Starting phenix.real_space_refine on Thu Jul 2 08:15:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yaj_33714/07_2026/7yaj_33714.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yaj_33714/07_2026/7yaj_33714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yaj_33714/07_2026/7yaj_33714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yaj_33714/07_2026/7yaj_33714.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yaj_33714/07_2026/7yaj_33714.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yaj_33714/07_2026/7yaj_33714.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yaj_33714/07_2026/7yaj_33714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yaj_33714/07_2026/7yaj_33714.map" } resolution = 3.16 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 3 5.49 5 S 55 5.16 5 C 4860 2.51 5 N 1283 2.21 5 O 1447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7649 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6675 Classifications: {'peptide': 874} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 34, 'TRANS': 839} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.67, per 1000 atoms: 0.22 Number of scatterers: 7649 At special positions: 0 Unit cell: (75.845, 82.74, 134.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 55 16.00 P 3 15.00 O 1447 8.00 N 1283 7.00 C 4860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 128 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 316.8 milliseconds 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 50.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.800A pdb=" N PHE A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 removed outlier: 3.864A pdb=" N GLN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 99 through 135 removed outlier: 3.630A pdb=" N ALA A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.972A pdb=" N ASN A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 239 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU A 240 " --> pdb=" O GLU A 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 240' Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.922A pdb=" N PHE A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 288 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 309 through 328 Processing helix chain 'A' and resid 335 through 341 removed outlier: 4.007A pdb=" N GLU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 407 Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 482 through 490 Processing helix chain 'A' and resid 503 through 521 Processing helix chain 'A' and resid 551 through 561 removed outlier: 3.761A pdb=" N ALA A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 595 through 602 Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.800A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 655 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 682 through 724 removed outlier: 3.760A pdb=" N MET A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 743 through 750 removed outlier: 3.975A pdb=" N LEU A 749 " --> pdb=" O PRO A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 772 through 798 Processing helix chain 'A' and resid 804 through 826 removed outlier: 3.988A pdb=" N THR A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 removed outlier: 3.663A pdb=" N ILE A 836 " --> pdb=" O SER A 832 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 832 through 837' Processing helix chain 'A' and resid 841 through 861 removed outlier: 3.505A pdb=" N CYS A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 868 Processing helix chain 'A' and resid 874 through 904 removed outlier: 4.546A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 151 removed outlier: 4.222A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 228 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 223 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N SER A 182 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS A 225 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASP A 180 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LYS A 227 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ALA A 178 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LYS A 229 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP A 172 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 332 removed outlier: 6.066A pdb=" N GLY A 658 " --> pdb=" O MET A 675 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU A 677 " --> pdb=" O GLY A 658 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 660 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A 639 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL A 659 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET A 