Starting phenix.real_space_refine on Thu Jun 4 18:50:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qww_53429/06_2026/9qww_53429.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qww_53429/06_2026/9qww_53429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qww_53429/06_2026/9qww_53429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qww_53429/06_2026/9qww_53429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qww_53429/06_2026/9qww_53429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qww_53429/06_2026/9qww_53429.map" } resolution = 3.8 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 9199 2.51 5 N 2482 2.21 5 O 2655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14400 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5830 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 689} Chain breaks: 1 Chain: "B" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1235 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 183} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 7, 'GLU:plan': 8, 'ASN:plan1': 6, 'TYR:plan': 6, 'GLN:plan1': 1, 'PHE:plan': 4, 'TRP:plan': 2, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 203 Chain: "D" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1505 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 184} Chain: "C" Number of atoms: 5830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5830 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 689} Chain breaks: 1 Time building chain proxies: 3.54, per 1000 atoms: 0.25 Number of scatterers: 14400 At special positions: 0 Unit cell: (154.88, 80, 124.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2655 8.00 N 2482 7.00 C 9199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 410 " - pdb=" SG CYS A 414 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 304 " distance=2.03 Simple disulfide: pdb=" SG CYS C 410 " - pdb=" SG CYS C 414 " distance=2.05 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: 1.20 Conformation dependent library (CDL) restraints added in 702.8 milliseconds 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3414 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 22 sheets defined 24.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 157 through 165 removed outlier: 4.016A pdb=" N ASP A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 295 through 301 removed outlier: 4.008A pdb=" N CYS A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 339 through 346 removed outlier: 3.819A pdb=" N SER A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.714A pdb=" N TRP A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 removed outlier: 4.072A pdb=" N LEU A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.683A pdb=" N LEU A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.745A pdb=" N MET A 492 " --> pdb=" O GLN A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 517 removed outlier: 3.841A pdb=" N THR A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.609A pdb=" N PHE A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 674 through 678 removed outlier: 3.771A pdb=" N CYS A 678 " --> pdb=" O PRO A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.848A pdb=" N ARG A 685 " --> pdb=" O GLU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 707 through 712 removed outlier: 3.662A pdb=" N LYS A 710 " --> pdb=" O SER A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 759 through 767 removed outlier: 4.036A pdb=" N SER A 762 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 838 removed outlier: 3.769A pdb=" N LEU A 835 " --> pdb=" O PRO A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 870 Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.004A pdb=" N ALA B 34 " --> pdb=" O TRP B 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'C' and resid 156 through 159 removed outlier: 3.982A pdb=" N GLU C 159 " --> pdb=" O GLY C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 159' Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.806A pdb=" N ASN C 193 " --> pdb=" O THR C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 248 through 252 removed outlier: 3.997A pdb=" N PHE C 252 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.565A pdb=" N GLN C 300 " --> pdb=" O LYS C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 4.074A pdb=" N TRP C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 346 removed outlier: 3.797A pdb=" N SER C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 368 through 382 removed outlier: 3.755A pdb=" N TRP C 372 " --> pdb=" O THR C 368 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY C 380 " --> pdb=" O ASP C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 401 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 480 through 487 Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.591A pdb=" N MET C 492 " --> pdb=" O GLN C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 517 removed outlier: 3.957A pdb=" N THR C 517 " --> pdb=" O ARG C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 533 Processing helix chain 'C' and resid 559 through 565 Processing helix chain 'C' and resid 582 through 588 removed outlier: 3.856A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 611 Processing helix chain 'C' and resid 674 through 678 removed outlier: 3.808A pdb=" N CYS C 678 " --> pdb=" O PRO C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 685 removed outlier: 3.612A pdb=" N ARG C 685 " --> pdb=" O GLU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 702 removed outlier: 3.890A pdb=" N LEU C 701 " --> pdb=" O LYS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 712 removed outlier: 3.704A pdb=" N LYS C 710 " --> pdb=" O SER C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 742 removed outlier: 3.534A pdb=" N ILE C 741 " --> pdb=" O PRO C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 767 removed outlier: 4.250A pdb=" N MET C 767 " --> pdb=" O ILE C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 838 removed outlier: 3.637A pdb=" N LEU C 835 " --> pdb=" O PRO C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 870 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 180 removed outlier: 7.725A pdb=" N VAL A 178 " --> pdb=" O LEU A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 212 Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 500 removed outlier: 3.696A pdb=" N GLN A 499 " --> pdb=" O ARG A 520 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 522 " --> pdb=" O GLN A 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 551 through 552 removed outlier: 6.781A pdb=" N ILE A 551 " --> pdb=" O ASN A 577 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A 597 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER A 575 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 