Starting phenix.real_space_refine on Sun Jul 5 22:12:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwq_47260/07_2026/9dwq_47260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwq_47260/07_2026/9dwq_47260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwq_47260/07_2026/9dwq_47260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwq_47260/07_2026/9dwq_47260.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwq_47260/07_2026/9dwq_47260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwq_47260/07_2026/9dwq_47260.cif" } resolution = 2.76 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= 0.021 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 76 5.16 5 C 10264 2.51 5 N 2452 2.21 5 O 2748 1.98 5 H 15384 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30925 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 7731 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 10, 'TRANS': 459} Chain breaks: 1 Chain: "B" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 7731 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 10, 'TRANS': 459} Chain breaks: 1 Chain: "C" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 7731 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 10, 'TRANS': 459} Chain breaks: 1 Chain: "D" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 7731 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 10, 'TRANS': 459} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 5.08, per 1000 atoms: 0.16 Number of scatterers: 30925 At special positions: 0 Unit cell: (116.135, 114.838, 103.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 76 16.00 O 2748 8.00 N 2452 7.00 C 10264 6.00 H 15384 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 731.2 milliseconds 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3608 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 64.3% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 214 through 241 removed outlier: 3.553A pdb=" N SER A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 258 removed outlier: 4.190A pdb=" N TYR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 334 through 338 removed outlier: 3.662A pdb=" N ARG A 338 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.508A pdb=" N TRP A 366 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 367 " --> pdb=" O THR A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 367' Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 498 removed outlier: 3.683A pdb=" N ILE A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 504 Processing helix chain 'A' and resid 505 through 530 Processing helix chain 'A' and resid 532 through 541 removed outlier: 3.546A pdb=" N LEU A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 580 through 620 removed outlier: 3.617A pdb=" N ALA A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 599 " --> pdb=" O LYS A 595 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 removed outlier: 3.994A pdb=" N ILE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.582A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 Processing helix chain 'A' and resid 672 through 692 removed outlier: 4.374A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 241 Processing helix chain 'B' and resid 243 through 259 removed outlier: 4.137A pdb=" N TYR B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.781A pdb=" N ILE B 367 " --> pdb=" O THR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 499 removed outlier: 3.833A pdb=" N ILE B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 504 Processing helix chain 'B' and resid 505 through 531 removed outlier: 3.523A pdb=" N CYS B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.790A pdb=" N ASP B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 593 through 620 removed outlier: 3.689A pdb=" N ILE B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 642 removed outlier: 4.019A pdb=" N ILE B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.571A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 672 through 692 removed outlier: 4.366A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 241 Processing helix chain 'C' and resid 243 through 259 removed outlier: 4.213A pdb=" N TYR C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 334 through 338 removed outlier: 3.673A pdb=" N ARG C 338 " --> pdb=" O GLN C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.742A pdb=" N ILE C 367 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 498 Processing helix chain 'C' and resid 501 through 504 Processing helix chain 'C' and resid 505 through 531 removed outlier: 3.536A pdb=" N CYS C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 