Starting phenix.real_space_refine on Thu Jun 26 16:30:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwq_47260/06_2025/9dwq_47260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwq_47260/06_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_47260/06_2025/9dwq_47260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwq_47260/06_2025/9dwq_47260.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwq_47260/06_2025/9dwq_47260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwq_47260/06_2025/9dwq_47260.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.75, per 1000 atoms: 0.48 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: 7.24 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.32 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: 11.43 Time building geometry restraints manager: 8.85 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: 4.420 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: 0.540 Extract box with map and model: 1.270 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 62.210 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.920 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP B 293 HIS 0.001 0.001 HIS D 498 PHE 0.020 0.001 PHE C 600 TYR 0.011 0.001 TYR B 247 ARG 0.002 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.15224 ( 974) hydrogen bonds : angle 5.48485 ( 2796) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.71829 ( 8) covalent geometry : bond 0.00249 (15952) covalent geometry : angle 0.49290 (21644) *********************** 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 : 2.344 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: 2.1620 time to fit residues: 472.0204 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 : 2.519 ------------------------------------------------------------------------------- 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 158 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN C 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106303 restraints weight = 48509.120| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.74 r_work: 0.3035 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15956 Z= 0.259 Angle : 0.561 10.778 21652 Z= 0.309 Chirality : 0.041 0.366 2420 Planarity : 0.005 0.040 2688 Dihedral : 5.994 87.294 2089 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.19), residues: 1864 helix: 2.17 (0.15), residues: 1068 sheet: -0.08 (0.36), residues: 200 loop : -0.71 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 507 HIS 0.004 0.001 HIS D 498 PHE 0.020 0.002 PHE A 600 TYR 0.019 0.002 TYR D 247 ARG 0.003 0.000 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.05877 ( 974) hydrogen bonds : angle 4.60074 ( 2796) SS BOND : bond 0.00078 ( 4) SS BOND : angle 0.63924 ( 8) covalent geometry : bond 0.00625 (15952) covalent geometry : angle 0.56126 (21644) *********************** 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 178 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7971 (mttt) cc_final: 0.7740 (mmmt) REVERT: A 596 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7798 (m-30) REVERT: B 342 LYS cc_start: 0.7955 (mttt) cc_final: 0.7728 (mmmt) REVERT: B 590 MET cc_start: 0.8094 (mmm) cc_final: 0.7675 (mtm) REVERT: B 596 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: C 596 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: C 677 LEU cc_start: 0.8426 (tp) cc_final: 0.7740 (mp) REVERT: D 305 ASN cc_start: 0.6240 (t0) cc_final: 0.5985 (t0) REVERT: D 342 LYS cc_start: 0.7994 (mttt) cc_final: 0.7652 (mptm) REVERT: D 590 MET cc_start: 0.8117 (mmm) cc_final: 0.7672 (mtp) outliers start: 31 outliers final: 22 residues processed: 170 average time/residue: 2.0026 time to fit residues: 391.2712 Evaluate side-chains 167 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 2.550 ------------------------------------------------------------------------------- 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 596 ASP 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 262 VAL Chi-restraints excluded: chain D residue 268 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 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 130 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.144270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108892 restraints weight = 48463.711| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.75 r_work: 0.3076 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15956 Z= 0.134 Angle : 0.465 8.776 21652 Z= 0.257 Chirality : 0.037 0.367 2420 Planarity : 0.004 0.040 2688 Dihedral : 5.559 87.069 2078 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.64 % Allowed : 12.85 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.19), residues: 1864 helix: 2.45 (0.15), residues: 1060 sheet: -0.08 (0.35), residues: 200 loop : -0.65 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 293 HIS 0.002 0.001 HIS D 498 PHE 0.020 0.001 PHE D 600 TYR 0.017 0.001 TYR D 247 ARG 0.001 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 