Starting phenix.real_space_refine on Thu Jul 2 21:09:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iws_60962/07_2026/9iws_60962.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iws_60962/07_2026/9iws_60962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iws_60962/07_2026/9iws_60962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iws_60962/07_2026/9iws_60962.map" model { file = "/net/cci-nas-00/data/ceres_data/9iws_60962/07_2026/9iws_60962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iws_60962/07_2026/9iws_60962.cif" } resolution = 2.86 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= 0.053 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: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 42 5.16 5 C 6738 2.51 5 N 1686 2.21 5 O 1870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10364 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 5102 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 1 Chain: "B" Number of atoms: 5102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 5102 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 1 Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'I7P': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'I7P': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.37, per 1000 atoms: 0.23 Number of scatterers: 10364 At special positions: 0 Unit cell: (107.8, 128.7, 104.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 28 15.00 O 1870 8.00 N 1686 7.00 C 6738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " 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: 1.64 Conformation dependent library (CDL) restraints added in 235.3 milliseconds 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.929A pdb=" N HIS A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 19 removed outlier: 5.355A pdb=" N LYS A 17 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 19 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.586A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 100 Processing helix chain 'A' and resid 119 through 167 removed outlier: 3.843A pdb=" N LYS A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 189 through 206 Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.901A pdb=" N ALA A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 258 removed outlier: 3.541A pdb=" N THR A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.974A pdb=" N ILE A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.647A pdb=" N ILE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.773A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.717A pdb=" N PHE A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRP A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.520A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 removed outlier: 4.286A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 470 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 503 removed outlier: 4.427A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 531 removed outlier: 3.774A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 516 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 521 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 583 removed outlier: 4.287A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 617 Proline residue: A 598 - end of helix removed outlier: 4.111A pdb=" N VAL A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 602 " --> pdb=" O PRO A 598 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'B' and resid 2 through 10 removed outlier: 3.932A pdb=" N HIS B 6 " --> pdb=" O LYS B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 19 removed outlier: 3.625A pdb=" N ARG B 16 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYS B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 19 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 43 through 100 Processing helix chain 'B' and resid 119 through 167 removed outlier: 3.797A pdb=" N LEU B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.965A pdb=" N ASP B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 189 through 206 removed outlier: 3.521A pdb=" N GLN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.937A pdb=" N ALA B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.444A pdb=" N ILE B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.653A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 337 removed outlier: 3.725A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.558A pdb=" N PHE B 372 " --> pdb=" O TYR B 368 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TRP B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.505A pdb=" N PHE B 394 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 419 