541 removed outlier: 3.610A pdb=" N LEU C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 577 Processing helix chain 'C' and resid 580 through 593 Processing helix chain 'C' and resid 593 through 620 removed outlier: 3.625A pdb=" N ILE C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 642 removed outlier: 4.006A pdb=" N ILE C 633 " --> pdb=" O SER C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.575A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 Processing helix chain 'C' and resid 672 through 692 removed outlier: 4.392A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 241 Processing helix chain 'D' and resid 243 through 258 removed outlier: 4.122A pdb=" N TYR D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 370 through 375 Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 499 Processing helix chain 'D' and resid 501 through 504 Processing helix chain 'D' and resid 505 through 531 removed outlier: 3.505A pdb=" N CYS D 509 " --> pdb=" O SER D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 541 removed outlier: 3.573A pdb=" N LEU D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 572 Processing helix chain 'D' and resid 573 through 577 Processing helix chain 'D' and resid 580 through 620 removed outlier: 3.554A pdb=" N ALA D 594 " --> pdb=" O MET D 590 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY D 599 " --> pdb=" O LYS D 595 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 642 removed outlier: 3.967A pdb=" N ILE D 633 " --> pdb=" O SER D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.571A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 670 Processing helix chain 'D' and resid 672 through 692 removed outlier: 4.388A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 394 removed outlier: 7.073A pdb=" N LEU A 316 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR A 429 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 318 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER A 427 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 421 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA3, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.999A pdb=" N LEU B 316 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N TYR B 429 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 318 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N SER B 427 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 421 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA5, first strand: chain 'C' and resid 391 through 394 removed outlier: 7.075A pdb=" N LEU C 316 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N TYR C 429 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 318 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER C 427 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 421 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'D' and resid 391 through 394 removed outlier: 7.052A pdb=" N LEU D 316 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR D 429 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL D 318 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER D 427 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 421 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 379 through 380 974 hydrogen bonds defined for protein. 2796 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: 8.08 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15356 1.03 - 1.23: 31 1.23 - 1.42: 7089 1.42 - 1.62: 8744 1.62 - 1.81: 116 Bond restraints: 31336 Sorted by residual: bond pdb=" C GLN C 458 " pdb=" O GLN C 458 " ideal model delta sigma weight residual 1.249 1.240 0.009 8.50e-03 1.38e+04 1.08e+00 bond pdb=" N ARG D 464 " pdb=" CA ARG D 464 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.24e-02 6.50e+03 8.78e-01 bond pdb=" N ARG C 464 " pdb=" CA ARG C 464 " ideal model delta sigma weight residual 1.457 1.468 -0.012 1.24e-02 6.50e+03 8.70e-01 bond pdb=" N ARG A 464 " pdb=" CA ARG A 464 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.24e-02 6.50e+03 7.98e-01 bond pdb=" CA PHE A 310 " pdb=" C PHE A 310 " ideal model delta sigma weight residual 1.529 1.517 0.012 1.44e-02 4.82e+03 7.49e-01 ... (remaining 31331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.94: 56292 6.94 - 13.89: 1 13.89 - 20.83: 0 20.83 - 27.78: 0 27.78 - 34.72: 3 Bond angle restraints: 56296 Sorted by residual: angle pdb=" C THR B 529 " pdb=" CA THR B 529 " pdb=" HA THR B 529 " ideal model delta sigma weight residual 109.00 74.28 34.72 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N THR B 529 " pdb=" CA THR B 529 " pdb=" HA THR B 529 " ideal model delta sigma