Starting phenix.real_space_refine on Fri Aug 22 21:36:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozm_17314/08_2025/8ozm_17314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozm_17314/08_2025/8ozm_17314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ozm_17314/08_2025/8ozm_17314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozm_17314/08_2025/8ozm_17314.map" model { file = "/net/cci-nas-00/data/ceres_data/8ozm_17314/08_2025/8ozm_17314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozm_17314/08_2025/8ozm_17314.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 5088 2.51 5 N 1452 2.21 5 O 1482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8052 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "C" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "D" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "E" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "F" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "G" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Time building chain proxies: 1.72, per 1000 atoms: 0.21 Number of scatterers: 8052 At special positions: 0 Unit cell: (117.72, 124.2, 84.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1482 8.00 N 1452 7.00 C 5088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.39 Conformation dependent library (CDL) restraints added in 310.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.836A pdb=" N SER B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 314 " --> pdb=" O ILE B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 330 Processing helix chain 'B' and resid 331 through 339 removed outlier: 3.601A pdb=" N GLY B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.527A pdb=" N GLY B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 384 removed outlier: 3.755A pdb=" N THR B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 removed outlier: 3.694A pdb=" N HIS B 389 " --> pdb=" O PHE B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 390 through 402 removed outlier: 3.683A pdb=" N GLN B 401 " --> pdb=" O GLY B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 416 removed outlier: 3.531A pdb=" N THR B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 430 removed outlier: 3.803A pdb=" N GLY B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 429 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 444 removed outlier: 3.520A pdb=" N VAL B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 455 through 468 removed outlier: 3.532A pdb=" N LEU B 467 " --> pdb=" O VAL B 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 323 through 331 removed outlier: 3.778A pdb=" N GLY C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 339 removed outlier: 3.520A pdb=" N ILE C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 356 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 370 through 384 Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 390 through 402 removed outlier: 3.506A pdb=" N VAL C 394 " --> pdb=" O GLN C 390 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 418 through 427 Processing helix chain 'C' and resid 432 through 445 removed outlier: 3.523A pdb=" N VAL C 436 " --> pdb=" O GLY C 432 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 455 through 467 Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.627A pdb=" N ILE D 310 " --> pdb=" O PRO D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 323 through 331 removed outlier: 3.651A pdb=" N TRP D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 339 Processing helix chain 'D' and resid 343 through 356 removed outlier: 3.686A pdb=" N ARG D 347 " --> pdb=" O THR D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 370 through 384 removed outlier: 3.595A pdb=" N VAL D 375 " --> pdb=" O TRP D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 402 removed outlier: 3.511A pdb=" N ASP D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 removed outlier: 3.614A pdb=" N THR D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 427 removed outlier: 3.530A pdb=" N GLY D 424 " --> pdb=" O GLN D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 446 removed outlier: 3.644A pdb=" N VAL D 436 " --> pdb=" O GLY D 432 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU D 446 " --> pdb=" O ARG D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 