Processing helix chain 'B' and resid 435 through 440 removed outlier: 4.214A pdb=" N CYS B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 471 removed outlier: 4.518A pdb=" N ILE B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 503 removed outlier: 4.540A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 485 " --> pdb=" O GLY B 481 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 531 removed outlier: 3.798A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP B 514 " --> pdb=" O PHE B 510 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 521 " --> pdb=" O PHE B 517 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 527 " --> pdb=" O CYS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 583 removed outlier: 4.285A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 Processing helix chain 'B' and resid 591 through 597 Processing helix chain 'B' and resid 598 through 617 removed outlier: 3.839A pdb=" N PHE B 602 " --> pdb=" O PRO B 598 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1573 1.30 - 1.43: 3101 1.43 - 1.56: 5880 1.56 - 1.69: 36 1.69 - 1.81: 66 Bond restraints: 10656 Sorted by residual: bond pdb=" O45 I7P A 701 " pdb=" PB5 I7P A 701 " ideal model delta sigma weight residual 1.732 1.590 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" O45 I7P A 702 " pdb=" PB5 I7P A 702 " ideal model delta sigma weight residual 1.732 1.590 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" O45 I7P B 701 " pdb=" PB5 I7P B 701 " ideal model delta sigma weight residual 1.732 1.590 0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" O45 I7P B 702 " pdb=" PB5 I7P B 702 " ideal model delta sigma weight residual 1.732 1.590 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C PRO B 184 " pdb=" O PRO B 184 " ideal model delta sigma weight residual 1.237 1.177 0.061 1.20e-02 6.94e+03 2.55e+01 ... (remaining 10651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 14179 2.90 - 5.80: 233 5.80 - 8.71: 56 8.71 - 11.61: 20 11.61 - 14.51: 8 Bond angle restraints: 14496 Sorted by residual: angle pdb=" N ASN A 432 " pdb=" CA ASN A 432 " pdb=" C ASN A 432 " ideal model delta sigma weight residual 112.57 103.94 8.63 1.13e+00 7.83e-01 5.83e+01 angle pdb=" N HIS A 587 " pdb=" CA HIS A 587 " pdb=" C HIS A 587 " ideal model delta sigma weight residual 114.62 106.21 8.41 1.14e+00 7.69e-01 5.45e+01 angle pdb=" CA PRO B 431 " pdb=" CB PRO B 431 " pdb=" CG PRO B 431 " ideal model delta sigma weight residual 104.50 91.48 13.02 1.90e+00 2.77e-01 4.70e+01 angle pdb=" N PRO B 431 " pdb=" CA PRO B 431 " pdb=" C PRO B 431 " ideal model delta sigma weight residual 112.47 125.21 -12.74 2.06e+00 2.36e-01 3.82e+01 angle pdb=" N PRO B 431 " pdb=" CA PRO B 431 " pdb=" CB PRO B 431 " ideal model delta sigma weight residual 103.25 97.27 5.98 1.05e+00 9.07e-01 3.24e+01 ... (remaining 14491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.59: 5838 28.59 - 57.18: 484 57.18 - 85.77: 37 85.77 - 114.36: 3 114.36 - 142.96: 6 Dihedral angle restraints: 6368 sinusoidal: 2726 harmonic: 3642 Sorted by residual: dihedral pdb=" CB CYS B 415 " pdb=" SG CYS B 415 " pdb=" SG CYS B 440 " pdb=" CB CYS B 440 " ideal model delta sinusoidal sigma weight residual 93.00 178.45 -85.45 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS A 415 " pdb=" SG CYS A 415 " pdb=" SG CYS A 440 " pdb=" CB CYS A 440 " ideal model delta sinusoidal sigma weight residual 93.00 171.98 -78.98 1 1.00e+01 1.00e-02 7.77e+01 dihedral pdb=" CA LEU B 430 " pdb=" C LEU B 430 " pdb=" N PRO B 431 " pdb=" CA PRO B 431 " ideal model delta harmonic sigma weight residual 180.00 -153.97 -26.03 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 6365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1337 0.057 - 0.114: 196 0.114 - 0.172: 22 0.172 - 0.229: 10 0.229 - 0.286: 5 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CA PRO A 586 " pdb=" N PRO A 586 " pdb=" C PRO A 586 " pdb=" CB PRO A 586 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA LEU B 430 " pdb=" N LEU B 430 " pdb=" C LEU B 430 " pdb=" CB LEU B 430 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ALA B 183 " pdb=" N ALA B 183 " pdb=" C ALA B 183 " pdb=" CB ALA B 183 " both_signs ideal model delta sigma weight residual False 2.48 2.74 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1567 not shown) Planarity restraints: 1776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 430 " -0.118 5.00e-02 4.00e+02 1.85e-01 5.50e+01 pdb=" N PRO B 431 " 0.321 5.00e-02 4.00e+02 pdb=" CA PRO B 431 " -0.104 5.00e-02 4.00e+02 pdb=" CD PRO B 431 " -0.098 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 585 " -0.077 5.00e-02 4.00e+02 1.21e-01 2.36e+01 pdb=" N PRO B 586 