Starting phenix.real_space_refine on Fri Jul 25 14:56:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kzc_62659/07_2025/9kzc_62659.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kzc_62659/07_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_62659/07_2025/9kzc_62659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kzc_62659/07_2025/9kzc_62659.map" model { file = "/net/cci-nas-00/data/ceres_data/9kzc_62659/07_2025/9kzc_62659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kzc_62659/07_2025/9kzc_62659.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.058 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.99, per 1000 atoms: 0.64 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: 1.96 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.93 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: 2.98 Time building geometry restraints manager: 2.35 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: 1.090 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.080 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP D 183 HIS 0.012 0.001 HIS B 374 PHE 0.015 0.001 PHE B 346 TYR 0.012 0.001 TYR B 345 ARG 0.002 0.000 ARG B 273 Details of bonding type rmsd hydrogen bonds : bond 0.20098 ( 220) hydrogen bonds : angle 7.92877 ( 588) SS BOND : bond 0.00183 ( 25) SS BOND : angle 0.88213 ( 50) covalent geometry : bond 0.00233 ( 8011) covalent geometry : angle 0.47438 (10826) *********************** 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 : 0.908 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 1.2236 time to fit residues: 127.6774 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 : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.0060 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.190918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.116223 restraints weight = 7233.816| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.05 r_work: 0.3022 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 8036 Z= 0.301 Angle : 0.637 11.763 10876 Z= 0.343 Chirality : 0.050 0.211 1187 Planarity : 0.004 0.066 1394 Dihedral : 5.060 41.321 1061 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.04 % Allowed : 9.50 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 985 helix: 0.83 (0.45), residues: 124 sheet: -0.30 (0.31), residues: 258 loop : -1.40 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 413 HIS 0.009 0.001 HIS B 374 PHE 0.023 0.002 PHE B 346 TYR 0.018 0.002 TYR A 602 ARG 0.007 0.001 ARG B 395 Details of bonding type rmsd hydrogen bonds : bond 0.05458 ( 220) hydrogen bonds : angle 6.17384 ( 588) SS BOND : bond 0.00399 ( 25) SS BOND : angle 1.02244 ( 50) covalent geometry : bond 0.00725 ( 8011) covalent geometry : angle 0.63516 (10826) *********************** 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: 18 poor density : 79 time to evaluate : 0.845 Fit side-chains REVERT: A 405 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.7040 (m-30) REVERT: A 661 MET cc_start: 0.6853 (tpp) cc_final: 0.6534 (tpp) outliers start: 18 outliers final: 10 residues processed: 89 average time/residue: 1.1489 time to fit residues: 109.4534 Evaluate side-chains 81 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain D residue 129 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.196805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122052 restraints weight = 7473.673| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.93 r_work: 0.3164 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1186 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= 0.116 Angle : 0.483 8.782 10876 Z= 0.263 Chirality : 0.044 0.147 1187 Planarity : 0.003 0.069 1394 Dihedral : 4.551 38.093 1061 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.92 % Allowed : 12.10 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 985 helix: 1.08 (0.46), residues: 125 sheet: -0.40 (0.31), residues: 256 loop : -1.34 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 183 HIS 0.003 0.001 HIS B 374 PHE 0.017 0.001 PHE B 346 TYR 0.013 0.001 TYR B 345 ARG 0.004 0.000 ARG B 533 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 220) hydrogen bonds : angle 5.65878 ( 588) SS BOND : bond 0.00179 ( 25) SS BOND : angle 0.58562 ( 50) covalent geometry : bond 0.00260 ( 8011) covalent geometry : angle 0.48252 (10826) *********************** 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 96 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6986 (m-30) REVERT: A 661 MET cc_start: 0.7031 (tpp) cc_final: 0.6575 (tpp) REVERT: B 292 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8247 (mt-10) outliers start: 17 outliers final: 8 residues processed: 89 average time/residue: 1.0997 time to fit residues: 104.7538 Evaluate side-chains 85 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 289 ILE Chi-restraints excluded: chain B residue 292 GLU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 40.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 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 = 0.4107 r_free = 0.4107 target = 0.194004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118189 restraints weight = 7354.548| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.93 r_work: 0.3116 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8036 Z= 0.233 Angle : 0.576 11.736 10876 Z= 0.306 Chirality : 0.047 0.182 1187 Planarity : 0.004 0.066 1394 Dihedral : 4.853 40.882 1061 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.94 % Allowed : 13.24 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 985 helix: 0.96 (0.45), residues: 125 sheet: -0.49 (0.30), residues: 259 loop : -1.36 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 413 HIS 0.005 0.001 HIS B 374 PHE 0.020 0.002 PHE B 346 TYR 0.015 0.002 TYR B 345 ARG 0.003 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 220) hydrogen bonds : angle 5.78168 ( 588) SS BOND : bond 0.00305 ( 25) SS BOND : angle 1.01466 ( 50) covalent geometry : bond 0.00557 ( 8011) covalent geometry : angle 0.57295 (10826) *********************** 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 102 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: A 661 MET cc_start: 0.6983 (tpp) cc_final: 0.6606 (tpp) REVERT: B 225 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7146 (pp20) outliers start: 26 outliers final: 