Processing helix chain 'D' and resid 455 through 467 removed outlier: 3.618A pdb=" N HIS D 459 " --> pdb=" O THR D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.542A pdb=" N VAL E 313 " --> pdb=" O HIS E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 323 through 339 removed outlier: 3.567A pdb=" N TRP E 327 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Proline residue: E 333 - end of helix Processing helix chain 'E' and resid 343 through 356 Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 370 through 384 removed outlier: 3.650A pdb=" N THR E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 403 removed outlier: 3.770A pdb=" N ASN E 393 " --> pdb=" O HIS E 389 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN E 401 " --> pdb=" O GLY E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 415 removed outlier: 3.563A pdb=" N ALA E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER E 415 " --> pdb=" O GLY E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 428 removed outlier: 4.126A pdb=" N GLY E 428 " --> pdb=" O GLY E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 445 removed outlier: 3.703A pdb=" N VAL E 436 " --> pdb=" O GLY E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 455 Processing helix chain 'E' and resid 455 through 468 Processing helix chain 'F' and resid 306 through 315 removed outlier: 3.582A pdb=" N ILE F 310 " --> pdb=" O PRO F 306 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER F 312 " --> pdb=" O GLN F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 339 removed outlier: 3.717A pdb=" N GLY F 329 " --> pdb=" O PRO F 325 " (cutoff:3.500A) Proline residue: F 333 - end of helix removed outlier: 3.579A pdb=" N GLY F 337 " --> pdb=" O PRO F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 356 Processing helix chain 'F' and resid 370 through 384 Processing helix chain 'F' and resid 386 through 389 Processing helix chain 'F' and resid 390 through 400 removed outlier: 3.870A pdb=" N GLY F 397 " --> pdb=" O ASN F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 416 Processing helix chain 'F' and resid 418 through 427 Processing helix chain 'F' and resid 428 through 430 No H-bonds generated for 'chain 'F' and resid 428 through 430' Processing helix chain 'F' and resid 432 through 446 removed outlier: 3.747A pdb=" N ARG F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP F 444 " --> pdb=" O GLN F 440 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 468 removed outlier: 5.801A pdb=" N ILE F 457 " --> pdb=" O ALA F 453 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLN F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA F 462 " --> pdb=" O GLN F 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 Processing helix chain 'G' and resid 323 through 331 removed outlier: 3.553A pdb=" N GLY G 329 " --> pdb=" O PRO G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 339 Processing helix chain 'G' and resid 343 through 355 Processing helix chain 'G' and resid 358 through 362 removed outlier: 3.792A pdb=" N SER G 362 " --> pdb=" O ILE G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 384 Processing helix chain 'G' and resid 387 through 389 No H-bonds generated for 'chain 'G' and resid 387 through 389' Processing helix chain 'G' and resid 390 through 402 removed outlier: 3.504A pdb=" N GLY G 397 " --> pdb=" O ASN G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 415 Processing helix chain 'G' and resid 418 through 429 removed outlier: 3.902A pdb=" N VAL G 422 " --> pdb=" O ASN G 418 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY G 428 " --> pdb=" O GLY G 424 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR G 429 " --> pdb=" O ILE G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 445 removed outlier: 3.560A pdb=" N VAL G 436 " --> pdb=" O GLY G 432 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 468 removed outlier: 3.506A pdb=" N GLU G 454 " --> pdb=" O GLN G 450 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE G 457 " --> pdb=" O ALA G 453 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLN G 458 " --> pdb=" O GLU G 454 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1413 1.32 - 1.45: 2011 1.45 - 1.59: 4736 1.59 - 1.72: 0 1.72 - 1.86: 48 Bond restraints: 8208 Sorted by residual: bond pdb=" N ILE G 305 " pdb=" CA ILE G 305 " ideal model delta sigma weight residual 1.460 1.497 -0.036 7.30e-03 1.88e+04 2.48e+01 bond pdb=" N PHE E 386 " pdb=" CA PHE E 386 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.40e-03 1.83e+04 2.23e+01 bond pdb=" N MET E 413 " pdb=" CA MET E 413 " ideal model delta sigma weight residual 1.459 1.510 -0.052 1.16e-02 7.43e+03 1.98e+01 bond pdb=" C ASP C 345 " pdb=" O ASP C 345 " ideal model delta sigma weight residual 1.236 1.287 -0.051 1.16e-02 7.43e+03 1.92e+01 bond pdb=" N VAL B 404 " pdb=" CA VAL B 404 " ideal model delta sigma weight residual 1.460 1.509 -0.049 1.19e-02 7.06e+03 1.72e+01 ... (remaining 8203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 9118 2.57 - 5.15: 1972 5.15 - 7.72: 102 7.72 - 10.29: 3 10.29 - 12.86: 1 Bond angle restraints: 11196 Sorted by residual: angle pdb=" CA GLY G 384 " pdb=" C GLY G 384 " pdb=" O GLY G 384 " ideal model delta sigma weight residual 122.22 118.38 3.84 6.50e-01 2.37e+00 3.48e+01 angle pdb=" CG ARG E 381 " pdb=" CD ARG E 381 " pdb=" NE ARG E 381 " ideal model delta sigma weight residual 112.00 99.14 12.86 2.20e+00 2.07e-01 3.42e+01 angle pdb=" C ILE C 359 " pdb=" N GLY C 360 " pdb=" CA GLY C 360 " ideal model delta sigma weight residual 119.99 126.46 -6.47 1.13e+00 7.83e-01 3.28e+01 angle pdb=" N PRO F 431 " pdb=" CA PRO F 431 " pdb=" CB PRO F 431 " ideal model delta sigma weight residual 102.28 98.07 4.21 7.50e-01 1.78e+00 3.15e+01 angle pdb=" N ILE D 351 " pdb=" CA ILE D 351 " pdb=" C ILE D 351 " ideal model delta sigma weight residual 110.30 104.88 5.42 9.70e-01 1.06e+00 3.13e+01 ... (remaining 11191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.60: 4243 15.60 - 31.20: 507 31.20 - 46.81: 108 46.81 - 62.41: 37 62.41 - 78.01: 13 Dihedral angle restraints: 4908 sinusoidal: 1956 harmonic: 2952 Sorted by residual: dihedral pdb=" CA LEU F 355 " pdb=" C LEU F 355 " pdb=" N GLY F 356 " pdb=" CA GLY F 356 " ideal model delta harmonic sigma weight residual 180.00 153.27 26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA GLU D 446 " pdb=" C GLU D 446 " pdb=" N ILE D 447 " pdb=" CA ILE D 447 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA PRO E 387 " pdb=" C PRO E 387 " pdb=" N MET E 388 " pdb=" CA MET E 388 " ideal model delta harmonic sigma weight residual -180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 4905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 609 0.060 - 0.120: 464 0.120 - 0.179: 188 0.179 - 0.239: 39 0.239 - 0.299: 14 Chirality restraints: 1314 Sorted by residual: chirality pdb=" CB VAL G 399 " pdb=" CA VAL G 399 " pdb=" CG1 VAL G 399 " pdb=" CG2 VAL G 399 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA VAL G 341 " pdb=" N VAL G 341 " pdb=" C VAL G 341 " pdb=" CB VAL G 341 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB VAL B 338 " pdb=" CA VAL B 338 " pdb=" CG1 VAL B 338 " pdb=" CG2 VAL B 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1311 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 408 " 0.044 2.00e-02 2.50e+03 2.28e-02 1.04e+01 pdb=" CG TYR F 408 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR F 408 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR F 408 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR F 408 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR F 408 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 408 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR F 408 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 390 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C GLN B 390 " -0.047 2.00e-02 2.50e+03 pdb=" O GLN B 390 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU B 391 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 408 " 0.009 2.00e-02 2.50e+03 1.87e-02 7.02e+00 pdb=" CG TYR D 408 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR D 408 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 408 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR D 408 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR D 408 " -0.024 2.00e-02 2.50e+03 pdb=" CZ TYR D 408 " -0.025 2.00e-02 2.50e+03 pdb=" OH TYR D 408 " 0.033 2.00e-02 2.50e+03 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 2485 2.89 - 3.39: 8040 3.39 - 3.89: 12633 3.89 - 4.40: 14552 4.40 - 4.90: 23656 Nonbonded interactions: 61366 