Starting phenix.real_space_refine on Mon Aug 25 20:57:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwq_47260/08_2025/9dwq_47260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwq_47260/08_2025/9dwq_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_47260/08_2025/9dwq_47260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwq_47260/08_2025/9dwq_47260.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwq_47260/08_2025/9dwq_47260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwq_47260/08_2025/9dwq_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-2.0-5787/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.75, per 1000 atoms: 0.19 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: 2.61 Conformation dependent library (CDL) restraints added in 938.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.71 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: 7.06 Time building geometry restraints manager: 3.65 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: 4.280 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: 0.190 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 29.190 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 aren 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 covalent geometry : bond 0.00249 (15952) covalent geometry : angle 0.49290 (21644) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.71829 ( 8) hydrogen bonds : bond 0.15224 ( 974) hydrogen bonds : angle 5.48485 ( 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 : 0.854 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: 1.1002 time to fit residues: 237.8062 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 : 0.697 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107875 restraints weight = 48482.383| |-----------------------------------------------------------------------------| 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: 0.2937 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0715 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= 0.196 Angle : 0.513 9.656 21652 Z= 0.283 Chirality : 0.039 0.360 2420 Planarity : 0.004 0.037 2688 Dihedral : 5.741 86.573 2089 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.17 % Allowed : 12.91 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.19), residues: 1864 helix: 2.37 (0.15), residues: 1064 sheet: 0.00 (0.36), residues: 200 loop : -0.61 (0.24), 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 0.020 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 covalent geometry : bond 0.00461 (15952) covalent geometry : angle 0.51274 (21644) SS BOND : bond 0.00019 ( 4) SS BOND : angle 0.62339 ( 8) hydrogen bonds : bond 0.05349 ( 974) hydrogen bonds : angle 4.52811 ( 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 169 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7978 (mttt) cc_final: 0.7751 (mmmt) REVERT: A 596 ASP cc_start: 0.8081 (m-30) cc_final: 0.7750 (m-30) REVERT: B 342 LYS cc_start: 0.7960 (mttt) cc_final: 0.7730 (mmmt) REVERT: B 590 MET cc_start: 0.8068 (mmm) cc_final: 0.7647 (mtp) REVERT: B 596 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: C 289 ASP cc_start: 0.8694 (m-30) cc_final: 0.8452 (m-30) REVERT: C 596 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: D 305 ASN cc_start: 0.6193 (t0) cc_final: 0.5954 (t0) REVERT: D 342 LYS cc_start: 0.8004 (mttt) cc_final: 0.7658 (mptm) REVERT: D 585 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6978 (mm110) REVERT: D 590 MET cc_start: 0.8051 (mmm) cc_final: 0.7622 (mtp) REVERT: D 596 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7757 (m-30) outliers start: 20 outliers final: 12 residues processed: 163 average time/residue: 0.9710 time to fit residues: 180.2938 Evaluate side-chains 162 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 275 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 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: 0.7980 chunk 8 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3604 r_free = 0.3604 target = 0.142842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.107462 restraints weight = 48514.010| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.75 r_work: 0.3054 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15956 Z= 0.190 Angle : 0.503 9.855 21652 Z= 0.278 Chirality : 0.038 0.370 2420 Planarity : 0.004 0.040 2688 Dihedral : 5.716 87.827 2078 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.46 % Allowed : 12.32 % Favored : 85.21 % 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 aren not related in a simple way. whole: 1.64 (0.19), residues: 1864 helix: 2.30 (0.15), residues: 1064 sheet: -0.04 (0.35), residues: 200 loop : -0.77 (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 0.003 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00451 (15952) covalent geometry : angle 0.50328 (21644) SS