Starting phenix.real_space_refine on Fri Nov 15 02:36:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozm_17314/11_2024/8ozm_17314.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozm_17314/11_2024/8ozm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozm_17314/11_2024/8ozm_17314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozm_17314/11_2024/8ozm_17314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozm_17314/11_2024/8ozm_17314.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozm_17314/11_2024/8ozm_17314.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 5.85, per 1000 atoms: 0.73 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: 2.06 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.79 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: 2.12 Time building geometry restraints manager: 2.26 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: 0.00 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: 2.030 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.270 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.220 ------------------------------------------------------------------------------- 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= 0.964 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (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 TRP 0.026 0.008 TRP E 327 HIS 0.017 0.004 HIS F 389 PHE 0.031 0.007 PHE E 386 TYR 0.044 0.010 TYR F 408 ARG 0.042 0.002 ARG E 311 *********************** 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 : 0.962 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: 0.2721 time to fit residues: 57.6168 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 : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.0170 chunk 92 optimal weight: 0.5980 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2229 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= 0.195 Angle : 0.642 6.116 11196 Z= 0.333 Chirality : 0.042 0.204 1314 Planarity : 0.005 0.042 1470 Dihedral : 4.827 19.123 1140 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.49 % Allowed : 10.11 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1038 helix: -0.12 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -2.02 (0.31), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 327 HIS 0.007 0.001 HIS G 389 PHE 0.012 0.001 PHE E 379 TYR 0.010 0.001 TYR E 419 ARG 0.004 0.001 ARG E 322 *********************** 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 158 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.945 Fit side-chains REVERT: B 358 ASN cc_start: 0.6341 (m-40) cc_final: 0.6070 (m-40) REVERT: B 452 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7449 (mtt90) REVERT: C 319 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7402 (mtm180) REVERT: C 322 ARG cc_start: 0.7259 (mtt180) cc_final: 0.6986 (mmm-85) REVERT: C 440 GLN cc_start: 0.6736 (tp40) cc_final: 0.6442 (tp40) REVERT: C 441 GLN cc_start: 0.6732 (mt0) cc_final: 0.6494 (tp40) REVERT: D 429 TYR cc_start: 0.8248 (m-80) cc_final: 0.8044 (m-80) REVERT: D 450 GLN cc_start: 0.7157 (mt0) cc_final: 0.6957 (tp-100) REVERT: E 415 SER cc_start: 0.8182 (t) cc_final: 0.7767 (p) REVERT: E 417 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7362 (mm-40) REVERT: F 412 MET cc_start: 0.8068 (mmm) cc_final: 0.7506 (mmt) REVERT: G 319 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7948 (mtm180) REVERT: G 450 GLN cc_start: 0.6861 (tp40) cc_final: 0.6660 (tp40) outliers start: 13 outliers final: 6 residues processed: 152 average time/residue: 0.2704 time to fit residues: 52.1968 Evaluate side-chains 116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.0170 chunk 77 optimal weight: 0.0170 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 74 optimal weight: 0.0000 chunk 91 optimal weight: 3.9990 overall best weight: 0.