641 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N MET A 661 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 638 " --> pdb=" O CYS A 344 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.522A pdb=" N GLU A 374 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY A 543 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE A 365 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 541 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N THR A 367 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU A 539 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N PHE A 538 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N SER A 529 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 540 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 525 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 464 " --> pdb=" O ALA A 450 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA A 450 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.522A pdb=" N GLU A 374 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY A 543 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE A 365 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 541 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N THR A 367 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU A 539 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A 492 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N GLY A 540 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 9.873A pdb=" N GLN A 494 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 13.486A pdb=" N VAL A 542 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 416 through 417 Processing sheet with id=AA6, first strand: chain 'A' and resid 592 through 594 removed outlier: 8.212A pdb=" N GLN A 592 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE A 617 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 594 " --> pdb=" O PHE A 617 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.825A pdb=" N LEU C 51 " --> pdb=" O MET C 115 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET C 115 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER C 103 " --> pdb=" O TYR C 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.831A pdb=" N PHE C 80 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG C 71 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP C 66 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 130 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR C 148 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.831A pdb=" N PHE C 80 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG C 71 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP C 66 " --> pdb=" O GLN C 131 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1466 1.33 - 1.45: 1767 1.45 - 1.58: 4450 1.58 - 1.70: 3 1.70 - 1.82: 90 Bond restraints: 7776 Sorted by residual: bond pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 1.698 1.608 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C3B ACP A1001 " pdb=" PG ACP A1001 " ideal model delta sigma weight residual 1.875 1.795 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" O5' ACP A1001 " pdb=" PA ACP A1001 " ideal model delta sigma weight residual 1.659 1.580 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" N ILE A 431 " pdb=" CA ILE A 431 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.17e-02 7.31e+03 1.00e+01 bond pdb=" N VAL A 415 " pdb=" CA VAL A 415 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.14e-02 7.69e+03 9.64e+00 ... (remaining 7771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 10308 2.79 - 5.58: 190 5.58 - 8.37: 23 8.37 - 11.16: 7 11.16 - 13.94: 4 Bond angle restraints: 10532 Sorted by residual: angle pdb=" PA ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 125.06 111.12 13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" N ALA A 407 " pdb=" CA ALA A 407 " pdb=" C ALA A 407 " ideal model delta sigma weight residual 113.19 108.48 4.71 1.19e+00 7.06e-01 1.57e+01 angle pdb=" CB MET A 97 " pdb=" CG MET A 97 " pdb=" SD MET A 97 " ideal model delta sigma weight residual 112.70 124.31 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" N GLN A 443 " pdb=" CA GLN A 443 " pdb=" C GLN A 443 " ideal model delta sigma weight residual 111.28 107.08 4.20 1.09e+00 8.42e-01 1.48e+01 angle pdb=" N LEU A 442 " pdb=" CA LEU A 442 " pdb=" C LEU A 442 " ideal model delta sigma weight residual 112.54 107.99 4.55 1.22e+00 6.72e-01 1.39e+01 ... (remaining 10527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.80: 4213 24.80 - 49.60: 429 49.60 - 74.40: 46 74.40 - 99.20: 5 99.20 - 124.00: 2 Dihedral angle restraints: 4695 sinusoidal: 1835 harmonic: 2860 Sorted