weight residual 110.00 75.57 34.43 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB THR B 529 " pdb=" CA THR B 529 " pdb=" HA THR B 529 " ideal model delta sigma weight residual 109.00 75.50 33.50 3.00e+00 1.11e-01 1.25e+02 angle pdb=" N VAL B 466 " pdb=" CA VAL B 466 " pdb=" C VAL B 466 " ideal model delta sigma weight residual 113.71 110.01 3.70 9.50e-01 1.11e+00 1.52e+01 angle pdb=" C ILE C 309 " pdb=" N PHE C 310 " pdb=" CA PHE C 310 " ideal model delta sigma weight residual 121.90 117.78 4.12 1.26e+00 6.30e-01 1.07e+01 ... (remaining 56291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13343 17.96 - 35.91: 1059 35.91 - 53.87: 289 53.87 - 71.83: 102 71.83 - 89.78: 47 Dihedral angle restraints: 14840 sinusoidal: 7636 harmonic: 7204 Sorted by residual: dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 344 " pdb=" CB CYS B 344 " ideal model delta sinusoidal sigma weight residual 93.00 153.44 -60.44 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 344 " pdb=" CB CYS A 344 " ideal model delta sinusoidal sigma weight residual 93.00 153.01 -60.01 1 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" CB CYS D 331 " pdb=" SG CYS D 331 " pdb=" SG CYS D 344 " pdb=" CB CYS D 344 " ideal model delta sinusoidal sigma weight residual 93.00 152.87 -59.87 1 1.00e+01 1.00e-02 4.78e+01 ... (remaining 14837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2311 0.079 - 0.158: 108 0.158 - 0.236: 0 0.236 - 0.315: 0 0.315 - 0.394: 1 Chirality restraints: 2420 Sorted by residual: chirality pdb=" CA THR B 529 " pdb=" N THR B 529 " pdb=" C THR B 529 " pdb=" CB THR B 529 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA ILE D 333 " pdb=" N ILE D 333 " pdb=" C ILE D 333 " pdb=" CB ILE D 333 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE C 333 " pdb=" N ILE C 333 " pdb=" C ILE C 333 " pdb=" CB ILE C 333 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 2417 not shown) Planarity restraints: 4520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 318 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO B 319 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 319 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 319 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 600 " 0.015 2.00e-02 2.50e+03 7.45e-03 1.67e+00 pdb=" CG PHE C 600 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE C 600 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 600 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 600 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 600 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 600 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE C 600 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE C 600 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE C 600 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE C 600 " 0.000 2.00e-02 2.50e+03 pdb=" HZ PHE C 600 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 600 " -0.014 2.00e-02 2.50e+03 7.25e-03 1.58e+00 pdb=" CG PHE D 600 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE D 600 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE D 600 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 600 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 600 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 600 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE D 600 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE D 600 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE D 600 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE D 600 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE D 600 " -0.001 2.00e-02 2.50e+03 ... (remaining 4517 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 2386 2.23 - 2.83: 67673 2.83 - 3.42: 81140 3.42 - 4.01: 112738 4.01 - 4.60: 174122 Nonbonded interactions: 438059 Sorted by model distance: nonbonded pdb=" HA THR B 529 " pdb=" HB THR B 529 " model vdw 1.642 1.952 nonbonded pdb=" H THR B 529 " pdb=" HA THR B 529 " model vdw 1.758 1.816 nonbonded pdb=" H SER B 396 " pdb=" HG1 THR B 402 " model vdw 1.857 2.100 nonbonded pdb=" H ASP C 416 " pdb=" HG1 THR C 419 " model vdw 1.872 2.100 nonbonded pdb=" H SER A 396 " pdb=" HG1 THR A 402 " model vdw 1.872 2.100 ... (remaining 438054 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 'A' and resid 214 through 693) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 5.550 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: 0.200 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 29.140 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:10.