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO B 586 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 586 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 586 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C PRO B 586 " 0.059 2.00e-02 2.50e+03 pdb=" O PRO B 586 " -0.022 2.00e-02 2.50e+03 pdb=" N HIS B 587 " -0.020 2.00e-02 2.50e+03 ... (remaining 1773 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 44 2.55 - 3.14: 7986 3.14 - 3.73: 16122 3.73 - 4.31: 21073 4.31 - 4.90: 35686 Nonbonded interactions: 80911 Sorted by model distance: nonbonded pdb=" N GLU A 14 " pdb=" OE1 GLU A 14 " model vdw 1.965 3.120 nonbonded pdb=" N GLU B 14 " pdb=" OE1 GLU B 14 " model vdw 2.033 3.120 nonbonded pdb=" N GLU A 5 " pdb=" OE1 GLU A 5 " model vdw 2.120 3.120 nonbonded pdb=" N GLU B 5 " pdb=" OE1 GLU B 5 " model vdw 2.120 3.120 nonbonded pdb=" O THR A 470 " pdb=" OG1 THR A 470 " model vdw 2.220 3.040 ... (remaining 80906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.670 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 9.780 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 0.005 0.142 10658 Z= 0.288 Angle : 0.970 14.511 14500 Z= 0.465 Chirality : 0.045 0.286 1570 Planarity : 0.006 0.185 1776 Dihedral : 19.179 142.956 4002 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.66 % Favored : 93.77 % Rotamer: Outliers : 3.85 % Allowed : 28.21 % Favored : 67.95 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.25), residues: 1220 helix: 2.25 (0.18), residues: 878 sheet: None (None), residues: 0 loop : -2.21 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 171 TYR 0.022 0.001 TYR A 443 PHE 0.015 0.001 PHE A 185 TRP 0.016 0.001 TRP B 423 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.29 (10656) covalent geometry : angle 0.96924 / 0.46 (14496) SS BOND : bond 0.00039 / 0.02 ( 2) SS BOND : angle 2.85596 / 1.52 ( 4) hydrogen bonds : bond 0.13899 / 9.48 ( 690) hydrogen bonds : angle 5.34083 / 3.78 ( 2049) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7506 (mmtt) cc_final: 0.6970 (mmpt) REVERT: A 17 LYS cc_start: 0.7444 (mmtm) cc_final: 0.7092 (ptpp) REVERT: A 82 ARG cc_start: 0.7861 (mtm180) cc_final: 0.7632 (ttm110) REVERT: A 160 LEU cc_start: 0.7556 (mt) cc_final: 0.7251 (mm) REVERT: A 177 VAL cc_start: 0.7868 (OUTLIER) cc_final: 0.7577 (m) REVERT: A 182 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7598 (p) REVERT: A 201 VAL cc_start: 0.6639 (OUTLIER) cc_final: 0.5998 (p) REVERT: A 205 GLU cc_start: 0.6181 (tp30) cc_final: 0.5860 (mp0) REVERT: A 258 LYS cc_start: 0.7190 (tptt) cc_final: 0.6531 (mptt) REVERT: A 430 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5718 (pt) REVERT: A 508 MET cc_start: 0.5321 (OUTLIER) cc_final: 0.4142 (ttm) REVERT: A 520 ILE cc_start: 0.8966 (mt) cc_final: 0.8733 (mp) REVERT: A 612 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8117 (mp) REVERT: B 17 LYS cc_start: 0.7441 (mmtm) cc_final: 0.7022 (ptpp) REVERT: B 82 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7598 (ttm110) REVERT: B 177 VAL cc_start: 0.7842 (t) cc_final: 0.7625 (m) REVERT: B 201 VAL cc_start: 0.6522 (OUTLIER) cc_final: 0.6003 (p) REVERT: B 205 GLU cc_start: 0.6271 (tp30) cc_final: 0.5906 (mp0) REVERT: B 258 LYS cc_start: 0.7448 (tttp) cc_final: 0.6461 (mptt) REVERT: B 461 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7561 (pt) REVERT: B 508 MET cc_start: 0.5268 (mmm) cc_final: 0.4143 (tmm) REVERT: B 520 ILE cc_start: 0.8958 (mt) cc_final: 0.8714 (mp) outliers start: 42 outliers final: 14 residues processed: 180 average time/residue: 0.4761 time to fit residues: 92.7980 Evaluate side-chains 142 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 431 PRO Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 630 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0470 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.211971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.176469 restraints weight = 11632.482| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.78 r_work: 0.3818 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 10658 Z= 0.163 Angle : 0.637 7.092 14500 Z= 0.332 Chirality : 0.041 0.190 1570 Planarity : 0.005 0.139 1776 Dihedral : 11.719 105.259 1629 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.51 % Favored : 95.25 % Rotamer: Outliers : 4.21 % Allowed : 26.37 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.25), residues: 1220 helix: 2.35 (0.17), residues: 892 sheet: None (None), residues: 0 loop : -2.16 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 171 TYR 0.016 0.002 TYR A 443 PHE 0.024 0.001 PHE A 394 TRP 0.015 0.001 TRP A 607 HIS 0.003 0.001 HIS B 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (10656) covalent