618 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A 598 " --> pdb=" O ASN A 620 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 625 through 627 removed outlier: 6.848A pdb=" N LEU A 626 " --> pdb=" O LYS A 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 694 through 696 removed outlier: 5.853A pdb=" N ILE A 694 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU A 751 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 756 through 757 removed outlier: 5.376A pdb=" N LEU A 756 " --> pdb=" O MET A 781 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 784 through 786 removed outlier: 6.738A pdb=" N TRP A 785 " --> pdb=" O LYS A 808 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 798 through 799 removed outlier: 5.426A pdb=" N ILE A 799 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N PHE A 882 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A 846 " --> pdb=" O PHE A 882 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.640A pdb=" N LEU B 100 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 195 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 48 through 50 removed outlier: 3.957A pdb=" N GLU D 49 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN D 59 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 84 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN D 168 " --> pdb=" O ASN D 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 68 through 71 removed outlier: 3.799A pdb=" N VAL D 70 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 196 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AB6, first strand: chain 'D' and resid 137 through 139 Processing sheet with id=AB7, first strand: chain 'C' and resid 209 through 212 removed outlier: 7.161A pdb=" N ILE C 209 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASP C 264 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL C 211 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AB9, first strand: chain 'C' and resid 551 through 552 removed outlier: 4.206A pdb=" N SER C 597 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER C 575 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 618 " --> pdb=" O ILE C 594 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER C 598 " --> pdb=" O ASN C 620 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU C 617 " --> pdb=" O HIS C 642 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 625 through 627 removed outlier: 6.793A pdb=" N LEU C 626 " --> pdb=" O LYS C 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 691 through 696 removed outlier: 3.899A pdb=" N GLY C 696 " --> pdb=" O ILE C 724 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS C 776 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU C 797 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE C 823 " --> pdb=" O LEU C 797 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE C 799 " --> pdb=" O ILE C 823 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N PHE C 882 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU C 846 " --> pdb=" O PHE C 882 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 756 through 757 removed outlier: 5.065A pdb=" N LEU C 756 " --> pdb=" O MET C 781 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 784 through 786 removed outlier: 6.678A pdb=" N TRP C 785 " --> pdb=" O LYS C 808 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 280 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4708 1.35 - 1.47: 3421 1.47 - 1.60: 6485 1.60 - 1.72: 0 1.72 - 1.85: 89 Bond restraints: 14703 Sorted by residual: bond pdb=" CA ILE C 558 " pdb=" CB ILE C 558 " ideal model delta sigma weight residual 1.537 1.545 -0.008 5.00e-03 4.00e+04 2.58e+00 bond pdb=" CB PRO A 199 " pdb=" CG PRO A 199 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.77e+00 bond pdb=" CB CYS C 410 " pdb=" SG CYS C 410 " ideal model delta sigma weight residual 1.808 1.849 -0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" C LEU C 260 " pdb=" N ILE C 261 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.24e-02 6.50e+03 1.41e+00 bond pdb=" CA ARG B 135 " pdb=" C ARG B 135 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.26e-02 6.30e+03 1.20e+00 ... (remaining 14698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 19394 2.24 - 4.47: 415 4.47 - 6.71: 49 6.71 - 8.94: 17 8.94 - 11.18: 4 Bond angle restraints: 19879 Sorted by residual: angle pdb=" N ILE A 458 " pdb=" CA ILE A 458 " pdb=" C ILE A 458 " ideal model delta sigma weight residual 112.96 107.76 5.20 1.00e+00 1.00e+00 2.70e+01 angle pdb=" C ASN C 283 " pdb=" CA ASN C 283 " pdb=" CB ASN C 283 " ideal model delta sigma weight residual 116.54 110.81 5.73 1.15e+00 7.56e-01 2.49e+01 angle pdb=" C LYS C 427 " pdb=" N LEU C 428 " pdb=" CA LEU C 428 " ideal model delta sigma weight residual 121.54 130.42 -8.88 1.91e+00 2.74e-01 2.16e+01 angle pdb=" C ASP A 200 " pdb=" CA ASP A 200 " pdb=" CB ASP A 200 " ideal model delta sigma weight residual 116.34 110.53 5.81 1.40e+00 5.10e-01 1.72e+01 angle pdb=" C LYS A 427 " pdb=" N LEU A 428 " pdb=" CA LEU A 428 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 ... (remaining 19874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7477 17.93 - 35.87: 1068 35.87 - 53.80: 258 53.80 - 71.73: 63 71.73 - 89.66: 28 Dihedral angle restraints: 8894 sinusoidal: 3609 harmonic: 5285 Sorted by residual: dihedral pdb=" CB CYS C 410 " pdb=" SG CYS C 410 " pdb=" SG CYS C 414 " pdb=" CB CYS C 414 " ideal model delta sinusoidal sigma weight residual 93.00 5.52 87.48 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CA PHE C 417 " pdb=" C PHE C 417 " pdb=" N PRO C 418 " pdb=" CA PRO C 418 " ideal model delta harmonic sigma weight residual -180.00 -146.14 -33.86 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA THR C 476 " pdb=" C THR C 476 " pdb=" N CYS C 477 " pdb=" CA CYS C 477 " ideal model delta harmonic sigma weight residual 180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 8891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1536 0.046 - 0.092: 510 0.092 - 0.137: 164 0.137 - 0.183: 7 0.183 - 0.229: 2 Chirality restraints: 2219 Sorted by residual: chirality pdb=" CG LEU A 383 " pdb=" CB LEU A 383 " pdb=" CD1 LEU A 383 " pdb=" CD2 LEU A 383 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO A 199 " pdb=" N PRO A 199 " pdb=" C PRO A 199 " pdb=" CB PRO A 199 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA TYR C 196 " pdb=" N TYR C 196 " pdb=" C TYR C 196 " pdb=" CB TYR C 196 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 2216 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 198 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO A 199 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 178 " 0.061 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO A 179 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 351 " 0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO C 352 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 352 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 352 " 0.048 5.00e-02 4.00e+02 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 6669 2.94 - 3.43: 15660 3.43 - 3.92: 25110 3.92 - 4.41: 28931 4.41 - 4.90: 44685 Nonbonded interactions: 121055 Sorted by model distance: nonbonded pdb=" O ASP A 557 " pdb=" OD1 ASP A 557 " model vdw 2.448 3.040 nonbonded pdb=" OD1 ASP C 331 " pdb=" N LYS C 332 " model vdw 2.458 3.120 nonbonded pdb=" O ASP C 557 " pdb=" OD1 ASP C 557 " model vdw 2.491 3.040 nonbonded pdb=" O ASP C 557 " pdb=" OG1 THR C 560 " model vdw 2.502 3.040 nonbonded pdb=" OH TYR C 212 " pdb=" O LEU C 479 " model vdw 2.538 3.040 ... (remaining 121050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 29 through 214) selection = (chain 'D' and (resid 37 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 43 or (resid 44 through 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 through 51 or (res \ id 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or r \ esid 57 through 60 or (resid 61 and (name N or name CA or name C or name O or na \ me CB )) or resid 62 or (resid 63 and (name N or name CA or name C or name O or \ name CB )) or resid 64 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 70 or (resid 71 through 73 and (na \ me N or name CA or name C or name O or name CB )) or resid 74 through 75 or (res \ id 76 through 78 and (name N or name CA or name C or name O or name CB )) or res \ id 79 or (resid 80 and (name N or name CA or name C or name O or name CB )) or r \ esid 81 through 82 or (resid 83 and (name N or name CA or name C or name O or na \ me CB )) or resid 84 or (resid 85 and (name N or name CA or name C or name O or \ name CB )) or resid 86 or (resid 87 and (name N or name CA or name C or name O o \ r name CB )) or resid 88 through 94 or (resid 95 through 98 and (name N or name \ CA or name C or name O or name CB )) or resid 99 through 103 or (resid 104 throu \ gh 106 and (name N or name CA or name C or name O or name CB )) or resid 107 or \ (resid 108 through 109 and (name N or name CA or name C or name O or name CB )) \ or resid 110 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 121 or (resid 122 and (name N or name CA or \ name C or name O or name CB )) or resid 123 or (resid 124 and (name N or name C \ A or name C or name O or name CB )) or resid 125 through 126 or (resid 127 throu \ gh 129 and (name N or name CA or name C or name O or name CB )) or resid 130 or \ (resid 131 and (name N or name CA or name C or name O or name CB )) or resid 132 \ through 135 or (resid 136 through 139 and (name N or name CA or name C or name \ O or name CB )) or resid 140 through 144 or (resid 145 and (name N or name CA or \ name C or name O or name CB )) or resid 146 or (resid 147 and (name N or name C \ A or name C or name O or name CB )) or resid 148 through 149 or (resid 150 and ( \ name N or name CA or name C or name O or name CB )) or resid 151 or (resid 152 t \ hrough 156 and (name N or name CA or name C or name O or name CB )) or resid 157 \ through 164 or (resid 165 and (name N or name CA or name C or name O or name CB \ )) or resid 166 or (resid 167 and (name N or name CA or name C or name O or nam \ e CB )) or resid 168 through 170 or (resid 171 and (name N or name CA or name C \ or name O or name CB )) or resid 172 or (resid 173 through 174 and (name N or na \ me CA or name C or name O or name CB )) or resid 175 or (resid 176 through 177 a \ nd (name N or name CA or name C or name O or name CB )) or resid 178 through 187 \ or (resid 188 through 191 and (name N or name CA or name C or name O or name CB \ )) or resid 192 through 200 or (resid 201 and (name N or name CA or name C or n \ ame O or name CB )) or resid 202 or (resid 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 205 or (resid 206 through 209 and ( \ name N or name CA or name C or name O or name CB )) or resid 210 through 212 or \ (resid 213 through 214 and (name N or name CA or name C or name O or name CB )) \ or resid 215 through 222)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 14.630 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5334 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 : 0.003 0.067 14707 Z= 0.155 Angle : 0.788 11.178 19887 Z= 0.412 Chirality : 0.048 0.229 2219 Planarity : 0.006 0.106 2547 Dihedral : 18.336 89.664 5468 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.93 % Allowed : 14.49 % Favored : 84.58 % Rotamer: Outliers : 3.53 % Allowed : 28.58 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.06 % Twisted Proline : 1.19 % 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: -3.37 (0.18), residues: 1822 helix: -2.83 (0.23), residues: 368 sheet: -2.03 (0.31), residues: 259 loop : -2.18 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 520 TYR 0.022 0.001 TYR A 196 PHE 0.041 0.002 PHE A 313 TRP 0.020 0.002 TRP A 432 HIS 0.013 0.001 HIS C 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (14703) covalent geometry : angle 0.78342 / 0.41 (19879) SS BOND : bond 0.00977 / 0.49 ( 4) SS BOND : angle 4.13901 / 1.79 ( 8) hydrogen bonds : bond 0.21659 / 13.88 ( 280) hydrogen bonds : angle 11.06922 / 7.66 ( 663) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 117 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.4825 (OUTLIER) cc_final: 0.4415 (mt0) REVERT: A 222 LEU cc_start: 0.8789 (mp) cc_final: 0.8209 (tt) REVERT: A 242 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 261 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8643 (pt) REVERT: A 272 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.5854 (m100) REVERT: A 403 LEU cc_start: 0.3729 (OUTLIER) cc_final: 0.3115 (mm) REVERT: D 84 PHE cc_start: -0.0876 (OUTLIER) cc_final: -0.4206 (t80) REVERT: D 106 MET cc_start: -0.1124 (tpp) cc_final: -0.1654 (tpt) REVERT: D 142 GLU cc_start: 0.6843 (tp30) cc_final: 0.5631 (tm-30) REVERT: D 184 LEU cc_start: 0.7558 (pt) cc_final: 0.6739 (mp) REVERT: D 197 SER cc_start: 0.7790 (OUTLIER) cc_final: 0.7423 (p) REVERT: C 228 SER cc_start: 0.4520 (OUTLIER) cc_final: 0.4309 (t) REVERT: C 272 TRP cc_start: 0.7794 (t60) cc_final: 0.6925 (t60) REVERT: C 403 LEU cc_start: 0.3643 (OUTLIER) cc_final: 0.3177 (mt) REVERT: C 691 LYS cc_start: 0.7520 (tttp) cc_final: 0.7254 (tmtt) outliers start: 55 outliers final: 42 residues processed: 163 average time/residue: 0.1078 time to fit residues: 27.5768 Evaluate side-chains 163 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 113 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 TYR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 711 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.0060 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.150468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.130153 restraints weight = 57442.