ILE 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: 0.6980 chunk 32 optimal weight: 4.9990 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: 8.9990 chunk 79 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.195636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120167 restraints weight = 7378.185| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.94 r_work: 0.3148 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8036 Z= 0.161 Angle : 0.518 10.520 10876 Z= 0.278 Chirality : 0.045 0.156 1187 Planarity : 0.003 0.068 1394 Dihedral : 4.580 39.037 1061 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.49 % Allowed : 12.78 % Favored : 84.73 % 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 aren not related in a simple way. whole: -1.09 (0.25), residues: 985 helix: 1.13 (0.46), residues: 126 sheet: -0.52 (0.31), residues: 257 loop : -1.26 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 171 TYR 0.014 0.001 TYR B 345 PHE 0.018 0.001 PHE B 346 TRP 0.007 0.001 TRP B 362 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8011) covalent geometry : angle 0.51707 (10826) SS BOND : bond 0.00237 ( 25) SS BOND : angle 0.72683 ( 50) hydrogen bonds : bond 0.03908 ( 220) hydrogen bonds : angle 5.54313 ( 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 92 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.7101 (m-30) REVERT: A 661 MET cc_start: 0.6995 (tpp) cc_final: 0.6555 (tpp) REVERT: B 225 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7248 (pp20) outliers start: 22 outliers final: 16 residues processed: 84 average time/residue: 0.4850 time to fit residues: 43.6388 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 : 0.307 ------------------------------------------------------------------------------- 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 254 GLN 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 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 129 SER Chi-restraints excluded: chain D residue 156 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 83 optimal weight: 0.4980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 520 GLN D 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.197947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123876 restraints weight = 7382.446| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.91 r_work: 0.3202 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8036 Z= 0.097 Angle : 0.462 8.517 10876 Z= 0.250 Chirality : 0.043 0.156 1187 Planarity : 0.003 0.066 1394 Dihedral : 4.242 37.245 1061 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.04 % Allowed : 13.46 % Favored : 84.50 % 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 aren not related in a simple way. whole: -0.94 (0.25), residues: 985 helix: 1.32 (0.46), residues: 126 sheet: -0.37 (0.31), residues: 255 loop : -1.19 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 171 TYR 0.011 0.001 TYR B 345 PHE 0.015 0.001 PHE B 346 TRP 0.007 0.001 TRP B 362 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8011) covalent geometry : angle 0.46115 (10826) SS BOND : bond 0.00159 ( 25) SS BOND : angle 0.54650 ( 50) hydrogen bonds : bond 0.03171 ( 220) hydrogen bonds : angle 5.21974 ( 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 92 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.198 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 86 average time/residue: 0.5035 time to fit residues: 46.3866 Evaluate side-chains 83 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 251 VAL Chi-restraints excluded: chain B residue 254 GLN 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 410 ILE 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 156 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 96 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.195102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123826 restraints weight = 7416.217| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.12 r_work: 0.3131 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8036 Z= 0.156 Angle : 0.514 10.330 10876 Z= 0.275 Chirality : 0.045 0.160 1187 Planarity : 0.003 0.066 1394 Dihedral : 4.463 38.977 1061 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.15 % Allowed : 14.37 % Favored : 83.48 % 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 aren not related in a simple way. whole: -0.97 (0.25), residues: 985 helix: 1.33 (0.46), residues: 125 sheet: -0.39 (0.31), residues: 258 loop : -1.22 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 395 TYR 0.015 0.001 TYR B 345 PHE 0.018 0.001 PHE B 346 TRP 0.007 0.001 TRP B 413 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8011) covalent geometry : angle 0.50974 (10826) SS BOND : bond 0.00247 ( 25) SS BOND : angle 1.09492 ( 50) hydrogen bonds : bond 0.03723 ( 220) hydrogen bonds : angle 5.34606 ( 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 91 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 661 MET cc_start: 0.6841 (tpp) cc_final: 0.6432 (tpp) REVERT: B 225 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7092 (pp20) outliers start: 19 outliers final: 15 residues processed: 85 average time/residue: 0.4884 time to fit residues: 44.5853 Evaluate side-chains 86 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 MET 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 254 GLN 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 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 156 LYS Chi-restraints excluded: chain D residue 198 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 35 optimal weight: 0.4980 chunk 84 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.197748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126201 restraints weight = 7447.316| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.11 r_work: 0.3208 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8036 Z= 0.099 Angle : 0.467 9.027 10876 Z= 0.252 Chirality : 0.043 0.152 1187 Planarity : 0.003 0.067 1394 Dihedral : 4.238 37.283 1061 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.26 % Allowed : 14.82 % Favored : 82.92 % 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 aren not related in a simple way. whole: -0.91 (0.26), residues: 985 helix: 1.41 (0.46), residues: 125 sheet: -0.40 (0.31), residues: 260 