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 441 GLN E 445 GLN F 440 GLN G 420 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8208 Z= 0.159 Angle : 0.515 5.769 11196 Z= 0.261 Chirality : 0.040 0.139 1314 Planarity : 0.004 0.036 1470 Dihedral : 4.001 17.066 1140 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.72 % Allowed : 12.18 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1038 helix: 1.18 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.49 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 327 HIS 0.004 0.001 HIS F 389 PHE 0.005 0.001 PHE E 339 TYR 0.008 0.001 TYR D 464 ARG 0.005 0.000 ARG C 452 *********************** 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 140 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.920 Fit side-chains REVERT: B 358 ASN cc_start: 0.6268 (m-40) cc_final: 0.5979 (m-40) REVERT: C 319 ARG cc_start: 0.7669 (mtt180) cc_final: 0.7376 (mtm180) REVERT: C 322 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6993 (mmm-85) REVERT: D 312 SER cc_start: 0.8019 (OUTLIER) cc_final: 0.7688 (p) REVERT: D 450 GLN cc_start: 0.7062 (mt0) cc_final: 0.6852 (tp-100) REVERT: E 415 SER cc_start: 0.8121 (t) cc_final: 0.7713 (p) REVERT: F 412 MET cc_start: 0.8044 (mmm) cc_final: 0.7453 (mmt) REVERT: G 319 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.7958 (mtm180) REVERT: G 450 GLN cc_start: 0.6840 (tp40) cc_final: 0.6604 (tp40) outliers start: 15 outliers final: 7 residues processed: 133 average time/residue: 0.2220 time to fit residues: 39.3476 Evaluate side-chains 110 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 312 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8208 Z= 0.176 Angle : 0.503 5.643 11196 Z= 0.252 Chirality : 0.040 0.151 1314 Planarity : 0.004 0.037 1470 Dihedral : 3.720 13.799 1140 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.64 % Allowed : 11.61 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 1038 helix: 1.50 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 327 HIS 0.005 0.001 HIS G 389 PHE 0.005 0.001 PHE B 456 TYR 0.006 0.001 TYR D 464 ARG 0.005 0.000 ARG G 472 *********************** 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 130 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.937 Fit side-chains REVERT: B 303 THR cc_start: 0.4839 (OUTLIER) cc_final: 0.4558 (t) REVERT: B 358 ASN cc_start: 0.6120 (m-40) cc_final: 0.5800 (m-40) REVERT: B 388 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7915 (tpp) REVERT: C 319 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7419 (mtm180) REVERT: C 322 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6997 (mmm-85) REVERT: D 450 GLN cc_start: 0.7024 (mt0) cc_final: 0.6824 (tp-100) REVERT: E 415 SER cc_start: 0.8192 (t) cc_final: 0.7759 (p) REVERT: F 412 MET cc_start: 0.8052 (mmm) cc_final: 0.7403 (mmt) REVERT: G 319 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7926 (mtm180) REVERT: G 450 GLN cc_start: 0.6884 (tp40) cc_final: 0.6620 (tp40) outliers start: 23 outliers final: 12 residues processed: 118 average time/residue: 0.2293 time to fit residues: 36.0118 Evaluate side-chains 118 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 388 MET 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 454 GLU Chi-restraints excluded: chain E residue 341 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3283 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= 0.188 Angle : 0.495 5.581 11196 Z= 0.249 Chirality : 0.040 0.193 1314 Planarity : 0.004 0.036 1470 Dihedral : 3.609 13.896 1140 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.95 % Allowed : 12.76 % 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 (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: 1.52 (0.27), residues: 1038 helix: 1.72 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -1.06 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 327 HIS 0.004 0.001 HIS F 389 PHE 0.006 0.001 PHE F 339 TYR 0.008 0.001 TYR B 429 ARG 0.006 0.000 ARG G 472 *********************** 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 122 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.894 Fit side-chains REVERT: B 303 THR cc_start: 0.4804 (OUTLIER) cc_final: 0.4534 (t) REVERT: B 358 ASN cc_start: 0.5911 (m-40) cc_final: 0.5544 (m-40) REVERT: C 319 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7403 (mtm180) REVERT: C 322 ARG cc_start: 0.7260 (mtt180) cc_final: 0.7012 (mmm-85) REVERT: D 450 GLN cc_start: 0.7029 (mt0) cc_final: 0.6826 (tp-100) REVERT: E 415 SER cc_start: 0.8244 (t) cc_final: 0.7817 (p) REVERT: F 412 MET cc_start: 0.8060 (mmm) cc_final: 0.7432 (mmt) REVERT: G 319 ARG cc_start: 0.8201 (mtt-85) cc_final: 0.7926 (mtm180) REVERT: G 450 GLN cc_start: 0.7067 (tp40) cc_final: 0.6856 (tp-100) outliers start: 17 outliers final: 13 residues processed: 111 average time/residue: 0.2261 time to fit residues: 33.5340 Evaluate side-chains 112 