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.133056 restraints weight = 36152.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.134986 restraints weight = 26155.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.136287 restraints weight = 20786.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.137208 restraints weight = 17620.124| |-----------------------------------------------------------------------------| r_work (final): 0.4752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5263 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14707 Z= 0.170 Angle : 0.748 9.594 19887 Z= 0.380 Chirality : 0.048 0.216 2219 Planarity : 0.006 0.101 2547 Dihedral : 9.622 83.240 2040 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.99 % Allowed : 15.42 % Favored : 83.59 % Rotamer: Outliers : 6.42 % Allowed : 25.95 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.06 % Twisted Proline : 1.19 % 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: -3.32 (0.18), residues: 1822 helix: -2.52 (0.24), residues: 371 sheet: -1.86 (0.32), residues: 257 loop : -2.29 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 520 TYR 0.014 0.002 TYR A 196 PHE 0.015 0.002 PHE D 152 TRP 0.016 0.002 TRP A 210 HIS 0.010 0.001 HIS C 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (14703) covalent geometry : angle 0.74523 / 0.38 (19879) SS BOND : bond 0.00816 / 0.41 ( 4) SS BOND : angle 3.49213 / 1.53 ( 8) hydrogen bonds : bond 0.04190 / 2.74 ( 280) hydrogen bonds : angle 8.54115 / 5.89 ( 663) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 117 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.5807 (OUTLIER) cc_final: 0.4503 (t) REVERT: A 204 GLN cc_start: 0.4476 (OUTLIER) cc_final: 0.4135 (mt0) REVERT: A 243 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6795 (tm-30) REVERT: A 261 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8545 (pt) REVERT: A 272 TRP cc_start: 0.7585 (OUTLIER) cc_final: 0.5793 (m100) REVERT: A 403 LEU cc_start: 0.3401 (OUTLIER) cc_final: 0.2897 (mm) REVERT: A 460 ARG cc_start: 0.3884 (OUTLIER) cc_final: 0.1824 (ttt180) REVERT: A 464 MET cc_start: 0.5723 (ppp) cc_final: 0.5455 (ptm) REVERT: A 757 GLU cc_start: 0.2769 (OUTLIER) cc_final: 0.1690 (tp30) REVERT: B 134 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7086 (tp30) REVERT: D 142 GLU cc_start: 0.6460 (tp30) cc_final: 0.5669 (tp30) REVERT: D 145 TYR cc_start: 0.2498 (OUTLIER) cc_final: 0.1890 (p90) REVERT: D 184 LEU cc_start: 0.7639 (pt) cc_final: 0.6809 (mp) REVERT: C 272 TRP cc_start: 0.7729 (OUTLIER) cc_final: 0.6952 (t60) REVERT: C 403 LEU cc_start: 0.3171 (OUTLIER) cc_final: 0.2845 (mt) REVERT: C 748 LYS cc_start: 0.5498 (OUTLIER) cc_final: 0.5214 (mmtt) outliers start: 100 outliers final: 58 residues processed: 204 average time/residue: 0.1167 time to fit residues: 36.6923 Evaluate side-chains 178 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 108 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 TYR Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 748 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 54 optimal weight: 0.5980 chunk 160 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 70 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 109 optimal weight: 0.0010 chunk 122 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.151338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.131860 restraints weight = 58830.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.134698 restraints weight = 36598.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.136566 restraints weight = 26267.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.137881 restraints weight = 20813.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.138723 restraints weight = 17458.857| |-----------------------------------------------------------------------------| r_work (final): 0.4769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14707 Z= 0.149 Angle : 0.718 9.636 19887 Z= 0.363 Chirality : 0.047 0.217 2219 Planarity : 0.005 0.096 2547 Dihedral : 9.293 83.395 2026 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.99 % Allowed : 14.82 % Favored : 84.19 % Rotamer: Outliers : 7.32 % Allowed : 26.33 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.06 % Twisted Proline : 1.19 % 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: -3.35 (0.18), residues: 1822 helix: -2.45 (0.24), residues: 371 sheet: -2.00 (0.31), residues: 272 loop : -2.30 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 520 TYR 0.019 0.001 TYR A 196 PHE 0.014 0.002 PHE D 152 TRP 0.014 0.002 TRP A 210 HIS 0.006 0.001 HIS C 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (14703) covalent geometry : angle 0.71684 / 0.36 (19879) SS BOND : bond 0.00624 / 0.31 ( 4) SS BOND : angle 2.20068 / 0.94 ( 8) hydrogen bonds : bond 0.03868 / 2.54 ( 280) hydrogen bonds : angle 8.14086 / 5.59 ( 663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 126 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.5471 (OUTLIER) cc_final: 0.3988 (t) REVERT: A 204 GLN cc_start: 0.4438 (OUTLIER) cc_final: 0.4129 (mt0) REVERT: A 243 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6829 (tm-30) REVERT: A 261 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8814 (pp) REVERT: A 272 TRP cc_start: 0.7546 (OUTLIER) cc_final: 0.5669 (m100) REVERT: A 403 LEU cc_start: 0.3298 (OUTLIER) cc_final: 0.2891 (mm) REVERT: A 460 ARG cc_start: 0.3685 (OUTLIER) cc_final: 0.1696 (ttt180) REVERT: A 600 THR cc_start: 0.5583 (p) cc_final: 0.5167 (t) REVERT: A 757 GLU cc_start: 0.2752 (OUTLIER) cc_final: 0.1642 (tp30) REVERT: D 142 GLU cc_start: 0.6438 (tp30) cc_final: 0.5381 (tm-30) REVERT: D 145 TYR cc_start: 0.2440 (OUTLIER) cc_final: 0.1855 (p90) REVERT: D 184 LEU cc_start: 0.7601 (pt) cc_final: 0.6743 (mp) REVERT: D 197 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7474 (p) REVERT: C 240 MET cc_start: 0.4925 (mmm) cc_final: 0.4309 (mpp) REVERT: C 272 TRP cc_start: 0.7678 (OUTLIER) cc_final: 0.6902 (t60) REVERT: C 383 LEU cc_start: 0.7910 (tt) cc_final: 0.7344 (tt) REVERT: C 403 LEU cc_start: 0.2855 (OUTLIER) cc_final: 0.2437 (mt) REVERT: C 748 LYS cc_start: 0.5546 (OUTLIER) cc_final: 0.5318 (mmtt) outliers start: 114 outliers final: 59 residues processed: 227 average time/residue: 0.1211 time to fit residues: 41.5667 Evaluate side-chains 185 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 114 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 426 TRP Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 TYR Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 748 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 76 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS ** C 622 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 = 0.4968 r_free = 0.4968 target = 0.153162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.133808 restraints weight = 59119.