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15956 Z= 0.125 Angle : 0.493 7.910 21652 Z= 0.303 Chirality : 0.036 0.394 2420 Planarity : 0.003 0.035 2688 Dihedral : 16.033 89.782 5612 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.29 % Allowed : 12.38 % Favored : 86.33 % 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 are not related in a simple way. whole: 2.06 (0.19), residues: 1864 helix: 2.66 (0.16), residues: 1032 sheet: -0.01 (0.38), residues: 192 loop : -0.37 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.011 0.001 TYR B 247 PHE 0.020 0.001 PHE C 600 TRP 0.005 0.001 TRP B 293 HIS 0.001 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (15952) covalent geometry : angle 0.49290 / 0.30 (21644) SS BOND : bond 0.00059 / 0.03 ( 4) SS BOND : angle 0.71829 / 0.34 ( 8) hydrogen bonds : bond 0.15224 / 10.05 ( 974) hydrogen bonds : angle 5.48485 / 3.90 ( 2796) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7956 (mttt) cc_final: 0.7754 (mmmt) REVERT: A 596 ASP cc_start: 0.8003 (m-30) cc_final: 0.7662 (m-30) REVERT: A 662 THR cc_start: 0.8834 (m) cc_final: 0.8377 (p) REVERT: B 278 ASP cc_start: 0.8731 (m-30) cc_final: 0.8525 (m-30) REVERT: B 342 LYS cc_start: 0.7940 (mttt) cc_final: 0.7716 (mmmt) REVERT: B 590 MET cc_start: 0.7937 (mmm) cc_final: 0.7585 (mtp) REVERT: B 596 ASP cc_start: 0.8087 (m-30) cc_final: 0.7694 (m-30) REVERT: B 662 THR cc_start: 0.8848 (m) cc_final: 0.8392 (p) REVERT: C 289 ASP cc_start: 0.8694 (m-30) cc_final: 0.8472 (m-30) REVERT: C 587 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8149 (m) REVERT: C 596 ASP cc_start: 0.8059 (m-30) cc_final: 0.7707 (m-30) REVERT: C 662 THR cc_start: 0.8853 (m) cc_final: 0.8400 (p) REVERT: D 342 LYS cc_start: 0.7998 (mttt) cc_final: 0.7678 (mptm) REVERT: D 425 ASP cc_start: 0.8411 (m-30) cc_final: 0.8095 (m-30) REVERT: D 585 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6964 (mm110) REVERT: D 590 MET cc_start: 0.7971 (mmm) cc_final: 0.7595 (mtp) REVERT: D 596 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: D 662 THR cc_start: 0.8830 (m) cc_final: 0.8402 (p) REVERT: D 677 LEU cc_start: 0.8259 (tp) cc_final: 0.8025 (tp) outliers start: 22 outliers final: 16 residues processed: 191 average time/residue: 0.9682 time to fit residues: 211.1609 Evaluate side-chains 176 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 585 GLN Chi-restraints excluded: chain D residue 596 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.108136 restraints weight = 48487.278| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.75 r_work: 0.3058 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15956 Z= 0.195 Angle : 0.512 9.632 21652 Z= 0.283 Chirality : 0.039 0.360 2420 Planarity : 0.004 0.036 2688 Dihedral : 5.732 86.603 2089 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.23 % Allowed : 12.79 % Favored : 85.97 % 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 are not related in a simple way. whole: 1.81 (0.19), residues: 1864 helix: 2.40 (0.15), residues: 1060 sheet: 0.01 (0.36), residues: 200 loop : -0.58 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 322 TYR 0.017 0.002 TYR D 247 PHE 0.020 0.002 PHE D 600 TRP 0.006 0.001 TRP B 293 HIS 0.004 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (15952) covalent geometry : angle 0.51162 / 0.28 (21644) SS BOND : bond 0.00020 / 0.01 ( 4) SS BOND : angle 0.62443 / 0.29 ( 8) hydrogen bonds : bond 0.05371 / 3.49 ( 974) hydrogen bonds : angle 4.53442 / 3.21 ( 2796) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7953 (mttt) cc_final: 0.7732 (mmmt) REVERT: A 596 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: B 342 LYS cc_start: 0.7959 (mttt) cc_final: 0.7731 (mmmt) REVERT: B 590 MET cc_start: 0.8067 (mmm) cc_final: 0.7648 (mtp) REVERT: B 596 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: C 289 ASP cc_start: 0.8697 (m-30) cc_final: 0.8455 (m-30) REVERT: C 596 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: D 305 ASN cc_start: 0.6200 (t0) cc_final: 0.5962 (t0) REVERT: D 342 LYS cc_start: 0.8001 (mttt) cc_final: 0.7657 (mptm) REVERT: D 585 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6976 (mm110) REVERT: D 590 MET cc_start: 0.8057 (mmm) cc_final: 0.7640 (mtp) REVERT: D 596 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7760 (m-30) outliers start: 21 outliers final: 12 residues processed: 163 average time/residue: 0.9653 time to fit residues: 181.4940 Evaluate side-chains 164 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 585 GLN Chi-restraints excluded: chain D residue 596 ASP Chi-restraints excluded: chain D residue 629 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 37 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 323 GLN B 543 ASN C 