by residual: dihedral pdb=" CB CYS C 55 " pdb=" SG CYS C 55 " pdb=" SG CYS C 128 " pdb=" CB CYS C 128 " ideal model delta sinusoidal sigma weight residual 93.00 166.99 -73.99 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CA HIS A 98 " pdb=" C HIS A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" O1A ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PA ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sinusoidal sigma weight residual -48.75 75.25 -124.00 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 4692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 987 0.061 - 0.122: 209 0.122 - 0.184: 36 0.184 - 0.245: 10 0.245 - 0.306: 1 Chirality restraints: 1243 Sorted by residual: chirality pdb=" CB ILE A 699 " pdb=" CA ILE A 699 " pdb=" CG1 ILE A 699 " pdb=" CG2 ILE A 699 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB VAL A 611 " pdb=" CA VAL A 611 " pdb=" CG1 VAL A 611 " pdb=" CG2 VAL A 611 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE A 685 " pdb=" N ILE A 685 " pdb=" C ILE A 685 " pdb=" CB ILE A 685 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1240 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 448 " 0.332 9.50e-02 1.11e+02 1.49e-01 1.35e+01 pdb=" NE ARG A 448 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 448 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 448 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 448 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 583 " -0.317 9.50e-02 1.11e+02 1.42e-01 1.24e+01 pdb=" NE ARG A 583 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 583 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 583 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 583 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 744 " -0.054 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO A 745 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 745 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 745 " -0.045 5.00e-02 4.00e+02 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 234 2.70 - 3.25: 7495 3.25 - 3.80: 13133 3.80 - 4.35: 16135 4.35 - 4.90: 26696 Nonbonded interactions: 63693 Sorted by model distance: nonbonded pdb=" OD2 ASP A 742 " pdb="MN MN A1002 " model vdw 2.150 2.320 nonbonded pdb=" O VAL A 303 " pdb="MN MN A1002 " model vdw 2.275 2.320 nonbonded pdb=" OE1 GLU A 513 " pdb=" OH TYR C 143 " model vdw 2.278 3.040 nonbonded pdb=" OG SER A 456 " pdb=" O2A ACP A1001 " model vdw 2.279 3.040 nonbonded pdb=" O SER C 145 " pdb=" OG SER C 145 " model vdw 2.279 3.040 ... (remaining 63688 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 7777 Z= 0.306 Angle : 0.947 13.944 10534 Z= 0.542 Chirality : 0.054 0.306 1243 Planarity : 0.009 0.149 1327 Dihedral : 18.196 124.004 2850 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.66 % Allowed : 30.37 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.24), residues: 987 helix: -0.23 (0.22), residues: 477 sheet: -0.85 (0.50), residues: 107 loop : -0.98 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 99 TYR 0.027 0.003 TYR C 143 PHE 0.020 0.002 PHE A 383 TRP 0.042 0.002 TRP C 149 HIS 0.008 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.31 ( 7776) covalent geometry : angle 0.94713 / 0.54 (10532) SS BOND : bond 0.00000 / 0.00 ( 1) SS BOND : angle 1.44202 / 0.76 ( 2) hydrogen bonds : bond 0.18399 / 11.64 ( 423) hydrogen bonds : angle 7.43052 / 5.29 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.315 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 101 ASP cc_start: 0.3003 (m-30) cc_final: 0.2693 (m-30) REVERT: A 725 PHE cc_start: 0.5297 (OUTLIER) cc_final: 0.4786 (t80) outliers start: 14 outliers final: 4 residues processed: 195 average time/residue: 0.0932 time to fit residues: 24.3293 Evaluate side-chains 140 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 884 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 HIS ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 ASN A 841 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.124260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.098116 restraints weight = 22105.690| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 4.21 r_work: 0.3665 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7777 Z= 0.143 Angle : 0.660 7.667 10534 Z= 0.342 Chirality : 0.043 0.157 1243 Planarity : 0.005 0.067 1327 Dihedral : 7.228 120.671 1068 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.15 % Allowed : 30.01 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 987 helix: 0.56 (0.22), residues: 481 sheet: -0.88 (0.44), residues: 130 loop : -0.69 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 99 TYR 0.022 0.002 TYR C 143 PHE 0.029 0.002 PHE