974) hydrogen bonds : angle 4.29074 ( 2796) SS BOND : bond 0.00019 ( 4) SS BOND : angle 0.71988 ( 8) covalent geometry : bond 0.00302 (15952) covalent geometry : angle 0.46462 (21644) *********************** 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 174 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7980 (mttt) cc_final: 0.7762 (mmmt) REVERT: A 596 ASP cc_start: 0.8093 (m-30) cc_final: 0.7775 (m-30) REVERT: B 342 LYS cc_start: 0.7944 (mttt) cc_final: 0.7725 (mmmt) REVERT: B 590 MET cc_start: 0.8049 (mmm) cc_final: 0.7654 (mtp) REVERT: B 596 ASP cc_start: 0.8214 (m-30) cc_final: 0.7870 (m-30) REVERT: C 289 ASP cc_start: 0.8680 (m-30) cc_final: 0.8445 (m-30) REVERT: C 596 ASP cc_start: 0.8239 (m-30) cc_final: 0.7882 (m-30) REVERT: C 677 LEU cc_start: 0.8349 (tp) cc_final: 0.7682 (mp) REVERT: D 342 LYS cc_start: 0.7974 (mttt) cc_final: 0.7632 (mptm) REVERT: D 585 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7024 (mm110) REVERT: D 590 MET cc_start: 0.8056 (mmm) cc_final: 0.7655 (mtp) REVERT: D 596 ASP cc_start: 0.8143 (m-30) cc_final: 0.7791 (m-30) outliers start: 28 outliers final: 12 residues processed: 168 average time/residue: 2.0907 time to fit residues: 403.5735 Evaluate side-chains 156 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 2.399 ------------------------------------------------------------------------------- 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 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 275 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 515 VAL 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 113 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3607 r_free = 0.3607 target = 0.142999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107684 restraints weight = 48553.594| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.75 r_work: 0.3037 rms_B_bonded: 2.08 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: 0.8426 moved from start: 0.0980 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= 0.182 Angle : 0.498 9.731 21652 Z= 0.274 Chirality : 0.038 0.370 2420 Planarity : 0.004 0.043 2688 Dihedral : 5.704 88.499 2076 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.58 % Allowed : 13.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.19), residues: 1864 helix: 2.34 (0.15), residues: 1064 sheet: -0.10 (0.35), residues: 200 loop : -0.79 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 293 HIS 0.003 0.001 HIS D 498 PHE 0.021 0.001 PHE D 600 TYR 0.017 0.002 TYR D 247 ARG 0.004 0.000 ARG C 592 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 974) hydrogen bonds : angle 4.25966 ( 2796) SS BOND : bond 0.00005 ( 4) SS BOND : angle 0.67299 ( 8) covalent geometry : bond 0.00430 (15952) covalent geometry : angle 0.49815 (21644) *********************** 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: 27 poor density : 148 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.8018 (mttt) cc_final: 0.7775 (mmmt) REVERT: A 596 ASP cc_start: 0.8100 (m-30) cc_final: 0.7773 (m-30) REVERT: B 342 LYS cc_start: 0.7950 (mttt) cc_final: 0.7629 (mptm) REVERT: B 590 MET cc_start: 0.8067 (mmm) cc_final: 0.7641 (mtp) REVERT: B 596 ASP cc_start: 0.8237 (m-30) cc_final: 0.7878 (m-30) REVERT: C 596 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: C 677 LEU cc_start: 0.8386 (tp) cc_final: 0.7731 (mp) REVERT: D 342 LYS cc_start: 0.7978 (mttt) cc_final: 0.7634 (mptm) REVERT: D 590 MET cc_start: 0.8072 (mmm) cc_final: 0.7650 (mtp) REVERT: D 596 ASP cc_start: 0.8123 (m-30) cc_final: 0.7770 (m-30) outliers start: 27 outliers final: 16 residues processed: 171 average time/residue: 2.3984 time to fit residues: 475.8205 Evaluate side-chains 162 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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 573 LEU Chi-restraints excluded: chain A residue 591 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 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 268 THR Chi-restraints excluded: chain D residue 515 VAL 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 77 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.142944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.107650 restraints weight = 48377.198| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.75 r_work: 0.3059 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1060 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= 0.176 Angle : 0.494 9.881 21652 Z= 0.271 Chirality : 0.038 0.372 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.764 88.971 2076 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.88 % Allowed : 13.