BOND : bond 0.00029 ( 4) SS BOND : angle 0.64462 ( 8) hydrogen bonds : bond 0.05195 ( 974) hydrogen bonds : angle 4.38160 ( 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 192 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7979 (mttt) cc_final: 0.7755 (mmmt) REVERT: A 596 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: B 342 LYS cc_start: 0.7955 (mttt) cc_final: 0.7727 (mmmt) REVERT: B 590 MET cc_start: 0.8080 (mmm) cc_final: 0.7655 (mtp) REVERT: B 596 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: C 289 ASP cc_start: 0.8696 (m-30) cc_final: 0.8471 (m-30) REVERT: C 596 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: D 305 ASN cc_start: 0.6334 (t0) cc_final: 0.6118 (t0) REVERT: D 342 LYS cc_start: 0.7963 (mttt) cc_final: 0.7631 (mptm) REVERT: D 585 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7053 (mm110) REVERT: D 590 MET cc_start: 0.8073 (mmm) cc_final: 0.7658 (mtp) REVERT: D 596 ASP cc_start: 0.8109 (m-30) cc_final: 0.7746 (m-30) outliers start: 42 outliers final: 21 residues processed: 183 average time/residue: 0.8914 time to fit residues: 188.3863 Evaluate side-chains 168 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107923 restraints weight = 48374.172| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.75 r_work: 0.3066 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1009 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= 0.164 Angle : 0.488 9.555 21652 Z= 0.268 Chirality : 0.038 0.370 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.704 88.440 2076 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.82 % Allowed : 12.85 % Favored : 85.33 % 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 aren not related in a simple way. whole: 1.69 (0.19), residues: 1864 helix: 2.37 (0.15), residues: 1064 sheet: -0.11 (0.35), residues: 200 loop : -0.75 (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 covalent geometry : bond 0.00384 (15952) covalent geometry : angle 0.48748 (21644) SS BOND : bond 0.00006 ( 4) SS BOND : angle 0.69083 ( 8) hydrogen bonds : bond 0.04831 ( 974) hydrogen bonds : angle 4.23579 ( 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 175 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.8003 (mttt) cc_final: 0.7777 (mmmt) REVERT: A 596 ASP cc_start: 0.8094 (m-30) cc_final: 0.7761 (m-30) REVERT: B 342 LYS cc_start: 0.7944 (mttt) cc_final: 0.7631 (mptm) REVERT: B 590 MET cc_start: 0.8066 (mmm) cc_final: 0.7673 (mtp) REVERT: B 596 ASP cc_start: 0.8229 (m-30) cc_final: 0.7891 (m-30) REVERT: C 289 ASP cc_start: 0.8674 (m-30) cc_final: 0.8449 (m-30) REVERT: C 596 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7856 (m-30) REVERT: D 342 LYS cc_start: 0.7976 (mttt) cc_final: 0.7631 (mptm) REVERT: D 590 MET cc_start: 0.8057 (mmm) cc_final: 0.7662 (mtp) REVERT: D 596 ASP cc_start: 0.8112 (m-30) cc_final: 0.7756 (m-30) outliers start: 31 outliers final: 18 residues processed: 169 average time/residue: 0.9066 time to fit residues: 177.4266 Evaluate side-chains 162 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105633 restraints weight = 47732.931| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.75 r_work: 0.3015 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1111 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= 0.206 Angle : 0.518 10.437 21652 Z= 0.284 Chirality : 0.039 0.373 2420 Planarity : 0.004 0.045 2688 Dihedral : 5.869 89.450 2076 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.41 % Allowed : 12.68 % Favored : 84.92 % 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 aren not related in a simple way. whole: 1.53 (0.19), residues: 1864 helix: 2.25 (0.15), residues: 1064 sheet: -0.16 (0.35), residues: 200 loop : -0.84 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 592 TYR 0.017 0.002 TYR D 247 PHE 0.021 0.002 PHE D 600 TRP 0.005 0.001 TRP A 554 HIS 0.004 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00493 (15952) covalent geometry : angle 0.51744 (21644) SS BOND : bond 0.00032 ( 4) SS BOND : angle 0.67369 ( 8) hydrogen bonds : bond 0.05117 ( 974) hydrogen bonds : angle 4.27506 ( 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 185 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.8003 (mttt) cc_final: 0.7761 (mmmt) REVERT: A 596 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: B 342 LYS cc_start: 0.7967 (mttt) cc_final: 0.7649 (mptm) REVERT: B 590 MET cc_start: 0.8061 (mmm) cc_final: 0.7655 (mtp) REVERT: B 596 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: C 289 ASP cc_start: 0.8695 (m-30) cc_final: 0.8473 (m-30) REVERT: C 596 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: C 613 GLN cc_start: 0.8493 (tt0) cc_final: 0.8188 (mm110) REVERT: D 342 LYS cc_start: 0.7988 (mttt) cc_final: 0.7648 (mptm) REVERT: D 590 MET cc_start: 0.8060 (mmm) cc_final: 0.7646 (mtp) REVERT: D 596 