Sorted by model distance: nonbonded pdb=" NE2 GLN F 440 " pdb=" OD1 ASP F 444 " model vdw 2.384 3.120 nonbonded pdb=" O HIS E 309 " pdb=" OG SER E 312 " model vdw 2.392 3.040 nonbonded pdb=" O HIS G 309 " pdb=" OG SER G 312 " model vdw 2.421 3.040 nonbonded pdb=" NH1 ARG E 311 " pdb=" OE2 GLU E 316 " model vdw 2.466 3.120 nonbonded pdb=" O GLN F 390 " pdb=" N ASN F 393 " model vdw 2.472 3.120 ... (remaining 61361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.320 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 : 0.015 0.060 8208 Z= 1.079 Angle : 1.933 12.862 11196 Z= 1.440 Chirality : 0.091 0.299 1314 Planarity : 0.006 0.043 1470 Dihedral : 15.029 78.012 3024 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.75 (0.19), residues: 1038 helix: -2.96 (0.14), residues: 710 sheet: None (None), residues: 0 loop : -3.15 (0.27), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.002 ARG E 311 TYR 0.044 0.010 TYR F 408 PHE 0.031 0.007 PHE E 386 TRP 0.026 0.008 TRP E 327 HIS 0.017 0.004 HIS F 389 Details of bonding type rmsd covalent geometry : bond 0.01457 ( 8208) covalent geometry : angle 1.93321 (11196) hydrogen bonds : bond 0.31039 ( 468) hydrogen bonds : angle 9.85646 ( 1380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.278 Fit side-chains REVERT: B 358 ASN cc_start: 0.6732 (m-40) cc_final: 0.6232 (m110) REVERT: B 381 ARG cc_start: 0.7513 (mtt180) cc_final: 0.7298 (mmt90) REVERT: B 472 ARG cc_start: 0.7974 (ttt180) cc_final: 0.7769 (ttm-80) REVERT: C 319 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7468 (mtm180) REVERT: C 322 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6933 (mmm-85) REVERT: D 429 TYR cc_start: 0.8357 (m-80) cc_final: 0.8143 (m-80) REVERT: D 450 GLN cc_start: 0.7588 (mt0) cc_final: 0.7373 (tp40) REVERT: E 308 GLN cc_start: 0.7610 (tt0) cc_final: 0.7060 (tt0) REVERT: E 415 SER cc_start: 0.8333 (t) cc_final: 0.7980 (t) REVERT: E 450 GLN cc_start: 0.7137 (tt0) cc_final: 0.6857 (tp-100) REVERT: F 402 GLU cc_start: 0.8044 (mp0) cc_final: 0.7693 (mm-30) REVERT: G 319 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.8013 (mtm180) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1126 time to fit residues: 23.8686 Evaluate side-chains 134 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN B 440 GLN B 441 GLN B 470 ASN C 440 GLN C 441 GLN D 440 GLN D 461 ASN F 389 HIS G 308 GLN G 441 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.097356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.083506 restraints weight = 11088.467| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.60 r_work: 0.2600 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8208 Z= 0.151 Angle : 0.645 5.894 11196 Z= 0.335 Chirality : 0.042 0.200 1314 Planarity : 0.005 0.041 1470 Dihedral : 4.836 19.626 1140 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.38 % Allowed : 10.46 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.24), residues: 1038 helix: -0.17 (0.18), residues: 752 sheet: None (None), residues: 0 loop : -2.05 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 322 TYR 0.009 0.001 TYR C 464 PHE 0.009 0.001 PHE E 379 TRP 0.013 0.001 TRP F 327 HIS 0.007 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8208) covalent geometry : angle 0.64497 (11196) hydrogen bonds : bond 0.05817 ( 468) hydrogen bonds : angle 5.00620 ( 1380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.278 Fit side-chains REVERT: B 358 ASN cc_start: 0.8034 (m-40) cc_final: 0.7653 (m-40) REVERT: C 319 ARG cc_start: 0.7853 (mtt180) cc_final: 0.7455 (mtm180) REVERT: C 322 ARG cc_start: 0.8642 (mtt180) cc_final: 0.8344 (mmm-85) REVERT: C 440 GLN cc_start: 0.8533 (tp40) cc_final: 0.8261 (tp40) REVERT: C 441 GLN cc_start: 0.8215 (mt0) cc_final: 0.8000 (tp40) REVERT: D 429 TYR cc_start: 0.9086 (m-80) cc_final: 0.8882 (m-80) REVERT: E 401 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7928 (mm110) REVERT: F 402 GLU cc_start: 0.8563 (mp0) cc_final: 0.8144 (mm-30) REVERT: F 412 MET cc_start: 0.9029 (mmm) cc_final: 0.8762 (mmt) REVERT: G 319 ARG cc_start: 0.8505 (mtt-85) cc_final: 0.8199 (mtm180) outliers start: 12 outliers final: 7 residues processed: 147 average time/residue: 0.0917 time to fit residues: 17.7814 Evaluate side-chains 121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain F residue 364 