C 100 TRP 0.027 0.002 TRP A 766 HIS 0.008 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 7776) covalent geometry : angle 0.65957 / 0.34 (10532) SS BOND : bond 0.00182 / 0.10 ( 1) SS BOND : angle 1.14206 / 0.65 ( 2) hydrogen bonds : bond 0.04481 / 2.97 ( 423) hydrogen bonds : angle 5.11778 / 3.64 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.7943 (mpp) cc_final: 0.7452 (mpp) REVERT: A 101 ASP cc_start: 0.3460 (m-30) cc_final: 0.2898 (m-30) REVERT: A 129 GLU cc_start: 0.9052 (tp30) cc_final: 0.8842 (pp20) REVERT: A 131 LEU cc_start: 0.7820 (tp) cc_final: 0.7604 (tp) REVERT: A 167 ASP cc_start: 0.5360 (OUTLIER) cc_final: 0.5134 (m-30) REVERT: A 320 LEU cc_start: 0.8573 (tt) cc_final: 0.8147 (pp) REVERT: A 339 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7877 (pt0) REVERT: A 412 ASN cc_start: 0.7268 (m-40) cc_final: 0.6744 (m110) REVERT: A 458 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: A 459 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7349 (ttmm) REVERT: A 718 SER cc_start: 0.8120 (t) cc_final: 0.7905 (p) REVERT: A 788 CYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7806 (p) REVERT: C 51 LEU cc_start: 0.7822 (tt) cc_final: 0.7369 (mp) REVERT: C 99 ARG cc_start: 0.8115 (ptt-90) cc_final: 0.6739 (ptt-90) outliers start: 35 outliers final: 16 residues processed: 177 average time/residue: 0.0907 time to fit residues: 21.7083 Evaluate side-chains 149 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain C residue 72 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 47 optimal weight: 0.0050 chunk 72 optimal weight: 10.0000 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN A 140 HIS A 506 GLN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.123570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.097124 restraints weight = 22106.636| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 4.25 r_work: 0.3656 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7777 Z= 0.132 Angle : 0.640 12.842 10534 Z= 0.327 Chirality : 0.042 0.150 1243 Planarity : 0.005 0.059 1327 Dihedral : 6.549 115.329 1062 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 5.22 % Allowed : 29.18 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 987 helix: 0.88 (0.22), residues: 484 sheet: -0.79 (0.44), residues: 128 loop : -0.61 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 78 TYR 0.017 0.002 TYR C 148 PHE 0.025 0.002 PHE A 218 TRP 0.028 0.002 TRP A 766 HIS 0.005 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7776) covalent geometry : angle 0.63994 / 0.33 (10532) SS BOND : bond 0.00222 / 0.12 ( 1) SS BOND : angle 1.20740 / 0.70 ( 2) hydrogen bonds : bond 0.04036 / 2.66 ( 423) hydrogen bonds : angle 4.83007 / 3.44 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.296 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 50 GLU cc_start: 0.3258 (OUTLIER) cc_final: 0.3026 (tt0) REVERT: A 101 ASP cc_start: 0.3442 (m-30) cc_final: 0.2765 (m-30) REVERT: A 129 GLU cc_start: 0.9063 (tp30) cc_final: 0.8826 (pp20) REVERT: A 167 ASP cc_start: 0.5402 (OUTLIER) cc_final: 0.5175 (m-30) REVERT: A 320 LEU cc_start: 0.8555 (tt) cc_final: 0.8164 (pp) REVERT: A 339 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: A 412 ASN cc_start: 0.7241 (m-40) cc_final: 0.6723 (m110) REVERT: A 413 ASP cc_start: 0.8139 (m-30) cc_final: 0.7693 (t0) REVERT: A 458 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: A 459 LYS cc_start: 0.7981 (mtmm) cc_final: 0.7325 (ttmm) REVERT: A 691 GLU cc_start: 0.7711 (pp20) cc_final: 0.7372 (pp20) REVERT: A 788 CYS cc_start: 0.8230 (m) cc_final: 0.7886 (p) REVERT: A 803 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6283 (tp) REVERT: A 871 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: C 51 LEU cc_start: 0.7922 (tt) cc_final: 0.7261 (mp) outliers start: 44 outliers final: 22 residues processed: 182 average time/residue: 0.0885 time to fit residues: 21.8546 Evaluate side-chains 161 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 884 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 84 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.0270 chunk 38 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 56 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 HIS A 140 HIS ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 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 = 0.4304 r_free = 0.4304 target = 0.123798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.097625 restraints weight = 22564.940| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 4.38 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7777 Z= 0.139 Angle : 0.662 15.365 10534 Z= 0.333 Chirality : 0.043 0.187 1243 Planarity : 0.005 