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7722 (m-30) outliers start: 41 outliers final: 29 residues processed: 177 average time/residue: 0.8944 time to fit residues: 182.4854 Evaluate side-chains 173 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 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 398 THR Chi-restraints excluded: chain B residue 488 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 274 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 398 THR 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 262 VAL 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 Chi-restraints excluded: chain D residue 596 ASP 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: 0.6980 chunk 133 optimal weight: 0.9990 chunk 49 optimal weight: 0.0970 chunk 72 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3642 r_free = 0.3642 target = 0.146042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111403 restraints weight = 48506.030| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.73 r_work: 0.3094 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15956 Z= 0.098 Angle : 0.427 7.696 21652 Z= 0.237 Chirality : 0.037 0.369 2420 Planarity : 0.004 0.045 2688 Dihedral : 5.505 88.647 2076 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.94 % Allowed : 13.91 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.19), residues: 1864 helix: 2.66 (0.15), residues: 1060 sheet: -0.13 (0.36), residues: 200 loop : -0.55 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 440 TYR 0.016 0.001 TYR D 247 PHE 0.020 0.001 PHE D 600 TRP 0.004 0.001 TRP C 455 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00207 (15952) covalent geometry : angle 0.42709 (21644) SS BOND : bond 0.00082 ( 4) SS BOND : angle 0.87343 ( 8) hydrogen bonds : bond 0.04035 ( 974) hydrogen bonds : angle 4.01614 ( 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 176 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7995 (mttt) cc_final: 0.7787 (mmmt) REVERT: A 596 ASP cc_start: 0.8068 (m-30) cc_final: 0.7760 (m-30) REVERT: A 662 THR cc_start: 0.8837 (m) cc_final: 0.8346 (p) REVERT: B 342 LYS cc_start: 0.7968 (mttt) cc_final: 0.7760 (mmmt) REVERT: B 590 MET cc_start: 0.8034 (mmm) cc_final: 0.7683 (mtp) REVERT: B 596 ASP cc_start: 0.8238 (m-30) cc_final: 0.7897 (m-30) REVERT: B 662 THR cc_start: 0.8849 (m) cc_final: 0.8351 (p) REVERT: C 289 ASP cc_start: 0.8630 (m-30) cc_final: 0.8389 (m-30) REVERT: C 596 ASP cc_start: 0.8225 (m-30) cc_final: 0.7894 (m-30) REVERT: C 662 THR cc_start: 0.8834 (m) cc_final: 0.8349 (p) REVERT: D 342 LYS cc_start: 0.7983 (mttt) cc_final: 0.7658 (mptm) REVERT: D 585 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.7089 (mm110) REVERT: D 590 MET cc_start: 0.8034 (mmm) cc_final: 0.7677 (mtp) REVERT: D 596 ASP cc_start: 0.8117 (m-30) cc_final: 0.7782 (m-30) REVERT: D 651 GLU cc_start: 0.8275 (tt0) cc_final: 0.7983 (tt0) REVERT: D 662 THR cc_start: 0.8828 (m) cc_final: 0.8341 (p) REVERT: D 677 LEU cc_start: 0.8210 (tp) cc_final: 0.7990 (tp) outliers start: 16 outliers final: 13 residues processed: 171 average time/residue: 0.9351 time to fit residues: 183.6877 Evaluate side-chains 172 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 274 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain D residue 244 SER 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: 5.9990 chunk 171 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108567 restraints weight = 48320.124| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.74 r_work: 0.3077 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15956 Z= 0.158 Angle : 0.471 9.081 21652 Z= 0.259 Chirality : 0.038 0.372 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.646 89.960 2076 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.17 % Allowed : 13.79 % 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 aren not related in a simple way. whole: 1.88 (0.19), residues: 1864 helix: 2.54 (0.15), residues: 1064 sheet: -0.18 (0.35), residues: 200 loop : -0.64 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 251 TYR 0.016 0.002 TYR D 247 PHE 0.021 0.001 PHE D 600 TRP 0.005 0.001 TRP C 293 HIS 0.003 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00370 (15952) covalent geometry : angle 0.47091 (21644) SS BOND : bond 0.00037 ( 4) SS BOND : angle 0.67704 ( 8) hydrogen bonds : bond 0.04540 ( 974) hydrogen bonds : angle 4.09410 ( 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 171 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.8001 (mttt) cc_final: 0.7796 (mmmt) REVERT: A 596 ASP cc_start: 0.8098 (m-30) cc_final: 0.7767 (m-30) REVERT: B 342 LYS cc_start: 0.7969 (mttt) cc_final: 0.7647 (mptm) REVERT: B 590 MET cc_start: 0.8053 (mmm) cc_final: 0.7679 (mtp) REVERT: B 596 ASP cc_start: 0.8228 (m-30) cc_final: 0.7843 (m-30) REVERT: C 289 ASP cc_start: 0.8675 (m-30) cc_final: 