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 0.0050 chunk 83 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 441 GLN F 440 GLN G 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.098435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.085174 restraints weight = 11029.978| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 1.52 r_work: 0.2627 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8208 Z= 0.120 Angle : 0.529 5.607 11196 Z= 0.269 Chirality : 0.040 0.153 1314 Planarity : 0.004 0.035 1470 Dihedral : 4.092 19.608 1140 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.30 % Allowed : 11.15 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.26), residues: 1038 helix: 1.07 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 472 TYR 0.007 0.001 TYR C 464 PHE 0.005 0.001 PHE F 339 TRP 0.010 0.001 TRP D 327 HIS 0.004 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8208) covalent geometry : angle 0.52909 (11196) hydrogen bonds : bond 0.04511 ( 468) hydrogen bonds : angle 4.30537 ( 1380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.302 Fit side-chains REVERT: B 358 ASN cc_start: 0.7910 (m-40) cc_final: 0.7528 (m-40) REVERT: B 420 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8047 (mp10) REVERT: C 319 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7502 (mtm180) REVERT: C 322 ARG cc_start: 0.8736 (mtt180) cc_final: 0.8422 (mmm-85) REVERT: D 312 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8634 (p) REVERT: D 447 ILE cc_start: 0.8489 (tp) cc_final: 0.8268 (tp) REVERT: E 441 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8358 (tm130) REVERT: F 402 GLU cc_start: 0.8467 (mp0) cc_final: 0.8140 (mm-30) REVERT: F 412 MET cc_start: 0.9018 (mmm) cc_final: 0.8704 (mmt) REVERT: G 319 ARG cc_start: 0.8426 (mtt-85) cc_final: 0.8216 (mtm180) REVERT: G 465 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8434 (mt-10) outliers start: 20 outliers final: 9 residues processed: 137 average time/residue: 0.0869 time to fit residues: 15.9150 Evaluate side-chains 114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain G residue 423 SER Chi-restraints excluded: chain G residue 465 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 401 GLN E 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.099423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.086071 restraints weight = 11245.634| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.56 r_work: 0.2642 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8208 Z= 0.107 Angle : 0.502 5.724 11196 Z= 0.252 Chirality : 0.039 0.149 1314 Planarity : 0.004 0.037 1470 Dihedral : 3.792 13.378 1140 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.76 % Allowed : 11.26 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.26), residues: 1038 helix: 1.40 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -1.41 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 472 TYR 0.007 0.001 TYR D 464 PHE 0.004 0.001 PHE F 456 TRP 0.009 0.001 TRP D 327 HIS 0.005 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8208) covalent geometry : angle 0.50159 (11196) hydrogen bonds : bond 0.03997 ( 468) hydrogen bonds : angle 4.10256 ( 1380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.289 Fit side-chains REVERT: B 358 ASN cc_start: 0.7851 (m-40) cc_final: 0.7427 (m-40) REVERT: C 319 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7525 (mtm180) REVERT: C 322 ARG cc_start: 0.8755 (mtt180) cc_final: 0.8372 (mmm-85) REVERT: E 441 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8508 (tm130) REVERT: F 402 GLU cc_start: 0.8450 (mp0) cc_final: 0.8132 (mm-30) REVERT: F 412 MET cc_start: 0.9014 (mmm) cc_final: 0.8648 (mmt) REVERT: G 319 ARG cc_start: 0.8404 (mtt-85) cc_final: 0.8140 (mtm180) REVERT: G 450 GLN cc_start: 0.7508 (tp40) cc_final: 0.7226 (tp40) REVERT: G 465 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8293 (mt-10) outliers start: 24 outliers final: 15 residues processed: 121 average time/residue: 0.0786 time to fit residues: 12.9756 Evaluate side-chains 121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain G residue 423 SER Chi-restraints excluded: chain G residue 465 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 441 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.099351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.086044 