loop : -1.16 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 171 TYR 0.011 0.001 TYR B 345 PHE 0.015 0.001 PHE B 346 TRP 0.007 0.001 TRP B 362 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8011) covalent geometry : angle 0.46458 (10826) SS BOND : bond 0.00178 ( 25) SS BOND : angle 0.79444 ( 50) hydrogen bonds : bond 0.03148 ( 220) hydrogen bonds : angle 5.10592 ( 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 94 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 513 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8258 (ttp80) REVERT: A 661 MET cc_start: 0.6511 (tpp) cc_final: 0.6020 (tpp) REVERT: B 225 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.6934 (pp20) REVERT: B 498 PHE cc_start: 0.8488 (m-80) cc_final: 0.8103 (m-80) REVERT: D 123 GLU cc_start: 0.8182 (pt0) cc_final: 0.7922 (pt0) outliers start: 20 outliers final: 17 residues processed: 89 average time/residue: 0.5233 time to fit residues: 49.8595 Evaluate side-chains 92 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 254 GLN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 284 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 16 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.194073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117581 restraints weight = 7386.646| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.97 r_work: 0.3120 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8036 Z= 0.207 Angle : 0.556 11.100 10876 Z= 0.296 Chirality : 0.046 0.170 1187 Planarity : 0.004 0.065 1394 Dihedral : 4.668 40.356 1061 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.60 % Allowed : 15.05 % Favored : 82.35 % 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 aren not related in a simple way. whole: -1.05 (0.25), residues: 985 helix: 1.18 (0.46), residues: 126 sheet: -0.49 (0.30), residues: 259 loop : -1.23 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 395 TYR 0.015 0.002 TYR B 345 PHE 0.019 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 covalent geometry : bond 0.00494 ( 8011) covalent geometry : angle 0.55348 (10826) SS BOND : bond 0.00298 ( 25) SS BOND : angle 0.94038 ( 50) hydrogen bonds : bond 0.04160 ( 220) hydrogen bonds : angle 5.48805 ( 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 96 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 393 LYS cc_start: 0.6703 (ttpt) cc_final: 0.6486 (ptpp) REVERT: A 405 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7118 (m-30) REVERT: A 661 MET cc_start: 0.6744 (tpp) cc_final: 0.6306 (tpp) REVERT: B 225 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7035 (pp20) outliers start: 23 outliers final: 16 residues processed: 89 average time/residue: 0.5203 time to fit residues: 49.6734 Evaluate side-chains 89 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 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 198 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 84 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.195261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.119436 restraints weight = 7394.223| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.96 r_work: 0.3156 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1565 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= 0.138 Angle : 0.506 9.896 10876 Z= 0.272 Chirality : 0.044 0.161 1187 Planarity : 0.003 0.068 1394 Dihedral : 4.511 38.822 1061 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.49 % Allowed : 15.27 % 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 aren not related in a simple way. whole: -1.00 (0.25), residues: 985 helix: 1.25 (0.46), residues: 126 sheet: -0.45 (0.31), residues: 258 loop : -1.21 (0.24), residues: 601 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 0.018 0.001 PHE B 346 TRP 0.007 0.001 TRP B 362 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8011) covalent geometry : angle 0.50386 (10826) SS BOND : bond 0.00220 ( 25) SS BOND : angle 0.79330 ( 50) hydrogen bonds : bond 0.03574 ( 220) hydrogen bonds : angle 5.31621 ( 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 94 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 393 LYS cc_start: 0.6617 (ttpt) cc_final: 0.6393 (ptpp) REVERT: A 405 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.7073 (m-30) REVERT: A 417 CYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8050 (m) REVERT: A 661 MET cc_start: 0.6759 (tpp) cc_final: 0.6316 (tpp) REVERT: B 225 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7036 (pp20) REVERT: D 123 GLU cc_start: 0.8365 (pt0) cc_final: 0.8150 (pt0) outliers start: 22 outliers final: 18 residues processed: 86 average time/residue: 0.4893 time to fit residues: 45.4043 Evaluate side-chains 91 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 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 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 198 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 63 optimal weight: 0.0470 chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 overall best weight: 1.2880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.195401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120127 restraints weight = 7388.561| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.92 r_work: 0.3161 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1595 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= 0.136 Angle : 0.502 9.860 10876 Z= 0.269 Chirality : 0.044 0.164 1187 Planarity : 0.003 0.066 1394 Dihedral : 4.467 39.007 1061 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.04 % Allowed : 15.61 % Favored : 82.35 % 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 aren not related in a simple way. whole: -0.99 (0.25), residues: 985 helix: 1.26 (0.46), residues: 126 sheet: -0.45 (0.31), residues: 258 loop : -1.20 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 171 TYR 0.014 0.001 TYR B 345 PHE 0.017 0.001 PHE B 346 TRP 0.007 0.001 TRP B 362 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8011) covalent geometry : angle 0.50004 (10826) SS BOND : bond 0.00216 ( 25) SS BOND : angle 0.77322 ( 50) hydrogen bonds : bond 0.03538 ( 220) hydrogen bonds : angle 5.26886 ( 588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3080.35 seconds wall clock time: 53 minutes 14.25 seconds (3194.25 seconds total)