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.136833 restraints weight = 35511.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.138885 restraints weight = 25001.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.140260 restraints weight = 19478.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.141049 restraints weight = 16226.749| |-----------------------------------------------------------------------------| r_work (final): 0.4812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5124 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14707 Z= 0.126 Angle : 0.707 9.712 19887 Z= 0.356 Chirality : 0.047 0.214 2219 Planarity : 0.005 0.093 2547 Dihedral : 8.940 84.136 2022 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.88 % Allowed : 14.05 % Favored : 85.07 % Rotamer: Outliers : 5.97 % Allowed : 27.04 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.06 % Twisted Proline : 1.19 % 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: -3.31 (0.18), residues: 1822 helix: -2.47 (0.24), residues: 371 sheet: -1.89 (0.32), residues: 253 loop : -2.29 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 520 TYR 0.020 0.001 TYR A 196 PHE 0.016 0.001 PHE A 313 TRP 0.014 0.001 TRP A 210 HIS 0.007 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (14703) covalent geometry : angle 0.70583 / 0.36 (19879) SS BOND : bond 0.00635 / 0.32 ( 4) SS BOND : angle 1.80744 / 0.80 ( 8) hydrogen bonds : bond 0.03485 / 2.31 ( 280) hydrogen bonds : angle 7.80168 / 5.30 ( 663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 124 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.5023 (OUTLIER) cc_final: 0.3387 (t) REVERT: A 243 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6796 (tm-30) REVERT: A 261 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8818 (pp) REVERT: A 272 TRP cc_start: 0.7529 (OUTLIER) cc_final: 0.5617 (m100) REVERT: A 403 LEU cc_start: 0.3247 (OUTLIER) cc_final: 0.2811 (mm) REVERT: A 460 ARG cc_start: 0.3597 (OUTLIER) cc_final: 0.1662 (ttt180) REVERT: A 464 MET cc_start: 0.5383 (ppp) cc_final: 0.4956 (ptm) REVERT: A 600 THR cc_start: 0.5596 (p) cc_final: 0.5158 (t) REVERT: A 757 GLU cc_start: 0.2681 (OUTLIER) cc_final: 0.1550 (tp30) REVERT: D 142 GLU cc_start: 0.6415 (tp30) cc_final: 0.5329 (tm-30) REVERT: D 145 TYR cc_start: 0.2391 (OUTLIER) cc_final: 0.1796 (p90) REVERT: D 184 LEU cc_start: 0.7557 (pt) cc_final: 0.6760 (mp) REVERT: D 197 SER cc_start: 0.7572 (OUTLIER) cc_final: 0.7342 (p) REVERT: C 240 MET cc_start: 0.4908 (mmm) cc_final: 0.4404 (mpp) REVERT: C 272 TRP cc_start: 0.7685 (OUTLIER) cc_final: 0.7014 (t60) REVERT: C 403 LEU cc_start: 0.2791 (OUTLIER) cc_final: 0.2303 (mt) outliers start: 93 outliers final: 59 residues processed: 205 average time/residue: 0.1207 time to fit residues: 37.5466 Evaluate side-chains 185 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 116 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 426 TRP Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 TYR Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 721 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 174 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.149431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.129886 restraints weight = 58986.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.132566 restraints weight = 37154.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.134444 restraints weight = 27016.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.135516 restraints weight = 21459.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.136486 restraints weight = 18305.681| |-----------------------------------------------------------------------------| r_work (final): 0.4731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5320 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14707 Z= 0.190 Angle : 0.773 9.653 19887 Z= 0.389 Chirality : 0.049 0.218 2219 Planarity : 0.005 0.090 2547 Dihedral : 8.918 83.661 2012 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 28.21 Ramachandran Plot: Outliers : 0.93 % Allowed : 15.26 % Favored : 83.81 % Rotamer: Outliers : 6.49 % Allowed : 27.10 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.06 % Twisted Proline : 1.19 % 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: -3.34 (0.18), residues: 1822 helix: -2.41 (0.25), residues: 363 sheet: -1.95 (0.33), residues: 253 loop : -2.34 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 478 TYR 0.025 0.002 TYR A 196 PHE 0.016 0.002 PHE D 152 TRP 0.012 0.002 TRP A 432 HIS 0.007 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (14703) covalent geometry : angle 0.77252 / 0.39 (19879) SS BOND : bond 0.00609 / 0.30 ( 4) SS BOND : angle 1.72922 / 0.73 ( 8) hydrogen bonds : bond 0.03754 / 2.43 ( 280) hydrogen bonds : angle 7.95088 / 5.40 ( 663) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 115 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6618 (tm-30) REVERT: A 260 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7558 (tt) REVERT: A 272 TRP cc_start: 0.7608 (OUTLIER) cc_final: 0.5663 (m100) REVERT: A 403 LEU cc_start: 0.3285 (OUTLIER) cc_final: 0.2881 (mm) REVERT: A 458 ILE cc_start: 0.1618 (OUTLIER) cc_final: 0.0226 (pt) REVERT: A 460 ARG cc_start: 0.3760 (OUTLIER) cc_final: 0.2025 (ttt90) REVERT: A 464 MET cc_start: 0.5669 (ppp) cc_final: 0.5407 (ptm) REVERT: A 757 GLU cc_start: 0.2959 (OUTLIER) cc_final: 0.1921 (tp30) REVERT: A 844 MET cc_start: -0.2193 (mmm) cc_final: -0.2422 (mmm) REVERT: D 142 GLU cc_start: 0.6514 (tp30) cc_final: 0.5355 (tm-30) REVERT: D 145 TYR cc_start: 0.2667 (OUTLIER) cc_final: 0.2074 (p90) REVERT: D 184 LEU cc_start: 0.7567 (pt) cc_final: 0.6652 (mp) REVERT: D 197 SER cc_start: 0.7871 (OUTLIER) cc_final: 0.7650 (p) REVERT: C 240 MET cc_start: 0.5265 (mmm) cc_final: 0.4552 (mpp) REVERT: C 261 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8408 (mp) REVERT: C 272 TRP cc_start: 0.7754 (t60) cc_final: 0.6895 (t60) REVERT: C 403 LEU cc_start: 0.2845 (OUTLIER) cc_final: 0.2349 (mt) REVERT: C 579 SER cc_start: 0.6428 (OUTLIER) cc_final: 0.5952 (m) outliers start: 101 outliers final: 70 residues processed: 203 average time/residue: 0.1227 time to fit residues: 37.4987 Evaluate side-chains 191 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 110 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 426 TRP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 TYR Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 718 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 71 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 156 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.148213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.128537 restraints weight = 59087.