restraints weight = 11201.117| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.53 r_work: 0.2643 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8208 Z= 0.110 Angle : 0.492 5.693 11196 Z= 0.246 Chirality : 0.040 0.183 1314 Planarity : 0.004 0.038 1470 Dihedral : 3.662 13.111 1140 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.53 % Allowed : 12.30 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.27), residues: 1038 helix: 1.63 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -1.22 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 472 TYR 0.009 0.001 TYR B 429 PHE 0.005 0.001 PHE F 339 TRP 0.008 0.001 TRP D 327 HIS 0.004 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8208) covalent geometry : angle 0.49160 (11196) hydrogen bonds : bond 0.03959 ( 468) hydrogen bonds : angle 4.00732 ( 1380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.202 Fit side-chains REVERT: B 319 ARG cc_start: 0.7411 (ptp-170) cc_final: 0.7097 (mtm-85) REVERT: B 358 ASN cc_start: 0.7788 (m-40) cc_final: 0.7331 (m-40) REVERT: C 319 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7464 (mtm180) REVERT: C 322 ARG cc_start: 0.8654 (mtt180) cc_final: 0.8323 (mmm-85) REVERT: E 441 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8508 (tm130) REVERT: F 402 GLU cc_start: 0.8426 (mp0) cc_final: 0.8114 (mm-30) REVERT: F 412 MET cc_start: 0.9024 (mmm) cc_final: 0.8657 (mmt) REVERT: G 319 ARG cc_start: 0.8411 (mtt-85) cc_final: 0.8137 (mtm180) REVERT: G 450 GLN cc_start: 0.7431 (tp40) cc_final: 0.7189 (tp40) outliers start: 22 outliers final: 14 residues processed: 118 average time/residue: 0.0825 time to fit residues: 12.9222 Evaluate side-chains 120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain G residue 423 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 HIS E 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.097133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.082928 restraints weight = 11199.967| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 1.72 r_work: 0.2591 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8208 Z= 0.141 Angle : 0.517 5.697 11196 Z= 0.261 Chirality : 0.040 0.156 1314 Planarity : 0.004 0.036 1470 Dihedral : 3.667 14.190 1140 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.07 % Allowed : 12.64 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.26), residues: 1038 helix: 1.65 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -1.22 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 472 TYR 0.007 0.001 TYR C 464 PHE 0.006 0.001 PHE F 339 TRP 0.009 0.001 TRP D 327 HIS 0.005 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8208) covalent geometry : angle 0.51748 (11196) hydrogen bonds : bond 0.04517 ( 468) hydrogen bonds : angle 4.03692 ( 1380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.184 Fit side-chains REVERT: B 319 ARG cc_start: 0.7426 (ptp-170) cc_final: 0.7089 (mtm-85) REVERT: B 358 ASN cc_start: 0.7675 (m-40) cc_final: 0.7106 (m-40) REVERT: B 401 GLN cc_start: 0.8670 (mt0) cc_final: 0.8455 (mt0) REVERT: C 319 ARG cc_start: 0.7926 (mtt180) cc_final: 0.7429 (mtm180) REVERT: C 322 ARG cc_start: 0.8636 (mtt180) cc_final: 0.8260 (mmm-85) REVERT: D 396 LYS cc_start: 0.8657 (tttt) cc_final: 0.8387 (tttp) REVERT: E 441 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8496 (tm130) REVERT: F 402 GLU cc_start: 0.8364 (mp0) cc_final: 0.8014 (mm-30) REVERT: F 412 MET cc_start: 0.9039 (mmm) cc_final: 0.8585 (mmt) REVERT: G 319 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.8110 (mtm180) REVERT: G 450 GLN cc_start: 0.7549 (tp40) cc_final: 0.7344 (tp40) outliers start: 18 outliers final: 16 residues processed: 117 average time/residue: 0.0879 time to fit residues: 13.4643 Evaluate side-chains 124 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain G residue 423 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 0.0470 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 441 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.098225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.083896 restraints weight = 11238.589| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 1.74 r_work: 0.2606 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8208 Z= 0.115 Angle : 0.491 5.604 11196 Z= 0.247 