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.19), residues: 1864 helix: 2.34 (0.15), residues: 1064 sheet: -0.20 (0.35), residues: 200 loop : -0.78 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 293 HIS 0.003 0.001 HIS D 498 PHE 0.021 0.001 PHE D 600 TYR 0.017 0.002 TYR D 247 ARG 0.002 0.000 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 974) hydrogen bonds : angle 4.22043 ( 2796) SS BOND : bond 0.00010 ( 4) SS BOND : angle 0.67868 ( 8) covalent geometry : bond 0.00414 (15952) covalent geometry : angle 0.49398 (21644) *********************** 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 175 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.8012 (mttt) cc_final: 0.7784 (mmmt) REVERT: A 596 ASP cc_start: 0.8088 (m-30) cc_final: 0.7760 (m-30) REVERT: B 342 LYS cc_start: 0.7959 (mttt) cc_final: 0.7640 (mptm) REVERT: B 590 MET cc_start: 0.8086 (mmm) cc_final: 0.7673 (mtp) REVERT: B 596 ASP cc_start: 0.8234 (m-30) cc_final: 0.7887 (m-30) REVERT: C 596 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: C 613 GLN cc_start: 0.8461 (tt0) cc_final: 0.8176 (mm110) REVERT: D 342 LYS cc_start: 0.7987 (mttt) cc_final: 0.7662 (mptm) REVERT: D 590 MET cc_start: 0.8084 (mmm) cc_final: 0.7671 (mtp) REVERT: D 596 ASP cc_start: 0.8113 (m-30) cc_final: 0.7763 (m-30) outliers start: 32 outliers final: 20 residues processed: 171 average time/residue: 1.9410 time to fit residues: 383.7268 Evaluate side-chains 161 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 2.165 ------------------------------------------------------------------------------- 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 398 THR Chi-restraints excluded: chain A residue 591 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 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 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 398 THR Chi-restraints excluded: chain D residue 515 VAL 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 43 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN C 543 ASN D 305 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 = 0.143010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.107735 restraints weight = 47571.869| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.74 r_work: 0.3043 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1064 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= 0.138 Angle : 0.464 9.015 21652 Z= 0.255 Chirality : 0.037 0.370 2420 Planarity : 0.004 0.045 2688 Dihedral : 5.666 89.200 2076 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.29 % Allowed : 13.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 1864 helix: 2.51 (0.15), residues: 1060 sheet: -0.24 (0.35), residues: 200 loop : -0.67 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 293 HIS 0.002 0.001 HIS D 498 PHE 0.021 0.001 PHE D 600 TYR 0.016 0.001 TYR D 247 ARG 0.002 0.000 ARG D 251 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 974) hydrogen bonds : angle 4.12282 ( 2796) SS BOND : bond 0.00031 ( 4) SS BOND : angle 0.72214 ( 8) covalent geometry : bond 0.00315 (15952) covalent geometry : angle 0.46385 (21644) *********************** 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 167 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.8016 (mttt) cc_final: 0.7787 (mmmt) REVERT: A 596 ASP cc_start: 0.8026 (m-30) cc_final: 0.7694 (m-30) REVERT: B 342 LYS cc_start: 0.7956 (mttt) cc_final: 0.7641 (mptm) REVERT: B 590 MET cc_start: 0.8036 (mmm) cc_final: 0.7651 (mtp) REVERT: B 596 ASP cc_start: 0.8177 (m-30) cc_final: 0.7818 (m-30) REVERT: B 613 GLN cc_start: 0.8474 (tt0) cc_final: 0.8140 (mm110) REVERT: C 596 ASP cc_start: 0.8181 (m-30) cc_final: 0.7847 (m-30) REVERT: C 613 GLN cc_start: 0.8460 (tt0) cc_final: 0.8166 (mm110) REVERT: D 342 LYS cc_start: 0.7982 (mttt) cc_final: 0.7661 (mptm) REVERT: D 585 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7090 (mm110) REVERT: D 590 MET cc_start: 0.8065 (mmm) cc_final: 0.7647 (mtp) REVERT: D 596 ASP cc_start: 0.8057 (m-30) cc_final: 0.7701 (m-30) outliers start: 22 outliers final: 20 residues processed: 164 average time/residue: 2.0721 time to fit residues: 392.2706 Evaluate side-chains 163 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 2.282 ------------------------------------------------------------------------------- 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 A residue 561 ILE Chi-restraints excluded: chain A residue 591 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 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 585 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.141531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.106248 restraints weight = 47827.494| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.73 r_work: 0.3026 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15956 Z= 0.193 Angle : 0.505 10.124 21652 Z= 0.277 Chirality : 0.038 0.373 2420 Planarity : 0.004 0.045 2688 Dihedral : 5.829 89.980 2076 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.53 % Allowed : 13.62 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 1864 helix: 2.33 (0.15), residues: 1064 sheet: -0.31 (0.35), residues: 200 loop : -0.79 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 293 HIS 0.004 0.001 HIS D 498 PHE 0.021 0.002 PHE D 600 TYR 0.017 0.002 TYR D 247 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 