geometry : angle 0.63688 / 0.33 (14496) SS BOND : bond 0.00479 / 0.25 ( 2) SS BOND : angle 1.60999 / 0.84 ( 4) hydrogen bonds : bond 0.05901 / 3.87 ( 690) hydrogen bonds : angle 3.72212 / 2.66 ( 2049) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.371 Fit side-chains REVERT: A 17 LYS cc_start: 0.7396 (mmtm) cc_final: 0.7039 (ptpp) REVERT: A 171 ARG cc_start: 0.5627 (OUTLIER) cc_final: 0.5125 (mpp-170) REVERT: A 205 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.5869 (mp0) REVERT: A 258 LYS cc_start: 0.7061 (tptt) cc_final: 0.6372 (mptt) REVERT: A 508 MET cc_start: 0.5294 (mmm) cc_final: 0.4138 (ttm) REVERT: A 565 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7681 (pp20) REVERT: B 17 LYS cc_start: 0.7657 (mmtm) cc_final: 0.7044 (ptpp) REVERT: B 28 MET cc_start: 0.6795 (ttt) cc_final: 0.6576 (ttt) REVERT: B 82 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7770 (ttm110) REVERT: B 189 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.6978 (mmtp) REVERT: B 258 LYS cc_start: 0.7424 (tttp) cc_final: 0.6508 (mptt) REVERT: B 268 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8225 (tp) REVERT: B 383 THR cc_start: 0.7175 (m) cc_final: 0.6682 (p) REVERT: B 472 ARG cc_start: 0.7134 (tmt-80) cc_final: 0.6843 (tmt-80) REVERT: B 508 MET cc_start: 0.5238 (OUTLIER) cc_final: 0.3972 (ttm) REVERT: B 576 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7422 (tm-30) outliers start: 46 outliers final: 9 residues processed: 157 average time/residue: 0.5423 time to fit residues: 91.6502 Evaluate side-chains 118 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 GLN Chi-restraints excluded: chain B residue 629 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN A 163 HIS A 288 ASN A 310 ASN A 314 GLN A 499 HIS B 288 ASN B 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.208911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.165400 restraints weight = 11931.987| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.99 r_work: 0.3718 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 10658 Z= 0.238 Angle : 0.720 12.023 14500 Z= 0.374 Chirality : 0.046 0.203 1570 Planarity : 0.006 0.135 1776 Dihedral : 10.438 80.885 1598 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.59 % Favored : 95.16 % Rotamer: Outliers : 6.78 % Allowed : 25.18 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1220 helix: 1.91 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -2.24 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 171 TYR 0.017 0.003 TYR A 553 PHE 0.027 0.002 PHE B 394 TRP 0.021 0.002 TRP B 266 HIS 0.009 0.002 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (10656) covalent geometry : angle 0.72023 / 0.37 (14496) SS BOND : bond 0.00244 / 0.12 ( 2) SS BOND : angle 1.24873 / 0.65 ( 4) hydrogen bonds : bond 0.07562 / 4.93 ( 690) hydrogen bonds : angle 3.96735 / 2.84 ( 2049) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 119 time to evaluate : 0.383 Fit side-chains REVERT: A 2 LYS cc_start: 0.7734 (mmpt) cc_final: 0.7261 (mmpt) REVERT: A 28 MET cc_start: 0.6871 (ttt) cc_final: 0.6610 (ttt) REVERT: A 168 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6766 (tt0) REVERT: A 171 ARG cc_start: 0.5802 (OUTLIER) cc_final: 0.5427 (mpp-170) REVERT: A 258 LYS cc_start: 0.7119 (tptt) cc_final: 0.6380 (mptt) REVERT: A 331 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7892 (tp) REVERT: A 423 TRP cc_start: 0.8042 (OUTLIER) cc_final: 0.7066 (m100) REVERT: A 452 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: A 508 MET cc_start: 0.4825 (mmm) cc_final: 0.3780 (ttm) REVERT: A 624 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7125 (ttt180) REVERT: B 2 LYS cc_start: 0.7751 (mmpt) cc_final: 0.7275 (mmpt) REVERT: B 28 MET cc_start: 0.6729 (ttt) cc_final: 0.6446 (ttt) REVERT: B 189 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7189 (mtmt) REVERT: B 258 LYS cc_start: 0.7291 (tttp) cc_final: 0.6339 (mptt) REVERT: B 268 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8171 (tp) REVERT: B 472 ARG cc_start: 0.7521 (tmt-80) cc_final: 0.7251 (tmt-80) REVERT: B 508 MET cc_start: 0.4559 (OUTLIER) cc_final: 0.3421 (tpp) REVERT: B 512 TYR cc_start: 0.5537 (OUTLIER) cc_final: 0.4410 (m-10) REVERT: B 576 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: B 624 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7218 (ttt180) outliers start: 74 outliers final: 23 residues processed: 177 average time/residue: 0.4946 time to fit residues: 94.5575 Evaluate side-chains 134 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 GLN Chi-restraints excluded: chain B residue 629 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 79 