Chirality : 0.039 0.142 1314 Planarity : 0.004 0.034 1470 Dihedral : 3.584 14.082 1140 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.30 % Allowed : 12.99 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.26), residues: 1038 helix: 1.77 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -1.13 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 472 TYR 0.006 0.001 TYR D 464 PHE 0.005 0.001 PHE F 339 TRP 0.009 0.001 TRP F 327 HIS 0.004 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8208) covalent geometry : angle 0.49075 (11196) hydrogen bonds : bond 0.04046 ( 468) hydrogen bonds : angle 3.95442 ( 1380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.203 Fit side-chains REVERT: B 319 ARG cc_start: 0.7414 (ptp-170) cc_final: 0.7092 (mtm-85) REVERT: B 358 ASN cc_start: 0.7758 (m-40) cc_final: 0.7207 (m-40) REVERT: C 319 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7427 (mtm180) REVERT: C 322 ARG cc_start: 0.8638 (mtt180) cc_final: 0.8263 (mmm-85) REVERT: D 396 LYS cc_start: 0.8668 (tttt) cc_final: 0.8394 (tttp) REVERT: E 305 ILE cc_start: 0.8982 (mm) cc_final: 0.8703 (mt) REVERT: E 441 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8498 (tm130) REVERT: F 402 GLU cc_start: 0.8350 (mp0) cc_final: 0.8022 (mm-30) REVERT: F 412 MET cc_start: 0.9035 (mmm) cc_final: 0.8588 (mmt) REVERT: G 319 ARG cc_start: 0.8459 (mtt-85) cc_final: 0.8102 (mtm180) outliers start: 20 outliers final: 15 residues processed: 113 average time/residue: 0.0913 time to fit residues: 13.6017 Evaluate side-chains 120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain G residue 423 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 450 GLN E 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.098944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.084706 restraints weight = 11073.565| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 1.72 r_work: 0.2617 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8208 Z= 0.109 Angle : 0.480 5.557 11196 Z= 0.241 Chirality : 0.039 0.137 1314 Planarity : 0.004 0.034 1470 Dihedral : 3.521 13.714 1140 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.07 % Allowed : 13.45 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.27), residues: 1038 helix: 1.87 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -1.03 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 472 TYR 0.005 0.001 TYR C 464 PHE 0.005 0.001 PHE D 456 TRP 0.009 0.001 TRP F 327 HIS 0.004 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8208) covalent geometry : angle 0.48015 (11196) hydrogen bonds : bond 0.03885 ( 468) hydrogen bonds : angle 3.90622 ( 1380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.230 Fit side-chains REVERT: B 319 ARG cc_start: 0.7471 (ptp-170) cc_final: 0.7127 (mtm-85) REVERT: B 358 ASN cc_start: 0.7808 (m-40) cc_final: 0.7269 (m-40) REVERT: C 319 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7428 (mtm180) REVERT: C 322 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8320 (mmm-85) REVERT: D 396 LYS cc_start: 0.8665 (tttt) cc_final: 0.8388 (tttp) REVERT: E 305 ILE cc_start: 0.8946 (mm) cc_final: 0.8682 (mt) REVERT: E 441 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8408 (tm130) REVERT: F 402 GLU cc_start: 0.8342 (mp0) cc_final: 0.8066 (mm-30) REVERT: F 412 MET cc_start: 0.9035 (mmm) cc_final: 0.8583 (mmt) REVERT: G 319 ARG cc_start: 0.8457 (mtt-85) cc_final: 0.8102 (mtm180) outliers start: 18 outliers final: 17 residues processed: 111 average time/residue: 0.0824 time to fit residues: 12.3166 Evaluate side-chains 120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain G residue 423 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 441 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.098413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.084049 restraints weight = 11222.043| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.74 r_work: 0.2610 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8208 Z= 0.119 Angle : 0.487 5.402 11196 Z= 0.243 Chirality : 0.040 0.149 1314 Planarity : 0.004 0.033 1470 Dihedral : 3.514 14.121 1140 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.07 % Allowed : 13.68 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.26), residues: 1038 helix: 1.85 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -1.02 