0.090 1327 Dihedral : 6.466 112.745 1061 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 5.46 % Allowed : 30.37 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.26), residues: 987 helix: 1.05 (0.23), residues: 484 sheet: -0.71 (0.44), residues: 127 loop : -0.51 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 99 TYR 0.017 0.001 TYR C 143 PHE 0.020 0.002 PHE A 218 TRP 0.029 0.002 TRP A 766 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 7776) covalent geometry : angle 0.66215 / 0.33 (10532) SS BOND : bond 0.00252 / 0.13 ( 1) SS BOND : angle 1.06373 / 0.62 ( 2) hydrogen bonds : bond 0.03852 / 2.55 ( 423) hydrogen bonds : angle 4.70601 / 3.34 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.308 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: symmetry clash REVERT: A 50 GLU cc_start: 0.3095 (OUTLIER) cc_final: 0.2858 (tt0) REVERT: A 63 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.5586 (p90) REVERT: A 101 ASP cc_start: 0.3270 (m-30) cc_final: 0.2792 (m-30) REVERT: A 167 ASP cc_start: 0.5255 (OUTLIER) cc_final: 0.4987 (m-30) REVERT: A 320 LEU cc_start: 0.8356 (tt) cc_final: 0.7954 (pp) REVERT: A 339 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: A 413 ASP cc_start: 0.8020 (m-30) cc_final: 0.7508 (t0) REVERT: A 437 MET cc_start: 0.8197 (tpt) cc_final: 0.7991 (tpt) REVERT: A 691 GLU cc_start: 0.7502 (pp20) cc_final: 0.7190 (pp20) REVERT: A 724 ASN cc_start: 0.7755 (t0) cc_final: 0.7042 (m-40) REVERT: A 788 CYS cc_start: 0.7700 (m) cc_final: 0.7461 (p) REVERT: A 803 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6306 (tp) REVERT: A 871 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: C 115 MET cc_start: 0.8698 (mmt) cc_final: 0.7757 (tmm) outliers start: 46 outliers final: 28 residues processed: 170 average time/residue: 0.0848 time to fit residues: 19.8090 Evaluate side-chains 165 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain C residue 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 16 optimal weight: 0.0370 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 0.0870 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN A 140 HIS A 724 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.124498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.098366 restraints weight = 22117.587| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 4.41 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7777 Z= 0.126 Angle : 0.663 16.341 10534 Z= 0.332 Chirality : 0.043 0.296 1243 Planarity : 0.005 0.056 1327 Dihedral : 6.345 108.482 1061 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 6.64 % Allowed : 29.54 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.26), residues: 987 helix: 1.17 (0.23), residues: 482 sheet: -0.78 (0.44), residues: 132 loop : -0.45 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 99 TYR 0.016 0.001 TYR C 143 PHE 0.031 0.002 PHE C 80 TRP 0.033 0.002 TRP A 766 HIS 0.002 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 7776) covalent geometry : angle 0.66340 / 0.33 (10532) SS BOND : bond 0.00007 / 0.00 ( 1) SS BOND : angle 0.61319 / 0.35 ( 2) hydrogen bonds : bond 0.03731 / 2.46 ( 423) hydrogen bonds : angle 4.62436 / 3.28 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.3181 (OUTLIER) cc_final: 0.2918 (tt0) REVERT: A 63 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.5524 (p90) REVERT: A 85 MET cc_start: 0.7666 (mpp) cc_final: 0.7449 (mpp) REVERT: A 101 ASP cc_start: 0.3285 (m-30) cc_final: 0.2891 (m-30) REVERT: A 167 ASP cc_start: 0.5272 (OUTLIER) cc_final: 0.4940 (m-30) REVERT: A 219 MET cc_start: 0.5989 (mmm) cc_final: 0.5739 (mmm) REVERT: A 320 LEU cc_start: 0.8306 (tt) cc_final: 0.7984 (pp) REVERT: A 339 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8143 (pt0) REVERT: A 437 MET cc_start: 0.8178 (tpt) cc_final: 0.7955 (tpt) REVERT: A 538 PHE cc_start: 0.7629 (t80) cc_final: 0.7416 (t80) REVERT: A 550 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8639 (p) REVERT: A 570 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7390 (p) REVERT: A 661 MET cc_start: 0.8417 (mmm) cc_final: 0.8176 (mmm) REVERT: A 691 GLU cc_start: 0.7406 (pp20) cc_final: 0.7193 (pp20) REVERT: A 718 SER cc_start: 0.7862 (t) cc_final: 0.7529 (p) REVERT: A 788 CYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7464 (p) REVERT: A 871 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7438 (pm20) REVERT: C 51 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7112 (tt) REVERT: C 115 MET cc_start: 0.8594 (mmt) cc_final: 0.7812 (tmm) outliers start: 56 outliers final: 28 residues processed: 174 average time/residue: 0.0841 time to fit residues: 20.3225 Evaluate side-chains 164 