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.213742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.168613 restraints weight = 11904.309| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.87 r_work: 0.3832 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 10658 Z= 0.141 Angle : 0.587 9.304 14500 Z= 0.304 Chirality : 0.040 0.173 1570 Planarity : 0.005 0.123 1776 Dihedral : 9.132 58.968 1596 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.67 % Favored : 95.16 % Rotamer: Outliers : 4.76 % Allowed : 26.37 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.25), residues: 1220 helix: 2.37 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -2.17 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 171 TYR 0.014 0.001 TYR A 443 PHE 0.017 0.001 PHE A 610 TRP 0.015 0.001 TRP A 607 HIS 0.002 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10656) covalent geometry : angle 0.58736 / 0.30 (14496) SS BOND : bond 0.00035 / 0.02 ( 2) SS BOND : angle 0.57801 / 0.29 ( 4) hydrogen bonds : bond 0.05558 / 3.65 ( 690) hydrogen bonds : angle 3.59204 / 2.55 ( 2049) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 114 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.6761 (ttt) cc_final: 0.6500 (ttt) REVERT: A 171 ARG cc_start: 0.5516 (OUTLIER) cc_final: 0.5170 (mpp-170) REVERT: A 258 LYS cc_start: 0.7028 (tptt) cc_final: 0.6256 (mptt) REVERT: A 318 GLU cc_start: 0.8397 (tt0) cc_final: 0.8079 (tt0) REVERT: A 331 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7650 (tp) REVERT: A 420 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6241 (tp30) REVERT: A 452 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: A 508 MET cc_start: 0.4545 (mmm) cc_final: 0.3407 (ttm) REVERT: B 28 MET cc_start: 0.6665 (ttt) cc_final: 0.6384 (ttt) REVERT: B 38 SER cc_start: 0.4507 (OUTLIER) cc_final: 0.4177 (p) REVERT: B 258 LYS cc_start: 0.7148 (tttp) cc_final: 0.6106 (mptt) REVERT: B 318 GLU cc_start: 0.8190 (tt0) cc_final: 0.7859 (tt0) REVERT: B 331 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7811 (tp) REVERT: B 508 MET cc_start: 0.4168 (OUTLIER) cc_final: 0.3061 (tpp) outliers start: 52 outliers final: 11 residues processed: 152 average time/residue: 0.5942 time to fit residues: 96.7240 Evaluate side-chains 124 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 629 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 117 optimal weight: 0.0570 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.214377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.169616 restraints weight = 11822.936| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.84 r_work: 0.3813 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 10658 Z= 0.129 Angle : 0.577 9.633 14500 Z= 0.295 Chirality : 0.039 0.191 1570 Planarity : 0.005 0.115 1776 Dihedral : 7.974 57.437 1596 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.02 % Favored : 95.82 % Rotamer: Outliers : 3.57 % Allowed : 27.38 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.25), residues: 1220 helix: 2.58 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -2.09 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 171 TYR 0.013 0.001 TYR A 443 PHE 0.017 0.001 PHE A 610 TRP 0.014 0.001 TRP A 607 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10656) covalent geometry : angle 0.57709 / 0.29 (14496) SS BOND : bond 0.00004 / 0.00 ( 2) SS BOND : angle 0.48024 / 0.24 ( 4) hydrogen bonds : bond 0.05203 / 3.42 ( 690) hydrogen bonds : angle 3.43547 / 2.44 ( 2049) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.6869 (ttt) cc_final: 0.6652 (ttt) REVERT: A 51 PHE cc_start: 0.5337 (OUTLIER) cc_final: 0.4298 (m-10) REVERT: A 164 ASP cc_start: 0.7018 (m-30) cc_final: 0.6816 (m-30) REVERT: A 171 ARG cc_start: 0.5646 (OUTLIER) cc_final: 0.5218 (mpp-170) REVERT: A 258 LYS cc_start: 0.7052 (tptt) cc_final: 0.6298 (mptt) REVERT: A 331 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7756 (tp) REVERT: A 508 MET cc_start: 0.4564 (mmm) cc_final: 0.3462 (ttm) REVERT: A 565 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7773 (pp20) REVERT: A 624 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7426 (ptt180) REVERT: B 38 SER cc_start: 0.4671 (OUTLIER) cc_final: 0.4401 (p) REVERT: B 186 TYR cc_start: 0.7388 (t80) cc_final: 0.7084 (t80) REVERT: B 258 LYS cc_start: 0.7190 (tttp) cc_final: 0.6188 (mptt) REVERT: B 268 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8079 (tp) REVERT: B 301 LEU cc_start: 0.8478 (tt) cc_final: 0.8128 (tp) REVERT: B 331 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7957 (tp) REVERT: B 417 TYR cc_start: 0.6933 (m-10) cc_final: 0.6659 (m-10) REVERT: B 508 MET cc_start: 0.4554 (OUTLIER) cc_final: 0.3590 (tpp) outliers start: 39 outliers