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.142502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107074 restraints weight = 48505.363| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.75 r_work: 0.3047 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15956 Z= 0.201 Angle : 0.513 10.113 21652 Z= 0.283 Chirality : 0.039 0.370 2420 Planarity : 0.004 0.040 2688 Dihedral : 5.763 87.867 2078 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.52 % Allowed : 12.32 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 1864 helix: 2.26 (0.15), residues: 1064 sheet: -0.05 (0.35), residues: 200 loop : -0.78 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 322 TYR 0.018 0.002 TYR D 247 PHE 0.021 0.002 PHE D 600 TRP 0.005 0.001 TRP C 554 HIS 0.004 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (15952) covalent geometry : angle 0.51261 / 0.28 (21644) SS BOND : bond 0.00042 / 0.02 ( 4) SS BOND : angle 0.65782 / 0.31 ( 8) hydrogen bonds : bond 0.05250 / 3.43 ( 974) hydrogen bonds : angle 4.39521 / 3.12 ( 2796) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7982 (mttt) cc_final: 0.7757 (mmmt) REVERT: A 596 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: B 342 LYS cc_start: 0.7958 (mttt) cc_final: 0.7632 (mptm) REVERT: B 590 MET cc_start: 0.8091 (mmm) cc_final: 0.7673 (mtp) REVERT: B 596 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7885 (m-30) REVERT: C 289 ASP cc_start: 0.8688 (m-30) cc_final: 0.8475 (m-30) REVERT: C 596 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: D 305 ASN cc_start: 0.6343 (t0) cc_final: 0.6121 (t0) REVERT: D 342 LYS cc_start: 0.7962 (mttt) cc_final: 0.7630 (mptm) REVERT: D 590 MET cc_start: 0.8086 (mmm) cc_final: 0.7669 (mtp) REVERT: D 596 ASP cc_start: 0.8105 (m-30) cc_final: 0.7744 (m-30) outliers start: 43 outliers final: 23 residues processed: 185 average time/residue: 0.9648 time to fit residues: 207.4112 Evaluate side-chains 168 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 585 GLN Chi-restraints excluded: chain D residue 629 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.143078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.107749 restraints weight = 48393.498| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.75 r_work: 0.3064 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15956 Z= 0.166 Angle : 0.491 9.672 21652 Z= 0.270 Chirality : 0.038 0.369 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.729 88.355 2076 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.82 % Allowed : 13.03 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.19), residues: 1864 helix: 2.33 (0.15), residues: 1064 sheet: -0.10 (0.35), residues: 200 loop : -0.77 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 592 TYR 0.017 0.002 TYR D 247 PHE 0.021 0.001 PHE D 600 TRP 0.005 0.001 TRP B 293 HIS 0.003 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (15952) covalent geometry : angle 0.49115 / 0.27 (21644) SS BOND : bond 0.00007 / 0.00 ( 4) SS BOND : angle 0.69822 / 0.33 ( 8) hydrogen bonds : bond 0.04864 / 3.18 ( 974) hydrogen bonds : angle 4.24519 / 3.02 ( 2796) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.8011 (mttt) cc_final: 0.7784 (mmmt) REVERT: A 596 ASP cc_start: 0.8078 (m-30) cc_final: 0.7750 (m-30) REVERT: B 342 LYS cc_start: 0.7948 (mttt) cc_final: 0.7638 (mptm) REVERT: B 590 MET cc_start: 0.8072 (mmm) cc_final: 0.7665 (mtp) REVERT: B 596 ASP cc_start: 0.8238 (m-30) cc_final: 0.7892 (m-30) REVERT: C 289 ASP cc_start: 0.8675 (m-30) cc_final: 0.8456 (m-30) REVERT: C 596 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: D 342 LYS cc_start: 0.7975 (mttt) cc_final: 0.7630 (mptm) REVERT: D 590 MET cc_start: 0.8055 (mmm) cc_final: 0.7649 (mtp) REVERT: D 596 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7751 (m-30) outliers start: 31 outliers final: 18 residues processed: 173 average time/residue: 0.8310 time to fit residues: 167.5733 Evaluate side-chains 166 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 585 GLN Chi-restraints excluded: chain D residue 596 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 68 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.143070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107823 restraints weight = 48316.274| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.74 r_work: 0.3041 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15956 Z= 0.166 Angle : 0.487 9.653 21652 Z= 0.268 Chirality : 0.038 0.371 2420 Planarity : 0.004 0.045 2688 Dihedral : 5.759 89.022 2076 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.05 % Allowed : 12.97 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.19), residues: 