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.131310 restraints weight = 37161.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.133159 restraints weight = 26897.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.134431 restraints weight = 21408.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.135227 restraints weight = 18127.036| |-----------------------------------------------------------------------------| r_work (final): 0.4731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5342 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14707 Z= 0.181 Angle : 0.763 9.856 19887 Z= 0.384 Chirality : 0.048 0.220 2219 Planarity : 0.005 0.088 2547 Dihedral : 8.909 83.682 2010 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.93 % Allowed : 15.59 % Favored : 83.48 % Rotamer: Outliers : 6.74 % Allowed : 27.17 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.06 % Twisted Proline : 1.19 % 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: -3.42 (0.18), residues: 1822 helix: -2.44 (0.25), residues: 359 sheet: -2.01 (0.33), residues: 246 loop : -2.41 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 520 TYR 0.027 0.002 TYR A 196 PHE 0.017 0.002 PHE C 421 TRP 0.013 0.002 TRP A 426 HIS 0.007 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (14703) covalent geometry : angle 0.76296 / 0.38 (19879) SS BOND : bond 0.00546 / 0.27 ( 4) SS BOND : angle 1.58196 / 0.66 ( 8) hydrogen bonds : bond 0.03708 / 2.40 ( 280) hydrogen bonds : angle 7.81699 / 5.30 ( 663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 119 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7670 (tt) REVERT: A 272 TRP cc_start: 0.7630 (OUTLIER) cc_final: 0.5621 (m100) REVERT: A 403 LEU cc_start: 0.3628 (OUTLIER) cc_final: 0.3181 (mm) REVERT: A 460 ARG cc_start: 0.3600 (OUTLIER) cc_final: 0.1691 (ttt180) REVERT: A 464 MET cc_start: 0.5802 (ppp) cc_final: 0.5433 (ptm) REVERT: A 481 ASP cc_start: 0.7442 (m-30) cc_final: 0.7130 (m-30) REVERT: A 600 THR cc_start: 0.5989 (p) cc_final: 0.5556 (t) REVERT: A 757 GLU cc_start: 0.3032 (OUTLIER) cc_final: 0.1766 (tp30) REVERT: B 176 LEU cc_start: 0.7008 (pt) cc_final: 0.6758 (pt) REVERT: D 142 GLU cc_start: 0.6531 (tp30) cc_final: 0.5368 (tm-30) REVERT: D 143 ARG cc_start: 0.5833 (OUTLIER) cc_final: 0.4160 (mmm160) REVERT: D 145 TYR cc_start: 0.2933 (OUTLIER) cc_final: 0.2378 (p90) REVERT: D 197 SER cc_start: 0.7976 (OUTLIER) cc_final: 0.7707 (p) REVERT: C 240 MET cc_start: 0.5185 (mmm) cc_final: 0.4440 (mpp) REVERT: C 260 LEU cc_start: 0.7810 (tt) cc_final: 0.7542 (tp) REVERT: C 272 TRP cc_start: 0.7830 (t60) cc_final: 0.6928 (t60) REVERT: C 403 LEU cc_start: 0.2916 (OUTLIER) cc_final: 0.2391 (mt) REVERT: C 579 SER cc_start: 0.6406 (OUTLIER) cc_final: 0.5942 (m) outliers start: 105 outliers final: 74 residues processed: 210 average time/residue: 0.1186 time to fit residues: 37.9404 Evaluate side-chains 197 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 113 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 426 TRP Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 TYR Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 761 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 179 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 62 optimal weight: 0.0870 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 30.0000 chunk 138 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.149693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.130158 restraints weight = 58755.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.133060 restraints weight = 36406.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.135006 restraints weight = 25969.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.136272 restraints weight = 20358.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.137125 restraints weight = 17167.817| |-----------------------------------------------------------------------------| r_work (final): 0.4769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5237 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14707 Z= 0.147 Angle : 0.740 11.205 19887 Z= 0.368 Chirality : 0.048 0.218 2219 Planarity : 0.005 0.088 2547 Dihedral : 8.758 84.140 2010 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 0.93 % Allowed : 14.71 % Favored : 84.36 % Rotamer: Outliers : 6.17 % Allowed : 27.81 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.06 % Twisted Proline : 1.19 % 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: -3.38 (0.18), residues: 1822 helix: -2.46 (0.24), residues: 371 sheet: -1.55 (0.35), residues: 233 loop : -2.45 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 520 TYR 0.025 0.001 TYR A 196 PHE 0.017 0.002 PHE C 223 TRP 0.015 0.002 TRP A 210 HIS 0.005 0.001 HIS A 480 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (14703) covalent geometry : angle 0.73997 / 0.37 (19879) SS BOND : bond 0.00496 / 0.25 ( 4) SS BOND : angle 1.38400 / 0.58 ( 8) hydrogen bonds : bond 0.03514 / 2.29 ( 280) hydrogen bonds : angle 7.67207 / 5.21 ( 663) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 118 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7542 (tp) REVERT: A 272 TRP cc_start: 0.7497 (OUTLIER) cc_final: 0.5554 (m100) REVERT: A 403 LEU cc_start: 0.3406 (OUTLIER) cc_final: 0.2982 (mm) REVERT: A 460 ARG cc_start: 0.3506 (OUTLIER) cc_final: 0.1541 (ttt180) REVERT: A 464 MET cc_start: 0.5807 (ppp) cc_final: 0.5416 (ptm) REVERT: A 481 ASP cc_start: 0.7249 (m-30) cc_final: 0.6970 (m-30) REVERT: A 600 THR cc_start: 0.5943 (p) cc_final: 0.5508 (t) REVERT: A 757 GLU cc_start: 0.3012 (OUTLIER) cc_final: 0.1901 (tp30) REVERT: D 142 GLU cc_start: 0.6427 (tp30) cc_final: 0.5210 (tm-30) REVERT: D 145 TYR cc_start: 0.2900 (OUTLIER) cc_final: 0.2202 (p90) REVERT: D 184 LEU cc_start: 0.7470 (pt) cc_final: 0.6547 (mp) REVERT: D 197 SER cc_start: 0.7838 (OUTLIER) cc_final: 0.7603 (p) REVERT: C 226 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7205 (mm) REVERT: C 240 MET cc_start: 0.5106 (mmm) cc_final: 0.4569 (mpp) REVERT: C 260 LEU cc_start: 0.7708 (tt) cc_final: 0.7426 (tp) REVERT: C 261 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8443 (mp) REVERT: C 272 TRP cc_start: 0.7754 (t60) cc_final: 0.6873 (t60) REVERT: C 363 ILE cc_start: 0.1434 (OUTLIER) cc_final: 0.1204 (tt) REVERT: C 403 LEU cc_start: 0.2811 (OUTLIER) cc_final: 0.2323 (mt) REVERT: C 685 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6788 (tpp-160) outliers start: 96 outliers final: 68 residues processed: 198 average time/residue: 0.1221 time to fit residues: 36.4195 Evaluate side-chains 190 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 110 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 426 TRP Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 685 ARG Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 TYR Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 426 TRP Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 685 ARG Chi-restraints excluded: chain C residue 761 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 25 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 167 optimal weight: 0.0870 chunk 154 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.149048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.129508 restraints weight = 58879.