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 472 TYR 0.006 0.001 TYR C 464 PHE 0.005 0.001 PHE F 339 TRP 0.009 0.001 TRP F 327 HIS 0.004 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8208) covalent geometry : angle 0.48731 (11196) hydrogen bonds : bond 0.04053 ( 468) hydrogen bonds : angle 3.91745 ( 1380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.250 Fit side-chains REVERT: B 319 ARG cc_start: 0.7485 (ptp-170) cc_final: 0.7132 (mtm-85) REVERT: B 358 ASN cc_start: 0.7842 (m-40) cc_final: 0.7314 (m-40) REVERT: C 319 ARG cc_start: 0.7914 (mtt180) cc_final: 0.7426 (mtm180) REVERT: C 322 ARG cc_start: 0.8650 (mtt180) cc_final: 0.8345 (mmm-85) REVERT: D 396 LYS cc_start: 0.8623 (tttt) cc_final: 0.8354 (tttp) REVERT: E 441 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8421 (tm130) REVERT: F 402 GLU cc_start: 0.8307 (mp0) cc_final: 0.8032 (mm-30) REVERT: F 412 MET cc_start: 0.9077 (mmm) cc_final: 0.8513 (mmt) REVERT: G 319 ARG cc_start: 0.8446 (mtt-85) cc_final: 0.8092 (mtm180) outliers start: 18 outliers final: 17 residues processed: 108 average time/residue: 0.0918 time to fit residues: 12.9958 Evaluate side-chains 118 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain G residue 423 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 95 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 450 GLN E 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.100019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.085719 restraints weight = 11143.448| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 1.72 r_work: 0.2632 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8208 Z= 0.097 Angle : 0.467 5.488 11196 Z= 0.233 Chirality : 0.039 0.133 1314 Planarity : 0.004 0.033 1470 Dihedral : 3.431 13.381 1140 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.95 % Allowed : 13.79 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.27), residues: 1038 helix: 1.98 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.94 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 472 TYR 0.005 0.001 TYR D 464 PHE 0.005 0.001 PHE D 456 TRP 0.010 0.001 TRP F 327 HIS 0.004 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 8208) covalent geometry : angle 0.46691 (11196) hydrogen bonds : bond 0.03565 ( 468) hydrogen bonds : angle 3.83047 ( 1380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.251 Fit side-chains REVERT: B 319 ARG cc_start: 0.7407 (ptp-170) cc_final: 0.7100 (mtm180) REVERT: B 420 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7905 (mp10) REVERT: C 319 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7343 (mtm180) REVERT: C 322 ARG cc_start: 0.8660 (mtt180) cc_final: 0.8376 (mmm-85) REVERT: D 396 LYS cc_start: 0.8637 (tttt) cc_final: 0.8373 (tttp) REVERT: E 305 ILE cc_start: 0.8934 (mm) cc_final: 0.8678 (mt) REVERT: F 402 GLU cc_start: 0.8290 (mp0) cc_final: 0.8038 (mm-30) REVERT: F 412 MET cc_start: 0.9034 (mmm) cc_final: 0.8420 (mmt) REVERT: G 319 ARG cc_start: 0.8438 (mtt-85) cc_final: 0.8089 (mtm180) outliers start: 17 outliers final: 16 residues processed: 113 average time/residue: 0.0834 time to fit residues: 12.5731 Evaluate side-chains 117 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain G residue 423 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.098006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.084466 restraints weight = 11183.992| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 1.59 r_work: 0.2616 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8208 Z= 0.132 Angle : 0.497 5.647 11196 Z= 0.248 Chirality : 0.040 0.149 1314 Planarity : 0.004 0.033 1470 Dihedral : 3.506 14.769 1140 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.07 % Allowed : 14.14 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.26), residues: 1038 helix: 1.89 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -1.02 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 472 TYR 0.007 0.001 TYR C 464 PHE 0.006 0.001 PHE F 339 TRP 0.009 0.001 TRP F 327 HIS 0.005 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8208) covalent geometry : angle 0.49730 (11196) hydrogen bonds : bond 0.04308 ( 468) hydrogen bonds : angle 3.91209 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1604.78 seconds wall clock time: 28 minutes 3.37 seconds (1683.37 seconds total)