16 residues processed: 95 average time/residue: 0.9928 time to fit residues: 101.6182 Evaluate side-chains 90 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 491 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 49 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.194443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118628 restraints weight = 7355.418| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.96 r_work: 0.3140 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1432 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= 0.160 Angle : 0.521 10.471 10876 Z= 0.280 Chirality : 0.045 0.160 1187 Planarity : 0.003 0.070 1394 Dihedral : 4.699 39.790 1061 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.05 % Allowed : 13.57 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.25), residues: 985 helix: 1.01 (0.46), residues: 126 sheet: -0.52 (0.31), residues: 257 loop : -1.32 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 183 HIS 0.004 0.001 HIS B 374 PHE 0.018 0.002 PHE B 346 TYR 0.014 0.001 TYR B 345 ARG 0.002 0.000 ARG D 171 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 220) hydrogen bonds : angle 5.60654 ( 588) SS BOND : bond 0.00235 ( 25) SS BOND : angle 0.73012 ( 50) covalent geometry : bond 0.00375 ( 8011) covalent geometry : angle 0.51955 (10826) *********************** 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 102 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.7074 (m-30) REVERT: B 225 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.6972 (pp20) outliers start: 27 outliers final: 19 residues processed: 95 average time/residue: 1.0182 time to fit residues: 103.9088 Evaluate side-chains 94 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 284 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 90 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 83 optimal weight: 0.0030 chunk 92 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.193677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117556 restraints weight = 7317.886| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.95 r_work: 0.3128 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1534 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= 0.197 Angle : 0.549 11.255 10876 Z= 0.293 Chirality : 0.046 0.166 1187 Planarity : 0.004 0.068 1394 Dihedral : 4.796 40.922 1061 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.28 % Allowed : 14.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 985 helix: 0.98 (0.45), residues: 126 sheet: -0.55 (0.30), residues: 257 loop : -1.31 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.004 0.001 HIS B 374 PHE 0.019 0.002 PHE B 346 TYR 0.015 0.002 TYR B 345 ARG 0.002 0.000 ARG D 171 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 220) hydrogen bonds : angle 5.63578 ( 588) SS BOND : bond 0.00259 ( 25) SS BOND : angle 0.78388 ( 50) covalent geometry : bond 0.00467 ( 8011) covalent geometry : angle 0.54765 (10826) *********************** 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 102 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 417 CYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8052 (m) REVERT: A 446 GLU cc_start: 0.6374 (mp0) cc_final: 0.6089 (mp0) REVERT: B 225 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7093 (pp20) outliers start: 29 outliers final: 18 residues processed: 96 average time/residue: 1.4414 time to fit residues: 147.9900 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 : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LYS 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 0.0470 chunk 13 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.196726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130127 restraints weight = 7403.135| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.87 r_work: 0.3214 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1501 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= 0.106 Angle : 0.480 9.239 10876 Z= 0.259 Chirality : 0.044 0.162 1187 Planarity : 0.003 0.070 1394 Dihedral : 4.456 39.031 1061 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.38 % Allowed : 16.29 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 985 helix: 1.23 (0.46), residues: 125 sheet: -0.47 (0.31), residues: 255 loop : -1.24 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 183 HIS 0.003 0.001 HIS B 374 PHE 0.015 0.001 PHE B 346 TYR 0.012 0.001 TYR B 345 ARG 0.002 0.000 ARG D 171 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 220) hydrogen bonds : angle 5.31993 ( 588) SS BOND : bond 0.00182 ( 25) SS BOND : angle 0.92667 ( 50) covalent geometry : bond 0.00240 ( 8011) covalent geometry : angle 0.47709 (10826) *********************** 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 98 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.833 Fit side-chains REVERT: A 417 CYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7825 (m) REVERT: A 513 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8313 (ttp80) REVERT: B 225 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.6868 (pp20) outliers start: 21 outliers final: 13 residues processed: 93 average time/residue: 0.9993 time to fit residues: 99.8860 Evaluate side-chains 92 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 410 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 545 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 97 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.195393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119959 restraints weight = 7385.799| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.95 r_work: 0.3157 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8036 Z= 0.134 Angle : 0.499 10.255 10876 Z= 0.268 Chirality : 0.044 0.162 1187 Planarity : 0.003 0.067 1394 Dihedral : 4.504 39.811 1061 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.38 % Allowed : 16.