0.8440 (m-30) REVERT: C 596 ASP cc_start: 0.8224 (m-30) cc_final: 0.7832 (m-30) REVERT: D 342 LYS cc_start: 0.7990 (mttt) cc_final: 0.7666 (mptm) REVERT: D 585 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7133 (mm110) REVERT: D 590 MET cc_start: 0.8047 (mmm) cc_final: 0.7677 (mtp) REVERT: D 596 ASP cc_start: 0.8121 (m-30) cc_final: 0.7775 (m-30) outliers start: 20 outliers final: 17 residues processed: 165 average time/residue: 1.0481 time to fit residues: 198.2938 Evaluate side-chains 165 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 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 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: 0.9990 chunk 6 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 137 optimal weight: 0.3980 chunk 96 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 543 ASN D 537 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.145650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.111009 restraints weight = 48535.539| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.72 r_work: 0.3063 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.002 0.026 15956 Z= 0.108 Angle : 0.436 8.193 21652 Z= 0.241 Chirality : 0.037 0.370 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.511 89.729 2076 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.00 % Allowed : 13.85 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.19), residues: 1864 helix: 2.70 (0.15), residues: 1060 sheet: -0.18 (0.36), residues: 200 loop : -0.52 (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 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00236 (15952) covalent geometry : angle 0.43602 (21644) SS BOND : bond 0.00063 ( 4) SS BOND : angle 0.75191 ( 8) hydrogen bonds : bond 0.04119 ( 974) hydrogen bonds : angle 4.00114 ( 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 176 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7992 (mttt) cc_final: 0.7697 (mptm) REVERT: A 596 ASP cc_start: 0.8101 (m-30) cc_final: 0.7791 (m-30) REVERT: A 662 THR cc_start: 0.8821 (m) cc_final: 0.8339 (p) REVERT: B 342 LYS cc_start: 0.7979 (mttt) cc_final: 0.7761 (mmmt) REVERT: B 590 MET cc_start: 0.8025 (mmm) cc_final: 0.7700 (mtp) REVERT: B 596 ASP cc_start: 0.8246 (m-30) cc_final: 0.7864 (m-30) REVERT: C 289 ASP cc_start: 0.8640 (m-30) cc_final: 0.8393 (m-30) REVERT: C 596 ASP cc_start: 0.8196 (m-30) cc_final: 0.7800 (m-30) REVERT: C 662 THR cc_start: 0.8836 (m) cc_final: 0.8348 (p) REVERT: D 342 LYS cc_start: 0.7989 (mttt) cc_final: 0.7662 (mptm) REVERT: D 585 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7097 (mm110) REVERT: D 590 MET cc_start: 0.7998 (mmm) cc_final: 0.7687 (mtp) REVERT: D 596 ASP cc_start: 0.8130 (m-30) cc_final: 0.7783 (m-30) REVERT: D 651 GLU cc_start: 0.8299 (tt0) cc_final: 0.8018 (tt0) REVERT: D 662 THR cc_start: 0.8829 (m) cc_final: 0.8352 (p) outliers start: 17 outliers final: 15 residues processed: 170 average time/residue: 1.0231 time to fit residues: 199.3124 Evaluate side-chains 174 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 275 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 515 VAL Chi-restraints excluded: chain B residue 585 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 46 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 117 optimal weight: 0.0050 chunk 119 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112248 restraints weight = 48534.547| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.72 r_work: 0.3083 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1149 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= 0.097 Angle : 0.419 7.925 21652 Z= 0.231 Chirality : 0.036 0.369 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.356 88.697 2076 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.00 % Allowed : 13.79 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.19), residues: 1864 helix: 2.86 (0.15), residues: 1060 sheet: -0.18 (0.36), residues: 200 loop : -0.45 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 251 TYR 0.014 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 covalent geometry : bond 0.00209 (15952) covalent geometry : angle 0.41900 (21644) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.79538 ( 8) hydrogen bonds : bond 0.03878 ( 974) hydrogen bonds : angle 3.91934 ( 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 183 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7989 (mttt) cc_final: 0.7691 (mptm) REVERT: A 596 ASP cc_start: 0.8072 (m-30) cc_final: 0.7766 (m-30) REVERT: A 662 THR cc_start: 0.8809 (m) cc_final: 0.8315 (p) REVERT: B 342 LYS cc_start: 0.7978 (mttt) cc_final: 0.7760 (mmmt) REVERT: B 590 MET cc_start: 0.7985 (mmm) cc_final: 0.7694 (mtp) REVERT: B 596 ASP cc_start: 0.8238 (m-30) cc_final: 0.7857 (m-30) REVERT: B 651 GLU cc_start: 0.8291 (tt0) cc_final: 0.8004 (tt0) REVERT: B 662 