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.132339 restraints weight = 36665.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.134222 restraints weight = 26338.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.135477 restraints weight = 20807.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.136280 restraints weight = 17607.446| |-----------------------------------------------------------------------------| r_work (final): 0.4752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5297 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 14707 Z= 0.168 Angle : 0.769 13.497 19887 Z= 0.386 Chirality : 0.048 0.216 2219 Planarity : 0.005 0.088 2547 Dihedral : 8.731 84.183 2007 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 26.37 Ramachandran Plot: Outliers : 0.93 % Allowed : 15.15 % Favored : 83.92 % Rotamer: Outliers : 5.78 % Allowed : 28.58 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.06 % Twisted Proline : 1.19 % Twisted General : 0.11 % 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: -3.40 (0.18), residues: 1822 helix: -2.51 (0.24), residues: 371 sheet: -1.57 (0.35), residues: 233 loop : -2.46 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 520 TYR 0.026 0.001 TYR A 196 PHE 0.015 0.002 PHE D 152 TRP 0.013 0.002 TRP A 210 HIS 0.006 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (14703) covalent geometry : angle 0.76088 / 0.38 (19879) SS BOND : bond 0.00517 / 0.26 ( 4) SS BOND : angle 5.61203 / 2.43 ( 8) hydrogen bonds : bond 0.03514 / 2.27 ( 280) hydrogen bonds : angle 7.63535 / 5.18 ( 663) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 114 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7617 (tp) REVERT: A 272 TRP cc_start: 0.7569 (OUTLIER) cc_final: 0.5580 (m100) REVERT: A 403 LEU cc_start: 0.3430 (OUTLIER) cc_final: 0.2990 (mm) REVERT: A 460 ARG cc_start: 0.3551 (OUTLIER) cc_final: 0.1526 (ttt180) REVERT: A 464 MET cc_start: 0.5845 (ppp) cc_final: 0.5529 (ptm) REVERT: A 481 ASP cc_start: 0.7240 (m-30) cc_final: 0.6956 (m-30) REVERT: A 600 THR cc_start: 0.6006 (p) cc_final: 0.5549 (t) REVERT: A 757 GLU cc_start: 0.3074 (OUTLIER) cc_final: 0.2032 (tp30) REVERT: D 142 GLU cc_start: 0.6491 (tp30) cc_final: 0.5290 (tm-30) REVERT: D 143 ARG cc_start: 0.5763 (OUTLIER) cc_final: 0.4069 (mmm160) REVERT: D 145 TYR cc_start: 0.3033 (OUTLIER) cc_final: 0.2481 (p90) REVERT: D 197 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7669 (p) REVERT: C 226 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7163 (mm) REVERT: C 240 MET cc_start: 0.5130 (mmm) cc_final: 0.4649 (mpp) REVERT: C 260 LEU cc_start: 0.7769 (tt) cc_final: 0.7464 (tp) REVERT: C 261 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8485 (mp) REVERT: C 272 TRP cc_start: 0.7823 (t60) cc_final: 0.6792 (t60) REVERT: C 403 LEU cc_start: 0.2834 (OUTLIER) cc_final: 0.2321 (mt) REVERT: C 685 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6782 (tpp-160) outliers start: 90 outliers final: 67 residues processed: 189 average time/residue: 0.1304 time to fit residues: 36.8260 Evaluate side-chains 193 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 114 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 426 TRP Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 685 ARG Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 TYR Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 685 ARG Chi-restraints excluded: chain C residue 761 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 97 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 92 optimal weight: 30.0000 chunk 177 optimal weight: 0.0270 chunk 72 optimal weight: 9.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.154183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.134886 restraints weight = 59254.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.138079 restraints weight = 35472.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.140143 restraints weight = 24713.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.141541 restraints weight = 19135.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.142467 restraints weight = 15900.016| |-----------------------------------------------------------------------------| r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5057 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 14707 Z= 0.126 Angle : 0.737 11.934 19887 Z= 0.365 Chirality : 0.047 0.237 2219 Planarity : 0.005 0.088 2547 Dihedral : 8.344 84.668 2007 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.93 % Allowed : 13.17 % Favored : 85.89 % Rotamer: Outliers : 4.56 % Allowed : 29.48 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.06 % Twisted Proline : 1.19 % 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: -3.15 (0.19), residues: 1822 helix: -2.19 (0.26), residues: 329 sheet: -1.32 (0.35), residues: 229 loop : -2.37 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 520 TYR 0.022 0.001 TYR A 196 PHE 0.027 0.001 PHE A 546 TRP 0.021 0.002 TRP A 210 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (14703) covalent geometry : angle 0.73256 / 0.36 (19879) SS BOND : bond 0.00563 / 0.28 ( 4) SS BOND : angle 4.09984 / 1.78 ( 8) hydrogen bonds : bond 0.03179 / 2.08 ( 280) hydrogen bonds : angle 7.30487 / 4.95 ( 663) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 133 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.5490 (m100) REVERT: A 403 LEU cc_start: 0.3333 (OUTLIER) cc_final: 0.2906 (mm) REVERT: A 460 ARG cc_start: 0.3266 (OUTLIER) cc_final: 0.1349 (ttt180) REVERT: A 481 ASP cc_start: 0.6859 (m-30) cc_final: 0.6446 (m-30) REVERT: A 600 THR cc_start: 0.5781 (p) cc_final: 0.5318 (t) REVERT: A 685 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.5829 (ttp-170) REVERT: A 757 GLU cc_start: 0.2844 (OUTLIER) cc_final: 0.2014 (tp30) REVERT: B 41 GLU cc_start: 0.3308 (mm-30) cc_final: 0.1383 (mt-10) REVERT: D 142 GLU cc_start: 0.6477 (tp30) cc_final: 0.5186 (tm-30) REVERT: D 184 LEU cc_start: 0.7429 (pt) cc_final: 0.6573 (mp) REVERT: D 197 SER cc_start: 0.7647 (OUTLIER) cc_final: 0.7405 (p) REVERT: C 226 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7438 (tp) REVERT: C 240 MET cc_start: 0.4961 (mmm) cc_final: 0.4620 (mpp) REVERT: C 260 LEU cc_start: 0.7617 (tt) cc_final: 0.7344 (tp) REVERT: C 272 TRP cc_start: 0.7691 (OUTLIER) cc_final: 0.6848 (t60) REVERT: C 363 ILE cc_start: 0.1392 (OUTLIER) cc_final: 0.1165 (tt) REVERT: C 403 LEU cc_start: 0.2623 (OUTLIER) cc_final: 0.2112 (mt) REVERT: C 685 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6805 (tpp-160) REVERT: C 761 MET cc_start: 0.2587 (OUTLIER) cc_final: 0.0812 (mmt) outliers start: 71 outliers final: 54 residues processed: 191 average time/residue: 0.1229 time to fit residues: 35.0046 Evaluate side-chains 187 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 121 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 426 TRP Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 685 ARG Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 TYR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 685 ARG Chi-restraints excluded: chain C residue 761 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 129 optimal weight: 0.8980 chunk 75 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 57 optimal weight: 0.3980 chunk 118 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 ASN ** 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 = 0.4988 r_free = 0.4988 target = 0.154510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.135318 restraints weight = 59020.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.138486 restraints weight = 35082.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.140496 restraints weight = 24427.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.141919 restraints weight = 18994.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.142789 restraints weight = 15777.820| |-----------------------------------------------------------------------------| r_work (final): 0.4846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5048 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14707 Z= 0.127 Angle : 0.757 15.457 19887 Z= 0.369 Chirality : 0.047 0.216 2219 Planarity : 0.005 0.088 2547 Dihedral : 7.982 84.879 2002 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.88 % Allowed : 13.06 % Favored : 86.06 % Rotamer: Outliers : 4.30 % Allowed : 30.38 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.06 % Twisted Proline : 1.19 % Twisted General : 0.06 % 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: -3.11 (0.19), residues: 1822 helix: -2.17 (0.26), residues: 341 sheet: -1.91 (0.32), residues: 279 loop : -2.17 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 520 TYR 0.020 0.001 TYR C 212 PHE 0.028 0.001 PHE C 530 TRP 0.022 0.002 TRP A 210 HIS 0.005 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (14703) covalent geometry : angle 0.75286 / 0.37 (19879) SS BOND : bond 0.00243 / 0.12 ( 4) SS BOND : angle 4.03027 / 1.72 ( 8) hydrogen bonds : bond 0.03156 / 2.06 ( 280) hydrogen bonds : angle 7.20904 / 4.86 ( 663) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 121 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 TRP cc_start: 0.7454 (OUTLIER) cc_final: 0.5541 (m100) REVERT: A 403 LEU cc_start: 0.3236 (OUTLIER) cc_final: 0.2797 (mm) REVERT: A 458 ILE cc_start: 0.1629 (OUTLIER) cc_final: 0.0388 (pt) REVERT: A 460 ARG cc_start: 0.3301 (OUTLIER) cc_final: 0.1384 (ttt180) REVERT: A 464 MET cc_start: 0.5306 (ppp) cc_final: 0.4624 (ptm) REVERT: A 600 THR cc_start: 0.5808 (p) cc_final: 0.5345 (t) REVERT: A 757 GLU cc_start: 0.2871 (OUTLIER) cc_final: 0.2010 (tp30) REVERT: B 41 GLU cc_start: 0.3328 (mm-30) cc_final: 0.1383 (mt-10) REVERT: D 184 LEU cc_start: 0.7440 (pt) cc_final: 0.6563 (mp) REVERT: D 197 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.7419 (p) REVERT: C 226 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7407 (tp) REVERT: C 240 MET cc_start: 0.5016 (mmm) cc_final: 0.4584 (mpp) REVERT: C 260 LEU cc_start: 0.7571 (tt) cc_final: 0.7306 (tp) REVERT: C 272 TRP cc_start: 0.7685 (OUTLIER) cc_final: 0.6746 (t60) REVERT: C 363 ILE cc_start: 0.1407 (OUTLIER) cc_final: 0.1196 (tt) REVERT: C 403 LEU cc_start: 0.2617 (OUTLIER) cc_final: 0.1419 (mp) REVERT: C 460 ARG cc_start: 0.3363 (tpt-90) cc_final: 0.2112 (ttt90) REVERT: C 685 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6820 (tpp-160) REVERT: C 761 MET cc_start: 0.2684 (OUTLIER) cc_final: 0.0840 (mmt) outliers start: 67 outliers final: 52 residues processed: 176 average time/residue: 0.1238 time to fit residues: 32.8442 Evaluate side-chains 181 residues out of total 1621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 117 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 426 TRP Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 TYR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 685 ARG Chi-restraints excluded: chain C residue 761 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 105 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 chunk 14 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 165 optimal weight: 0.0060 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.156219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.137083 restraints weight = 59258.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.140332 restraints weight = 34970.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.142485 restraints weight = 24230.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.143911 restraints weight = 18722.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.144888 restraints weight = 15475.876| |-----------------------------------------------------------------------------| r_work (final): 0.4880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4947 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14707 Z= 0.122 Angle : 0.738 12.559 19887 Z= 0.361 Chirality : 0.047 0.214 2219 Planarity : 0.005 0.088 2547 Dihedral : 7.571 55.975 1999 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.77 % Allowed : 12.07 % Favored : 87.16 % Rotamer: Outliers : 3.79 % Allowed : 30.96 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.06 % Twisted Proline : 1.19 % 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: -3.04 (0.19), residues: 1822 helix: -2.03 (0.26), residues: 331 sheet: -1.80 (0.32), residues: 282 loop : -2.18 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 520 TYR 0.017 0.001 TYR C 212 PHE 0.022 0.001 PHE C 530 TRP 0.021 0.001 TRP A 210 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (14703) covalent geometry : angle 0.73502 / 0.36 (19879) SS BOND : bond 0.00351 / 0.18 ( 4) SS BOND : angle 3.53807 / 1.52 ( 8) hydrogen bonds : bond 0.03035 / 1.99 ( 280) hydrogen bonds : angle 7.03897 / 4.76 ( 663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3200.96 seconds wall clock time: 56 minutes 7.47 seconds (3367.47 seconds total)