974) hydrogen bonds : angle 4.20117 ( 2796) SS BOND : bond 0.00010 ( 4) SS BOND : angle 0.66896 ( 8) covalent geometry : bond 0.00461 (15952) covalent geometry : angle 0.50497 (21644) *********************** 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 170 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.8007 (mttt) cc_final: 0.7788 (mmmt) REVERT: A 596 ASP cc_start: 0.8037 (m-30) cc_final: 0.7695 (m-30) REVERT: B 342 LYS cc_start: 0.7968 (mttt) cc_final: 0.7647 (mptm) REVERT: B 590 MET cc_start: 0.8056 (mmm) cc_final: 0.7676 (mtp) REVERT: B 596 ASP cc_start: 0.8192 (m-30) cc_final: 0.7835 (m-30) REVERT: B 613 GLN cc_start: 0.8511 (tt0) cc_final: 0.8163 (mm110) REVERT: C 596 ASP cc_start: 0.8172 (m-30) cc_final: 0.7777 (m-30) REVERT: C 613 GLN cc_start: 0.8487 (tt0) cc_final: 0.8180 (mm110) REVERT: D 342 LYS cc_start: 0.7989 (mttt) cc_final: 0.7663 (mptm) REVERT: D 590 MET cc_start: 0.8062 (mmm) cc_final: 0.7638 (mtp) REVERT: D 596 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7714 (m-30) outliers start: 26 outliers final: 24 residues processed: 166 average time/residue: 2.0254 time to fit residues: 386.6590 Evaluate side-chains 164 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 2.177 ------------------------------------------------------------------------------- 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 A residue 573 LEU Chi-restraints excluded: chain A residue 591 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 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 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 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 585 GLN Chi-restraints excluded: chain D residue 596 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.143479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.107834 restraints weight = 47776.986| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.77 r_work: 0.3037 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1108 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= 0.123 Angle : 0.454 8.566 21652 Z= 0.250 Chirality : 0.037 0.370 2420 Planarity : 0.004 0.045 2688 Dihedral : 5.658 89.739 2076 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.23 % Allowed : 13.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 1864 helix: 2.56 (0.15), residues: 1060 sheet: -0.26 (0.35), residues: 200 loop : -0.62 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 293 HIS 0.002 0.001 HIS D 498 PHE 0.021 0.001 PHE D 600 TYR 0.016 0.001 TYR D 247 ARG 0.001 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 974) hydrogen bonds : angle 4.07498 ( 2796) SS BOND : bond 0.00039 ( 4) SS BOND : angle 0.77127 ( 8) covalent geometry : bond 0.00276 (15952) covalent geometry : angle 0.45352 (21644) *********************** 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 167 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7999 (mttt) cc_final: 0.7692 (mptm) REVERT: A 596 ASP cc_start: 0.8024 (m-30) cc_final: 0.7690 (m-30) REVERT: B 342 LYS cc_start: 0.7947 (mttt) cc_final: 0.7736 (mmmt) REVERT: B 590 MET cc_start: 0.8007 (mmm) cc_final: 0.7642 (mtp) REVERT: B 596 ASP cc_start: 0.8183 (m-30) cc_final: 0.7802 (m-30) REVERT: C 596 ASP cc_start: 0.8163 (m-30) cc_final: 0.7773 (m-30) REVERT: D 342 LYS cc_start: 0.7990 (mttt) cc_final: 0.7665 (mptm) REVERT: D 585 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7097 (mm110) REVERT: D 590 MET cc_start: 0.8031 (mmm) cc_final: 0.7657 (mtp) REVERT: D 596 ASP cc_start: 0.8049 (m-30) cc_final: 0.7696 (m-30) outliers start: 21 outliers final: 19 residues processed: 161 average time/residue: 2.0181 time to fit residues: 373.6240 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 : 2.201 ------------------------------------------------------------------------------- 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 A residue 591 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 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 268 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 116 optimal weight: 0.0870 chunk 117 optimal weight: 0.7980 overall best weight: 1.7764 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.142505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107229 restraints weight = 47559.306| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.74 r_work: 0.3043 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.004 0.032 15956 Z= 0.153 Angle : 0.475 9.338 21652 Z= 0.260 Chirality : 0.037 0.371 2420 Planarity : 0.004 0.045 2688 Dihedral : 5.712 89.588 2076 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.23 % Allowed : 13.91 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.19), residues: 1864 helix: 2.52 (0.15), residues: 1060 sheet: -0.29 (0.35), residues: 200 loop : -0.72 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 293 HIS 0.003 0.001 HIS D 498 PHE 0.021 0.001 PHE D 600 TYR 0.016 0.002 TYR B 247 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 974) hydrogen bonds : angle 4.10508 ( 2796) SS