THR cc_start: 0.8829 (m) cc_final: 0.8328 (p) REVERT: C 289 ASP cc_start: 0.8618 (m-30) cc_final: 0.8405 (m-30) REVERT: C 596 ASP cc_start: 0.8210 (m-30) cc_final: 0.7812 (m-30) REVERT: C 662 THR cc_start: 0.8825 (m) cc_final: 0.8340 (p) REVERT: D 342 LYS cc_start: 0.7992 (mttt) cc_final: 0.7664 (mptm) REVERT: D 585 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7076 (mm110) REVERT: D 590 MET cc_start: 0.8005 (mmm) cc_final: 0.7693 (mtp) REVERT: D 596 ASP cc_start: 0.8109 (m-30) cc_final: 0.7768 (m-30) REVERT: D 651 GLU cc_start: 0.8276 (tt0) cc_final: 0.7992 (tt0) REVERT: D 662 THR cc_start: 0.8813 (m) cc_final: 0.8324 (p) outliers start: 17 outliers final: 14 residues processed: 176 average time/residue: 0.8824 time to fit residues: 178.7487 Evaluate side-chains 175 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 515 VAL Chi-restraints excluded: chain B residue 585 GLN 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 398 THR Chi-restraints excluded: chain D residue 515 VAL 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: 3.9990 chunk 144 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 186 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110479 restraints weight = 48351.103| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.73 r_work: 0.3078 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1146 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= 0.129 Angle : 0.447 8.575 21652 Z= 0.245 Chirality : 0.037 0.370 2420 Planarity : 0.004 0.043 2688 Dihedral : 5.446 88.031 2076 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.00 % Allowed : 14.03 % 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 aren not related in a simple way. whole: 2.15 (0.19), residues: 1864 helix: 2.77 (0.15), residues: 1060 sheet: -0.17 (0.36), residues: 200 loop : -0.48 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 251 TYR 0.015 0.001 TYR D 247 PHE 0.021 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 covalent geometry : bond 0.00294 (15952) covalent geometry : angle 0.44725 (21644) SS BOND : bond 0.00064 ( 4) SS BOND : angle 0.68245 ( 8) hydrogen bonds : bond 0.04182 ( 974) hydrogen bonds : angle 3.97499 ( 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: 17 poor density : 161 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7991 (mttt) cc_final: 0.7693 (mptm) REVERT: A 596 ASP cc_start: 0.8082 (m-30) cc_final: 0.7762 (m-30) REVERT: B 342 LYS cc_start: 0.7972 (mttt) cc_final: 0.7757 (mmmt) REVERT: B 590 MET cc_start: 0.7971 (mmm) cc_final: 0.7681 (mtp) REVERT: B 596 ASP cc_start: 0.8225 (m-30) cc_final: 0.7838 (m-30) REVERT: C 289 ASP cc_start: 0.8657 (m-30) cc_final: 0.8449 (m-30) REVERT: C 596 ASP cc_start: 0.8209 (m-30) cc_final: 0.7808 (m-30) REVERT: D 342 LYS cc_start: 0.7992 (mttt) cc_final: 0.7659 (mptm) REVERT: D 585 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7114 (mm110) REVERT: D 590 MET cc_start: 0.7973 (mmm) cc_final: 0.7650 (mtp) REVERT: D 596 ASP cc_start: 0.8135 (m-30) cc_final: 0.7795 (m-30) REVERT: D 651 GLU cc_start: 0.8315 (tt0) cc_final: 0.8042 (tt0) outliers start: 17 outliers final: 15 residues processed: 172 average time/residue: 0.9160 time to fit residues: 180.7389 Evaluate side-chains 174 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 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 515 VAL Chi-restraints excluded: chain B residue 585 GLN 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 398 THR Chi-restraints excluded: chain D residue 515 VAL 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: 0.6980 chunk 182 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 172 optimal weight: 0.3980 chunk 151 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 8 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.147823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113333 restraints weight = 48803.050| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.74 r_work: 0.3143 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15956 Z= 0.087 Angle : 0.408 7.501 21652 Z= 0.225 Chirality : 0.036 0.369 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.248 87.746 2076 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.94 % Allowed : 13.91 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.19), residues: 1864 helix: 2.95 (0.15), residues: 1060 sheet: -0.15 (0.37), residues: 200 loop : -0.37 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 592 TYR 0.013 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 covalent geometry : bond 0.00182 (15952) covalent geometry : angle 0.40760 (21644) SS BOND : bond 0.00061 ( 4) SS BOND : angle 0.79725 ( 8) hydrogen bonds : bond 0.03696 ( 974) hydrogen bonds : angle 3.86516 ( 2796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8396.59 seconds wall clock time: 142 minutes 40.17 seconds (8560.17 seconds total)