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 400 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8208 Z= 0.225 Angle : 0.511 5.484 11196 Z= 0.257 Chirality : 0.040 0.151 1314 Planarity : 0.004 0.035 1470 Dihedral : 3.617 13.458 1140 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.84 % Allowed : 13.10 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.26), residues: 1038 helix: 1.73 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -1.05 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 327 HIS 0.005 0.001 HIS F 389 PHE 0.007 0.001 PHE F 339 TYR 0.008 0.001 TYR B 429 ARG 0.006 0.000 ARG G 472 *********************** 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 120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.116 Fit side-chains REVERT: B 303 THR cc_start: 0.4793 (OUTLIER) cc_final: 0.4518 (t) REVERT: B 358 ASN cc_start: 0.6220 (m-40) cc_final: 0.5821 (m-40) REVERT: C 319 ARG cc_start: 0.7720 (mtt180) cc_final: 0.7420 (mtm180) REVERT: C 322 ARG cc_start: 0.7276 (mtt180) cc_final: 0.7025 (mmm-85) REVERT: D 450 GLN cc_start: 0.7032 (mt0) cc_final: 0.6830 (tp-100) REVERT: F 412 MET cc_start: 0.8080 (mmm) cc_final: 0.7453 (mmt) REVERT: G 319 ARG cc_start: 0.8241 (mtt-85) cc_final: 0.7969 (mtm180) outliers start: 16 outliers final: 13 residues processed: 111 average time/residue: 0.2247 time to fit residues: 33.5979 Evaluate side-chains 120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 THR 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 312 SER 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 F residue 336 ASP Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 475 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8208 Z= 0.217 Angle : 0.503 5.365 11196 Z= 0.253 Chirality : 0.040 0.146 1314 Planarity : 0.004 0.033 1470 Dihedral : 3.582 13.718 1140 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.30 % Allowed : 13.22 % 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 (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: 1.54 (0.26), residues: 1038 helix: 1.77 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -1.02 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 327 HIS 0.005 0.001 HIS F 389 PHE 0.007 0.001 PHE F 339 TYR 0.008 0.001 TYR B 429 ARG 0.007 0.000 ARG G 472 *********************** 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 127 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.961 Fit side-chains REVERT: B 303 THR cc_start: 0.4835 (OUTLIER) cc_final: 0.4551 (t) REVERT: C 319 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7296 (mtm180) REVERT: C 322 ARG cc_start: 0.7414 (mtt180) cc_final: 0.7170 (mmm-85) REVERT: D 450 GLN cc_start: 0.7035 (mt0) cc_final: 0.6834 (tp-100) REVERT: F 412 MET cc_start: 0.8145 (mmm) cc_final: 0.7405 (mmt) REVERT: G 319 ARG cc_start: 0.8241 (mtt-85) cc_final: 0.7973 (mtm180) outliers start: 20 outliers final: 17 residues processed: 115 average time/residue: 0.2224 time to fit residues: 34.6120 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 : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 THR 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 312 SER 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 423 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8208 Z= 0.262 Angle : 0.525 5.390 11196 Z= 0.264 Chirality : 0.041 0.158 1314 Planarity : 0.004 0.033 1470 Dihedral : 3.657 14.664 1140 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.72 % Allowed : 13.68 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.26), residues: 1038 helix: 1.68 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -1.05 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 327 HIS 0.005 0.001 HIS F 389 PHE 0.008 0.001 PHE F 339 TYR 0.009 0.001 TYR B 429 ARG 0.005 0.000 ARG G 472 *********************** 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 117 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.023 Fit side-chains REVERT: B 303 THR cc_start: 0.4858 (OUTLIER) cc_final: 0.4559 (t) REVERT: B 358 ASN cc_start: 0.6548 (m-40) cc_final: 0.6274 (m-40) REVERT: C 319 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7301 (mtm180) REVERT: C 322 ARG cc_start: 0.7413 (mtt180) cc_final: 0.7171 (mmm-85) REVERT: F 412 MET cc_start: 0.8125 (mmm) cc_final: 0.7375 (mmt) REVERT: G 319 ARG cc_start: 0.8282 (mtt-85) cc_final: 0.8012 (mtm180) outliers start: 15 