BOND : bond 0.00029 ( 4) SS BOND : angle 0.69401 ( 8) covalent geometry : bond 0.00358 (15952) covalent geometry : angle 0.47506 (21644) *********************** 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 167 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7998 (mttt) cc_final: 0.7694 (mptm) REVERT: A 596 ASP cc_start: 0.8036 (m-30) cc_final: 0.7692 (m-30) REVERT: B 342 LYS cc_start: 0.7955 (mttt) cc_final: 0.7634 (mptm) REVERT: B 590 MET cc_start: 0.8012 (mmm) cc_final: 0.7650 (mtp) REVERT: B 596 ASP cc_start: 0.8186 (m-30) cc_final: 0.7800 (m-30) REVERT: C 596 ASP cc_start: 0.8167 (m-30) cc_final: 0.7779 (m-30) REVERT: C 613 GLN cc_start: 0.8461 (tt0) cc_final: 0.8162 (mm110) REVERT: D 342 LYS cc_start: 0.7991 (mttt) cc_final: 0.7668 (mptm) REVERT: D 585 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7097 (mm110) REVERT: D 590 MET cc_start: 0.8032 (mmm) cc_final: 0.7642 (mtp) REVERT: D 596 ASP cc_start: 0.8062 (m-30) cc_final: 0.7703 (m-30) outliers start: 21 outliers final: 20 residues processed: 162 average time/residue: 2.1148 time to fit residues: 398.1089 Evaluate side-chains 165 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 2.549 ------------------------------------------------------------------------------- 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 A residue 591 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 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 585 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 107 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.143840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108241 restraints weight = 47732.984| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.76 r_work: 0.3025 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15956 Z= 0.120 Angle : 0.446 8.544 21652 Z= 0.246 Chirality : 0.037 0.370 2420 Planarity : 0.004 0.045 2688 Dihedral : 5.597 89.519 2076 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 1864 helix: 2.67 (0.15), residues: 1056 sheet: -0.25 (0.36), residues: 200 loop : -0.58 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 293 HIS 0.003 0.001 HIS D 498 PHE 0.020 0.001 PHE D 600 TYR 0.015 0.001 TYR B 247 ARG 0.001 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 974) hydrogen bonds : angle 4.02662 ( 2796) SS BOND : bond 0.00040 ( 4) SS BOND : angle 0.77181 ( 8) covalent geometry : bond 0.00268 (15952) covalent geometry : angle 0.44630 (21644) ********************** 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 170 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.7997 (mttt) cc_final: 0.7681 (mptm) REVERT: A 596 ASP cc_start: 0.8012 (m-30) cc_final: 0.7678 (m-30) REVERT: B 342 LYS cc_start: 0.7963 (mttt) cc_final: 0.7749 (mmmt) REVERT: B 590 MET cc_start: 0.7974 (mmm) cc_final: 0.7658 (mtp) REVERT: B 596 ASP cc_start: 0.8187 (m-30) cc_final: 0.7807 (m-30) REVERT: C 596 ASP cc_start: 0.8180 (m-30) cc_final: 0.7782 (m-30) REVERT: D 342 LYS cc_start: 0.7993 (mttt) cc_final: 0.7662 (mptm) REVERT: D 585 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7069 (mm110) REVERT: D 590 MET cc_start: 0.7984 (mmm) cc_final: 0.7642 (mtp) REVERT: D 596 ASP cc_start: 0.8042 (m-30) cc_final: 0.7687 (m-30) REVERT: D 651 GLU cc_start: 0.8267 (tt0) cc_final: 0.7980 (tt0) outliers start: 20 outliers final: 18 residues processed: 164 average time/residue: 2.0235 time to fit residues: 380.6936 Evaluate side-chains 167 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 2.141 ------------------------------------------------------------------------------- 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 591 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 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 585 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 162 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 105 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.143361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108149 restraints weight = 47866.954| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.74 r_work: 0.3020 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15956 Z= 0.139 Angle : 0.462 8.814 21652 Z= 0.253 Chirality : 0.037 0.371 2420 Planarity : 0.004 0.044 2688 Dihedral : 5.626 89.042 2076 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.29 % Allowed : 13.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.19), residues: 1864 helix: 2.61 (0.15), residues: 1060 sheet: -0.26 (0.36), residues: 200 loop : -0.64 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 293 HIS 0.003 0.001 HIS D 498 PHE 0.020 0.001 PHE D 600 TYR 0.016 0.001 TYR B 247 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 974) hydrogen bonds : angle 4.04820 ( 2796) SS BOND : bond 0.00035 ( 4) SS BOND : angle 0.72068 ( 8) covalent geometry : bond 0.00320 (15952) covalent geometry : angle 0.46143 (21644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17653.67 seconds wall clock time: 301 minutes 1.81 seconds (18061.81 seconds total)