1864 helix: 2.35 (0.15), residues: 1064 sheet: -0.14 (0.35), residues: 200 loop : -0.78 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 592 TYR 0.017 0.002 TYR D 247 PHE 0.021 0.001 PHE D 600 TRP 0.005 0.001 TRP B 293 HIS 0.003 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (15952) covalent geometry : angle 0.48703 / 0.27 (21644) SS BOND : bond 0.00008 / 0.00 ( 4) SS BOND : angle 0.69009 / 0.33 ( 8) hydrogen bonds : bond 0.04776 / 3.12 ( 974) hydrogen bonds : angle 4.19877 / 2.98 ( 2796) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.8011 (mttt) cc_final: 0.7781 (mmmt) REVERT: A 596 ASP cc_start: 0.8083 (m-30) cc_final: 0.7757 (m-30) REVERT: B 342 LYS cc_start: 0.7974 (mttt) cc_final: 0.7652 (mptm) REVERT: B 590 MET cc_start: 0.8078 (mmm) cc_final: 0.7693 (mtp) REVERT: B 596 ASP cc_start: 0.8237 (m-30) cc_final: 0.7890 (m-30) REVERT: C 289 ASP cc_start: 0.8680 (m-30) cc_final: 0.8466 (m-30) REVERT: C 596 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: C 613 GLN cc_start: 0.8481 (tt0) cc_final: 0.8192 (mm110) REVERT: D 342 LYS cc_start: 0.7997 (mttt) cc_final: 0.7656 (mptm) REVERT: D 590 MET cc_start: 0.8061 (mmm) cc_final: 0.7662 (mtp) REVERT: D 596 ASP cc_start: 0.8120 (m-30) cc_final: 0.7774 (m-30) outliers start: 35 outliers final: 24 residues processed: 172 average time/residue: 0.9138 time to fit residues: 182.7854 Evaluate side-chains 169 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 585 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 323 GLN D 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.145533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.110967 restraints weight = 48469.570| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.72 r_work: 0.3083 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15956 Z= 0.107 Angle : 0.435 7.792 21652 Z= 0.241 Chirality : 0.037 0.369 2420 Planarity : 0.004 0.045 2688 Dihedral : 5.538 89.026 2076 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.00 % Allowed : 13.97 % Favored : 85.04 % 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 are not related in a simple way. whole: 1.99 (0.19), residues: 1864 helix: 2.64 (0.15), residues: 1060 sheet: -0.16 (0.36), residues: 200 loop : -0.59 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 251 TYR 0.015 0.001 TYR D 247 PHE 0.020 0.001 PHE D 600 TRP 0.005 0.001 TRP C 293 HIS 0.002 0.000 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (15952) covalent geometry : angle 0.43526 / 0.24 (21644) SS BOND : bond 0.00060 / 0.03 ( 4) SS BOND : angle 0.77994 / 0.38 ( 8) hydrogen bonds : bond 0.04148 / 2.72 ( 974) hydrogen bonds : angle 4.03562 / 2.87 ( 2796) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.8003 (mttt) cc_final: 0.7795 (mmmt) REVERT: A 596 ASP cc_start: 0.8085 (m-30) cc_final: 0.7767 (m-30) REVERT: A 662 THR cc_start: 0.8834 (m) cc_final: 0.8340 (p) REVERT: B 342 LYS cc_start: 0.7969 (mttt) cc_final: 0.7657 (mptm) REVERT: B 590 MET cc_start: 0.8034 (mmm) cc_final: 0.7690 (mtp) REVERT: B 596 ASP cc_start: 0.8240 (m-30) cc_final: 0.7903 (m-30) REVERT: B 662 THR cc_start: 0.8849 (m) cc_final: 0.8350 (p) REVERT: C 289 ASP cc_start: 0.8640 (m-30) cc_final: 0.8406 (m-30) REVERT: C 596 ASP cc_start: 0.8223 (m-30) cc_final: 0.7827 (m-30) REVERT: C 662 THR cc_start: 0.8845 (m) cc_final: 0.8350 (p) REVERT: D 342 LYS cc_start: 0.7984 (mttt) cc_final: 0.7659 (mptm) REVERT: D 585 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7088 (mm110) REVERT: D 590 MET cc_start: 0.8039 (mmm) cc_final: 0.7681 (mtp) REVERT: D 596 ASP cc_start: 0.8120 (m-30) cc_final: 0.7778 (m-30) REVERT: D 651 GLU cc_start: 0.8286 (tt0) cc_final: 0.7996 (tt0) outliers start: 17 outliers final: 15 residues processed: 171 average time/residue: 0.9191 time to fit residues: 182.0227 Evaluate side-chains 172 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 585 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 146 optimal weight: 0.0670 chunk 100 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 543 ASN D 305 ASN D 537 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108589 restraints weight = 48311.852| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.73 r_work: 0.3054 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15956 Z= 0.155 Angle : 0.473 9.119 21652 Z= 0.259 Chirality : 0.037 0.372 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.650 89.746 2076 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.35 % Allowed : 13.67 % Favored : 84.98 % 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 are not related in a simple way. whole: 1.86 (0.19), residues: 1864 helix: 2.53 (0.15), residues: 1064 