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.25), residues: 985 helix: 1.20 (0.46), residues: 126 sheet: -0.42 (0.31), residues: 256 loop : -1.21 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 362 HIS 0.003 0.001 HIS B 374 PHE 0.017 0.001 PHE B 346 TYR 0.014 0.001 TYR B 345 ARG 0.003 0.000 ARG D 171 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 220) hydrogen bonds : angle 5.31139 ( 588) SS BOND : bond 0.00196 ( 25) SS BOND : angle 0.83434 ( 50) covalent geometry : bond 0.00315 ( 8011) covalent geometry : angle 0.49691 (10826) *********************** 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 96 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.909 Fit side-chains REVERT: A 417 CYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8047 (m) REVERT: B 225 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.6966 (pp20) REVERT: D 123 GLU cc_start: 0.8295 (pt0) cc_final: 0.8081 (pt0) outliers start: 21 outliers final: 16 residues processed: 90 average time/residue: 1.1159 time to fit residues: 108.2480 Evaluate side-chains 91 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 289 ILE Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 387 ILE 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 466 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 0.0670 chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 overall best weight: 1.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 254 GLN ** 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 = 0.4117 r_free = 0.4117 target = 0.194940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.118944 restraints weight = 7500.287| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.97 r_work: 0.3144 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8036 Z= 0.155 Angle : 0.518 10.571 10876 Z= 0.279 Chirality : 0.045 0.165 1187 Planarity : 0.004 0.068 1394 Dihedral : 4.585 40.136 1061 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.71 % Allowed : 16.52 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 985 helix: 1.19 (0.46), residues: 126 sheet: -0.48 (0.31), residues: 259 loop : -1.23 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 398 HIS 0.004 0.001 HIS B 374 PHE 0.018 0.001 PHE B 346 TYR 0.014 0.001 TYR B 345 ARG 0.012 0.000 ARG A 513 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 220) hydrogen bonds : angle 5.35784 ( 588) SS BOND : bond 0.00207 ( 25) SS BOND : angle 0.80957 ( 50) covalent geometry : bond 0.00369 ( 8011) covalent geometry : angle 0.51659 (10826) *********************** 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 97 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.907 Fit side-chains REVERT: A 417 CYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8078 (m) REVERT: B 225 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.6965 (pp20) outliers start: 24 outliers final: 21 residues processed: 91 average time/residue: 1.1569 time to fit residues: 114.1889 Evaluate side-chains 94 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 2.578 ------------------------------------------------------------------------------- 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 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 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 387 ILE 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 466 GLN 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 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 55 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** B 254 GLN ** 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 = 0.4124 r_free = 0.4124 target = 0.195663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.125255 restraints weight = 7415.843| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.10 r_work: 0.3157 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8036 Z= 0.124 Angle : 0.496 9.596 10876 Z= 0.267 Chirality : 0.044 0.162 1187 Planarity : 0.003 0.068 1394 Dihedral : 4.475 39.466 1061 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.60 % Allowed : 16.86 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 985 helix: 1.22 (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 TRP 0.014 0.001 TRP A 398 HIS 0.003 0.001 HIS B 374 PHE 0.017 0.001 PHE B 346 TYR 0.013 0.001 TYR B 345 ARG 0.009 0.000 ARG A 513 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 220) hydrogen bonds : angle 5.26551 ( 588) SS BOND : bond 0.00172 ( 25) SS BOND : angle 0.76966 ( 50) covalent geometry : bond 0.00291 ( 8011) covalent geometry : angle 0.49389 (10826) ********************** 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 97 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.916 Fit side-chains REVERT: A 417 CYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8064 (m) REVERT: B 225 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7004 (pp20) outliers start: 23 outliers final: 19 residues processed: 93 average time/residue: 0.9720 time to fit residues: 98.3765 Evaluate side-chains 92 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 387 ILE 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 466 GLN 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 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 20 optimal weight: 0.0010 chunk 97 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 0.0020 chunk 63 optimal weight: 0.5980 chunk 24 optimal weight: 30.0000 overall best weight: 1.3198 ------------------------------------------------------------------------------- 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** ** B 254 GLN ** 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 = 0.4121 r_free = 0.4121 target = 0.195375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119546 restraints weight = 7398.254| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.28 r_work: 0.3127 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8036 Z= 0.139 Angle : 0.512 10.398 10876 Z= 0.276 Chirality : 0.044 0.164 1187 Planarity : 0.004 0.068 1394 Dihedral : 4.509 39.981 1061 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.49 % Allowed : 16.97 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 985 helix: 1.21 (0.46), residues: 126 sheet: -0.47 (0.31), residues: 258 loop : -1.21 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 398 HIS 0.003 0.001 HIS B 374 PHE 0.017 0.001 PHE B 346 TYR 0.014 0.001 TYR B 345 ARG 0.009 0.000 ARG A 513 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 220) hydrogen bonds : angle 5.29013 ( 588) SS BOND : bond 0.00180 ( 25) SS BOND : angle 0.75663 ( 50) covalent geometry : bond 0.00329 ( 8011) covalent geometry : angle 0.51075 (10826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6883.25 seconds wall clock time: 122 minutes 24.58 seconds (7344.58 seconds total)