outliers final: 14 residues processed: 108 average time/residue: 0.2210 time to fit residues: 32.1553 Evaluate side-chains 118 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 THR 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 312 SER 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 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 39 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8208 Z= 0.158 Angle : 0.473 5.280 11196 Z= 0.236 Chirality : 0.039 0.134 1314 Planarity : 0.004 0.033 1470 Dihedral : 3.478 13.129 1140 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.07 % Allowed : 13.56 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.27), residues: 1038 helix: 1.92 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.89 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 327 HIS 0.004 0.001 HIS G 389 PHE 0.005 0.001 PHE D 456 TYR 0.006 0.001 TYR B 429 ARG 0.005 0.000 ARG G 472 *********************** 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 121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.935 Fit side-chains REVERT: B 303 THR cc_start: 0.4687 (OUTLIER) cc_final: 0.4366 (t) REVERT: B 358 ASN cc_start: 0.6497 (m-40) cc_final: 0.6231 (m-40) REVERT: C 319 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7283 (mtm180) REVERT: C 322 ARG cc_start: 0.7365 (mtt180) cc_final: 0.7137 (mmm-85) REVERT: F 412 MET cc_start: 0.8049 (mmm) cc_final: 0.7269 (mmt) REVERT: G 319 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7908 (mtm180) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 0.2270 time to fit residues: 33.7779 Evaluate side-chains 117 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 THR 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 312 SER 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 423 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 101 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3639 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= 0.189 Angle : 0.485 5.793 11196 Z= 0.241 Chirality : 0.039 0.159 1314 Planarity : 0.004 0.033 1470 Dihedral : 3.463 13.369 1140 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.95 % Allowed : 14.02 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.27), residues: 1038 helix: 1.90 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.93 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 327 HIS 0.005 0.001 HIS G 389 PHE 0.005 0.001 PHE F 339 TYR 0.007 0.001 TYR B 429 ARG 0.005 0.000 ARG G 472 ********************** 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 119 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.945 Fit side-chains REVERT: B 303 THR cc_start: 0.4756 (OUTLIER) cc_final: 0.4491 (t) REVERT: B 358 ASN cc_start: 0.6306 (m-40) cc_final: 0.6013 (m-40) REVERT: C 319 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7249 (mtm180) REVERT: C 322 ARG cc_start: 0.7326 (mtt180) cc_final: 0.7100 (mmm-85) REVERT: F 412 MET cc_start: 0.8119 (mmm) cc_final: 0.7366 (mmt) REVERT: G 319 ARG cc_start: 0.8216 (mtt-85) cc_final: 0.7905 (mtm180) outliers start: 17 outliers final: 15 residues processed: 109 average time/residue: 0.2296 time to fit residues: 33.5241 Evaluate side-chains 118 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 476 ILE 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 D residue 380 ILE Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 423 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 22 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.100382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.086794 restraints weight = 11023.935| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 1.60 r_work: 0.2655 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8208 Z= 0.150 Angle : 0.465 5.700 11196 Z= 0.230 Chirality : 0.039 0.132 1314 Planarity : 0.004 0.033 1470 Dihedral : 3.379 12.460 1140 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.72 % Allowed : 14.25 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.27), residues: 1038 helix: 2.02 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.90 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 327 HIS 0.004 0.001 HIS G 389 PHE 0.005 0.001 PHE D 456 TYR 0.005 0.001 TYR D 464 ARG 0.005 0.000 ARG G 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1872.50 seconds wall clock time: 34 minutes 53.26 seconds (2093.26 seconds total)