sheet: -0.20 (0.35), residues: 200 loop : -0.66 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.016 0.002 TYR D 247 PHE 0.021 0.001 PHE D 600 TRP 0.005 0.001 TRP B 293 HIS 0.003 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (15952) covalent geometry : angle 0.47256 / 0.26 (21644) SS BOND : bond 0.00041 / 0.02 ( 4) SS BOND : angle 0.66142 / 0.31 ( 8) hydrogen bonds : bond 0.04546 / 2.97 ( 974) hydrogen bonds : angle 4.09763 / 2.91 ( 2796) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7996 (mttt) cc_final: 0.7701 (mptm) REVERT: A 596 ASP cc_start: 0.8093 (m-30) cc_final: 0.7763 (m-30) REVERT: B 342 LYS cc_start: 0.7975 (mttt) cc_final: 0.7657 (mptm) REVERT: B 590 MET cc_start: 0.8057 (mmm) cc_final: 0.7680 (mtp) REVERT: B 596 ASP cc_start: 0.8224 (m-30) cc_final: 0.7842 (m-30) REVERT: C 289 ASP cc_start: 0.8673 (m-30) cc_final: 0.8437 (m-30) REVERT: C 596 ASP cc_start: 0.8229 (m-30) cc_final: 0.7846 (m-30) REVERT: D 342 LYS cc_start: 0.7995 (mttt) cc_final: 0.7667 (mptm) REVERT: D 585 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7144 (mm110) REVERT: D 590 MET cc_start: 0.8031 (mmm) cc_final: 0.7700 (mtp) REVERT: D 596 ASP cc_start: 0.8119 (m-30) cc_final: 0.7767 (m-30) REVERT: D 677 LEU cc_start: 0.8312 (tp) cc_final: 0.8029 (tp) outliers start: 23 outliers final: 18 residues processed: 170 average time/residue: 0.9735 time to fit residues: 190.5805 Evaluate side-chains 172 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 585 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN D 537 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.141303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105921 restraints weight = 47909.762| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.74 r_work: 0.3035 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15956 Z= 0.166 Angle : 0.484 9.660 21652 Z= 0.265 Chirality : 0.038 0.373 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.723 89.487 2076 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.47 % Allowed : 13.67 % Favored : 84.86 % 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 are not related in a simple way. whole: 1.80 (0.19), residues: 1864 helix: 2.47 (0.15), residues: 1064 sheet: -0.21 (0.35), residues: 200 loop : -0.68 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 251 TYR 0.016 0.002 TYR D 247 PHE 0.021 0.001 PHE D 600 TRP 0.005 0.001 TRP B 293 HIS 0.003 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (15952) covalent geometry : angle 0.48359 / 0.27 (21644) SS BOND : bond 0.00012 / 0.01 ( 4) SS BOND : angle 0.63285 / 0.30 ( 8) hydrogen bonds : bond 0.04657 / 3.04 ( 974) hydrogen bonds : angle 4.12452 / 2.93 ( 2796) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.8001 (mttt) cc_final: 0.7685 (mptm) REVERT: A 596 ASP cc_start: 0.8039 (m-30) cc_final: 0.7703 (m-30) REVERT: B 342 LYS cc_start: 0.7976 (mttt) cc_final: 0.7653 (mptm) REVERT: B 590 MET cc_start: 0.8011 (mmm) cc_final: 0.7638 (mtp) REVERT: B 596 ASP cc_start: 0.8171 (m-30) cc_final: 0.7791 (m-30) REVERT: B 613 GLN cc_start: 0.8493 (tt0) cc_final: 0.8150 (mm110) REVERT: C 289 ASP cc_start: 0.8692 (m-30) cc_final: 0.8460 (m-30) REVERT: C 596 ASP cc_start: 0.8174 (m-30) cc_final: 0.7777 (m-30) REVERT: C 677 LEU cc_start: 0.8317 (tp) cc_final: 0.7655 (mp) REVERT: D 342 LYS cc_start: 0.7982 (mttt) cc_final: 0.7657 (mptm) REVERT: D 585 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7143 (mm110) REVERT: D 590 MET cc_start: 0.8044 (mmm) cc_final: 0.7669 (mtp) REVERT: D 596 ASP cc_start: 0.8068 (m-30) cc_final: 0.7714 (m-30) outliers start: 25 outliers final: 23 residues processed: 165 average time/residue: 0.9809 time to fit residues: 187.2953 Evaluate side-chains 167 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 585 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 46 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108419 restraints weight = 47914.103| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.74 r_work: 0.3049 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15956 Z= 0.126 Angle : 0.460 8.776 21652 Z= 0.252 Chirality : 0.037 0.371 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.639 89.455 2076 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.23 % Allowed : 13.97 % Favored : 84.80 % 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 are not related in a simple way. whole: 1.94 (0.19), residues: 1864 helix: 2.59 (0.15), residues: 1060 sheet: -0.19 (0.36), residues: 200 loop : -0.59 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 322 TYR 0.015 0.001 TYR D 247 PHE 0.021 0.001 PHE D 600 TRP 0.005 0.001 TRP B 293 