final: 10 residues processed: 139 average time/residue: 0.4965 time to fit residues: 74.3157 Evaluate side-chains 125 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 629 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 387 HIS ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.213862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.167922 restraints weight = 11890.519| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.94 r_work: 0.3826 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 10658 Z= 0.138 Angle : 0.583 9.886 14500 Z= 0.298 Chirality : 0.039 0.171 1570 Planarity : 0.005 0.107 1776 Dihedral : 7.778 56.845 1596 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.51 % Favored : 95.33 % Rotamer: Outliers : 4.03 % Allowed : 27.38 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.25), residues: 1220 helix: 2.60 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -2.07 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 176 TYR 0.012 0.001 TYR A 443 PHE 0.016 0.001 PHE A 610 TRP 0.014 0.001 TRP A 607 HIS 0.004 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (10656) covalent geometry : angle 0.58316 / 0.30 (14496) SS BOND : bond 0.00037 / 0.02 ( 2) SS BOND : angle 0.39940 / 0.19 ( 4) hydrogen bonds : bond 0.05297 / 3.48 ( 690) hydrogen bonds : angle 3.43599 / 2.45 ( 2049) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.6689 (ttt) cc_final: 0.6476 (ttt) REVERT: A 51 PHE cc_start: 0.5300 (OUTLIER) cc_final: 0.4340 (m-10) REVERT: A 171 ARG cc_start: 0.5788 (OUTLIER) cc_final: 0.5372 (mpp-170) REVERT: A 258 LYS cc_start: 0.7011 (tptt) cc_final: 0.6209 (mptt) REVERT: A 331 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7643 (tp) REVERT: A 452 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7952 (mt0) REVERT: A 508 MET cc_start: 0.4130 (mmm) cc_final: 0.3324 (ttp) REVERT: A 565 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7841 (pp20) REVERT: B 38 SER cc_start: 0.4531 (OUTLIER) cc_final: 0.4296 (p) REVERT: B 186 TYR cc_start: 0.7319 (t80) cc_final: 0.6993 (t80) REVERT: B 258 LYS cc_start: 0.7162 (tttp) cc_final: 0.6118 (mptt) REVERT: B 268 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7970 (tp) REVERT: B 318 GLU cc_start: 0.8039 (tt0) cc_final: 0.7786 (tt0) REVERT: B 331 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7813 (tp) REVERT: B 417 TYR cc_start: 0.6835 (m-10) cc_final: 0.6578 (m-10) REVERT: B 508 MET cc_start: 0.4470 (OUTLIER) cc_final: 0.3540 (tpp) outliers start: 44 outliers final: 13 residues processed: 139 average time/residue: 0.5242 time to fit residues: 78.1953 Evaluate side-chains 125 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 629 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 107 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.212406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.166469 restraints weight = 11773.282| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.89 r_work: 0.3799 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 10658 Z= 0.156 Angle : 0.621 9.899 14500 Z= 0.317 Chirality : 0.040 0.175 1570 Planarity : 0.005 0.119 1776 Dihedral : 7.681 56.251 1596 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.51 % Favored : 95.33 % Rotamer: Outliers : 4.40 % Allowed : 26.56 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.25), residues: 1220 helix: 2.54 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -2.05 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 171 TYR 0.012 0.002 TYR A 553 PHE 0.017 0.001 PHE B 610 TRP 0.014 0.002 TRP A 607 HIS 0.005 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (10656) covalent geometry : angle 0.62149 / 0.32 (14496) SS BOND : bond 0.00045 / 0.02 ( 2) SS BOND : angle 0.37630 / 0.18 ( 4) hydrogen bonds : bond 0.05681 / 3.71 ( 690) hydrogen bonds : angle 3.46582 / 2.47 ( 2049) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 51 PHE cc_start: 0.5378 (OUTLIER) cc_final: 0.4338 (m-10) REVERT: A 258 LYS cc_start: 0.7083 (tptt) cc_final: 0.6337 (mptt) REVERT: A 331 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7696 (tp) REVERT: A 448 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6620 (mmt180) REVERT: A 452 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: A 508 MET cc_start: 0.4260 (mmm) cc_final: 0.3713 (ttp) REVERT: A 624 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7375 (ptt90) REVERT: B 51 PHE cc_start: 0.5212 (OUTLIER) cc_final: 0.4261 (m-10) REVERT: B 168 GLU cc_start: 0.6507 (mt-10) cc_final: 0.6222 (mt-10) REVERT: B 186 TYR cc_start: 0.7315 (t80) cc_final: 0.6998 (t80) REVERT: B 258 LYS cc_start: 0.7242 (tttp) cc_final: 0.6254 (mptt) REVERT: B 268 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7941 (tp) REVERT: B 318 GLU cc_start: 0.8056 (tt0) cc_final: 0.7828 (tt0) REVERT: B 331 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7870 (tp) REVERT: B 369 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7858 (mttm) REVERT: B 508 MET cc_start: 0.4309 (OUTLIER) cc_final: 0.3537 (tpp) REVERT: B 565 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7388 (tt0) outliers start: 48 outliers final: 17 residues processed: 139 average time/residue: 0.5546 time to fit residues: 82.8521 Evaluate side-chains 128 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 629 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.0030 chunk 67 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 107 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.215100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.169898 restraints weight = 11732.499| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.96 r_work: 0.3804 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 10658 Z= 0.126 Angle : 0.576 10.392 14500 Z= 0.293 Chirality : 0.038 0.182 1570 Planarity : 0.005 0.108 1776 Dihedral : 7.573 58.618 1596 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.18 % Favored : 95.66 % Rotamer: Outliers : 3.39 % Allowed : 27.75 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.25), residues: 1220 helix: 2.66 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -1.98 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 176 TYR 0.012 0.001 TYR A 518 PHE 0.016 0.001 PHE A 54 TRP 0.013 0.001 TRP A 607 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (10656) covalent geometry : angle 0.57612 / 0.29 (14496) SS BOND : bond 0.00031 / 0.02 ( 2) SS BOND : angle 0.40864 / 0.20 ( 4) hydrogen bonds : bond 0.04922 / 3.23 ( 690) hydrogen bonds : angle 3.35987 / 2.38 ( 2049) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7155 (mmpt) REVERT: A 51 PHE cc_start: 0.5357 (OUTLIER) cc_final: 0.4308 (m-10) REVERT: A 258 LYS cc_start: 0.7079 (tptt) cc_final: 0.6350 (mptt) REVERT: A 331 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7665 (tp) REVERT: A 410 LEU cc_start: 0.7826 (tp) cc_final: 0.7595 (tm) REVERT: A 448 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6438 (mmt180) REVERT: A 452 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: A 508 MET cc_start: 0.4121 (mmm) cc_final: 0.3743 (ttp) REVERT: A 565 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7629 (pp20) REVERT: A 624 ARG cc_start: 0.7741 (ttp80) cc_final: 0.7406 (ptt90) REVERT: B 51 PHE cc_start: 0.5380 (OUTLIER) cc_final: 0.4310 (m-10) REVERT: B 186 TYR cc_start: 0.7374 (t80) cc_final: 0.7075 (t80) REVERT: B 258 LYS cc_start: 0.7239 (tttp) cc_final: 0.6268 (mptt) REVERT: B 268 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7966 (tp) REVERT: B 318 GLU cc_start: 0.7799 (tt0) cc_final: 0.7565 (tt0) REVERT: B 331 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7832 (tp) REVERT: B 369 LYS cc_start: 0.8154 (mtmt) cc_final: 0.7884 (mttm) REVERT: B 508 MET cc_start: 0.4129 (OUTLIER) cc_final: 0.3712 (tpp) outliers start: 37 outliers final: 15 residues processed: 130 average time/residue: 0.5578 time to fit residues: 77.6495 Evaluate side-chains 126 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 629 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.213492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.167710 restraints weight = 11756.861| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.91 r_work: 0.3785 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10658 Z= 0.142 Angle : 0.600 11.008 14500 Z= 0.303 Chirality : 0.039 0.175 1570 Planarity : 0.005 0.130 1776 Dihedral : 7.534 57.912 1596 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.39 % Allowed : 27.84 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.25), residues: 1220 helix: 2.60 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -1.93 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 171 TYR 0.017 0.001 TYR B 417 PHE 0.016 0.001 PHE B 610 TRP 0.014 0.001 TRP A 607 HIS 0.004 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10656) covalent geometry : angle 0.60046 / 0.30 (14496) SS BOND : bond 0.00013 / 0.01 ( 2) SS BOND : angle 0.41965 / 0.20 ( 4) hydrogen bonds : bond 0.05318 / 3.48 ( 690) hydrogen bonds : angle 3.39934 / 2.42 ( 2049) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7255 (mmpt) REVERT: A 51 PHE cc_start: 0.5379 (OUTLIER) cc_final: 0.4327 (m-10) REVERT: A 258 LYS cc_start: 0.7063 (tptt) cc_final: 0.6375 (mptt) REVERT: A 331 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7753 (tp) REVERT: A 448 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6499 (mmt180) REVERT: A 452 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: A 508 MET cc_start: 0.4118 (mmm) cc_final: 0.3850 (ttp) REVERT: A 624 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7431 (ptt90) REVERT: B 51 PHE cc_start: 0.5286 (OUTLIER) cc_final: 0.4182 (m-10) REVERT: B 186 TYR cc_start: 0.7393 (t80) cc_final: 0.7099 (t80) REVERT: B 258 LYS cc_start: 0.7227 (tttp) cc_final: 0.6273 (mptt) REVERT: B 268 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7995 (tp) REVERT: B 318 GLU cc_start: 0.7829 (tt0) cc_final: 0.7596 (tt0) REVERT: B 331 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7868 (tp) REVERT: B 369 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7912 (mttm) REVERT: B 508 MET cc_start: 0.3948 (OUTLIER) cc_final: 0.3609 (tpp) outliers start: 37 outliers final: 15 residues processed: 126 average time/residue: 0.5654 time to fit residues: 76.4581 Evaluate side-chains 120 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 629 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 11 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 42 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.214971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.169704 restraints weight = 11702.864| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.86 r_work: 0.3806 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10658 Z= 0.128 Angle : 0.588 11.478 14500 Z= 0.299 Chirality : 0.038 0.177 1570 Planarity : 0.005 0.139 1776 Dihedral : 7.486 59.129 1596 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.75 % Allowed : 29.03 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.25), residues: 1220 helix: 2.63 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -1.93 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 171 TYR 0.012 0.001 TYR A 518 PHE 0.015 0.001 PHE A 610 TRP 0.014 0.001 TRP A 607 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10656) covalent geometry : angle 0.58832 / 0.30 (14496) SS BOND : bond 0.00016 / 0.01 ( 2) SS BOND : angle 0.53847 / 0.26 ( 4) hydrogen bonds : bond 0.04979 / 3.27 ( 690) hydrogen bonds : angle 3.35992 / 2.39 ( 2049) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7496 (mmpt) REVERT: A 51 PHE cc_start: 0.5389 (OUTLIER) cc_final: 0.4327 (m-10) REVERT: A 217 ARG cc_start: 0.7017 (ttm-80) cc_final: 0.6441 (ttp80) REVERT: A 258 LYS cc_start: 0.7008 (tptt) cc_final: 0.6269 (mptt) REVERT: A 331 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7785 (tp) REVERT: A 410 LEU cc_start: 0.7915 (tp) cc_final: 0.7686 (tm) REVERT: A 448 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.5135 (tmt170) REVERT: A 452 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: A 508 MET cc_start: 0.4157 (mmm) cc_final: 0.3806 (ttp) REVERT: A 565 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7734 (pp20) REVERT: A 624 ARG cc_start: 0.7644 (ttp80) cc_final: 0.7363 (ptt90) REVERT: B 51 PHE cc_start: 0.5433 (OUTLIER) cc_final: 0.4383 (m-10) REVERT: B 186 TYR cc_start: 0.7417 (t80) cc_final: 0.6984 (t80) REVERT: B 258 LYS cc_start: 0.7183 (tttp) cc_final: 0.6171 (mptt) REVERT: B 318 GLU cc_start: 0.8017 (tt0) cc_final: 0.7784 (tt0) REVERT: B 331 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7935 (tp) REVERT: B 369 LYS cc_start: 0.8309 (mtmt) cc_final: 0.8011 (mttm) REVERT: B 417 TYR cc_start: 0.6758 (m-10) cc_final: 0.6517 (m-10) outliers start: 30 outliers final: 10 residues processed: 118 average time/residue: 0.6338 time to fit residues: 80.0038 Evaluate side-chains 113 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 629 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 95 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.213797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.168392 restraints weight = 11821.908| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.88 r_work: 0.3788 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10658 Z= 0.142 Angle : 0.603 11.320 14500 Z= 0.306 Chirality : 0.039 0.172 1570 Planarity : 0.005 0.145 1776 Dihedral : 7.425 58.283 1596 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.38 % Allowed : 29.12 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.25), residues: 1220 helix: 2.60 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 171 TYR 0.011 0.001 TYR A 518 PHE 0.016 0.001 PHE B 610 TRP 0.013 0.001 TRP A 607 HIS 0.005 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (10656) covalent geometry : angle 0.60313 / 0.31 (14496) SS BOND : bond 0.00035 / 0.02 ( 2) SS BOND : angle 0.55009 / 0.25 ( 4) hydrogen bonds : bond 0.05280 / 3.46 ( 690) hydrogen bonds : angle 3.37863 / 2.41 ( 2049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3501.04 seconds wall clock time: 60 minutes 18.06 seconds (3618.06 seconds total)