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15952) covalent geometry : angle 0.45992 / 0.25 (21644) SS BOND : bond 0.00040 / 0.02 ( 4) SS BOND : angle 0.69108 / 0.33 ( 8) hydrogen bonds : bond 0.04362 / 2.85 ( 974) hydrogen bonds : angle 4.06888 / 2.89 ( 2796) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7992 (mttt) cc_final: 0.7681 (mptm) REVERT: A 596 ASP cc_start: 0.8019 (m-30) cc_final: 0.7688 (m-30) REVERT: B 342 LYS cc_start: 0.7960 (mttt) cc_final: 0.7644 (mptm) REVERT: B 590 MET cc_start: 0.8020 (mmm) cc_final: 0.7666 (mtp) REVERT: B 596 ASP cc_start: 0.8173 (m-30) cc_final: 0.7784 (m-30) REVERT: C 289 ASP cc_start: 0.8677 (m-30) cc_final: 0.8444 (m-30) REVERT: C 596 ASP cc_start: 0.8177 (m-30) cc_final: 0.7787 (m-30) REVERT: D 342 LYS cc_start: 0.7987 (mttt) cc_final: 0.7661 (mptm) REVERT: D 585 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7078 (mm110) REVERT: D 590 MET cc_start: 0.7983 (mmm) cc_final: 0.7640 (mtp) REVERT: D 596 ASP cc_start: 0.8083 (m-30) cc_final: 0.7738 (m-30) outliers start: 21 outliers final: 18 residues processed: 167 average time/residue: 1.0204 time to fit residues: 196.8543 Evaluate side-chains 171 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 585 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN D 537 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.144135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109244 restraints weight = 48325.534| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.73 r_work: 0.3082 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15956 Z= 0.139 Angle : 0.464 8.955 21652 Z= 0.254 Chirality : 0.037 0.371 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.646 89.195 2076 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.41 % Allowed : 13.79 % Favored : 84.80 % 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 are not related in a simple way. whole: 1.90 (0.19), residues: 1864 helix: 2.56 (0.15), residues: 1064 sheet: -0.20 (0.36), residues: 200 loop : -0.64 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 251 TYR 0.016 0.001 TYR D 247 PHE 0.021 0.001 PHE D 600 TRP 0.005 0.001 TRP A 293 HIS 0.003 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (15952) covalent geometry : angle 0.46367 / 0.25 (21644) SS BOND : bond 0.00037 / 0.02 ( 4) SS BOND : angle 0.67706 / 0.32 ( 8) hydrogen bonds : bond 0.04418 / 2.89 ( 974) hydrogen bonds : angle 4.06639 / 2.89 ( 2796) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7995 (mttt) cc_final: 0.7692 (mptm) REVERT: A 596 ASP cc_start: 0.8079 (m-30) cc_final: 0.7747 (m-30) REVERT: B 342 LYS cc_start: 0.7972 (mttt) cc_final: 0.7656 (mptm) REVERT: B 590 MET cc_start: 0.8038 (mmm) cc_final: 0.7705 (mtp) REVERT: B 596 ASP cc_start: 0.8222 (m-30) cc_final: 0.7839 (m-30) REVERT: C 289 ASP cc_start: 0.8671 (m-30) cc_final: 0.8440 (m-30) REVERT: C 596 ASP cc_start: 0.8209 (m-30) cc_final: 0.7829 (m-30) REVERT: D 342 LYS cc_start: 0.8000 (mttt) cc_final: 0.7677 (mptm) REVERT: D 585 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7128 (mm110) REVERT: D 590 MET cc_start: 0.8003 (mmm) cc_final: 0.7695 (mtp) REVERT: D 596 ASP cc_start: 0.8109 (m-30) cc_final: 0.7752 (m-30) outliers start: 24 outliers final: 21 residues processed: 170 average time/residue: 1.0096 time to fit residues: 198.0891 Evaluate side-chains 174 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 585 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 184 optimal weight: 0.5980 chunk 182 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111274 restraints weight = 48787.545| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.73 r_work: 0.3090 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15956 Z= 0.106 Angle : 0.431 8.527 21652 Z= 0.238 Chirality : 0.037 0.370 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.486 89.001 2076 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.17 % Allowed : 13.97 % Favored : 84.86 % 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 are not related in a simple way. whole: 2.12 (0.19), residues: 1864 helix: 2.74 (0.15), residues: 1060 sheet: -0.16 (0.36), residues: 200 loop : -0.50 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 251 TYR 0.014 0.001 TYR B 247 PHE 0.020 0.001 PHE D 600 TRP 0.005 0.001 TRP C 293 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (15952) covalent geometry : angle 0.43093 / 0.24 (21644) SS BOND : bond 0.00056 / 0.03 ( 4) SS BOND : angle 0.76141 / 0.37 ( 8) hydrogen bonds : bond 0.04023 / 2.64 ( 974) hydrogen bonds : angle 3.96251 / 2.81 ( 2796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8515.13 seconds wall clock time: 144 minutes 52.24 seconds (8692.24 seconds total)