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 112 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN A 53 HIS A 140 HIS A 471 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.122092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.096848 restraints weight = 22519.194| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 4.32 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7777 Z= 0.152 Angle : 0.673 16.258 10534 Z= 0.336 Chirality : 0.042 0.154 1243 Planarity : 0.005 0.055 1327 Dihedral : 6.289 107.919 1061 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 5.81 % Allowed : 29.89 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.26), residues: 987 helix: 1.22 (0.23), residues: 484 sheet: -0.59 (0.45), residues: 127 loop : -0.45 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 796 TYR 0.022 0.001 TYR C 143 PHE 0.038 0.002 PHE C 80 TRP 0.033 0.003 TRP A 766 HIS 0.008 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 7776) covalent geometry : angle 0.67289 / 0.34 (10532) SS BOND : bond 0.00094 / 0.05 ( 1) SS BOND : angle 0.44526 / 0.25 ( 2) hydrogen bonds : bond 0.03814 / 2.51 ( 423) hydrogen bonds : angle 4.62054 / 3.26 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.5551 (p90) REVERT: A 101 ASP cc_start: 0.3237 (m-30) cc_final: 0.2840 (m-30) REVERT: A 167 ASP cc_start: 0.5330 (OUTLIER) cc_final: 0.4989 (m-30) REVERT: A 320 LEU cc_start: 0.8302 (tt) cc_final: 0.8030 (pp) REVERT: A 339 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8114 (pt0) REVERT: A 458 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: A 496 LYS cc_start: 0.9465 (mmmt) cc_final: 0.9227 (tppt) REVERT: A 517 MET cc_start: 0.5729 (OUTLIER) cc_final: 0.5394 (mmp) REVERT: A 538 PHE cc_start: 0.7704 (t80) cc_final: 0.7395 (t80) REVERT: A 570 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7440 (p) REVERT: A 661 MET cc_start: 0.8475 (mmm) cc_final: 0.8061 (mmm) REVERT: A 691 GLU cc_start: 0.7462 (pp20) cc_final: 0.7171 (pp20) REVERT: A 718 SER cc_start: 0.7807 (t) cc_final: 0.7465 (p) REVERT: A 760 ARG cc_start: 0.7800 (tmm160) cc_final: 0.7518 (ttp80) REVERT: A 788 CYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7554 (p) REVERT: A 803 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6456 (tp) REVERT: A 871 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: C 51 LEU cc_start: 0.7511 (mp) cc_final: 0.6928 (tt) REVERT: C 115 MET cc_start: 0.8595 (mmt) cc_final: 0.7643 (tmm) outliers start: 49 outliers final: 35 residues processed: 162 average time/residue: 0.0886 time to fit residues: 19.6336 Evaluate side-chains 169 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 112 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN C 114 GLN ** C 151 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 = 0.4261 r_free = 0.4261 target = 0.120452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.094508 restraints weight = 22618.315| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 4.50 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7777 Z= 0.158 Angle : 0.684 17.573 10534 Z= 0.341 Chirality : 0.042 0.173 1243 Planarity : 0.005 0.055 1327 Dihedral : 6.278 105.422 1061 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 6.52 % Allowed : 30.37 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.26), residues: 987 helix: 1.22 (0.23), residues: 484 sheet: -0.58 (0.44), residues: 137 loop : -0.41 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 99 TYR 0.022 0.002 TYR C 143 PHE 0.029 0.002 PHE C 80 TRP 0.037 0.003 TRP A 766 HIS 0.002 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 7776) covalent geometry : angle 0.68365 / 0.34 (10532) SS BOND : bond 0.00113 / 0.06 ( 1) SS BOND : angle 0.21210 / 0.11 ( 2) hydrogen bonds : bond 0.03865 / 2.56 ( 423) hydrogen bonds : angle 4.69317 / 3.31 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8619 (mm110) cc_final: 0.8193 (tm-30) REVERT: A 63 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.5561 (p90) REVERT: A 101 ASP cc_start: 0.3309 (m-30) cc_final: 0.2919 (m-30) REVERT: A 167 ASP cc_start: 0.5632 (OUTLIER) cc_final: 0.5271 (m-30) REVERT: A 243 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: A 294 MET cc_start: 0.8389 (ttm) cc_final: 0.8107 (ttm) REVERT: A 320 LEU cc_start: 0.8369 (tt) cc_final: 0.8083 (pp) REVERT: A 339 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8081 (pt0) REVERT: A 360 MET cc_start: 0.8437 (mtt) cc_final: 0.8125 (mtt) REVERT: A 458 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: A 496 LYS cc_start: 0.9450 (mmmt) cc_final: 0.9211 (tppt) REVERT: A 538 PHE cc_start: 0.7666 (t80) cc_final: 0.7379 (t80) REVERT: A 570 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7454 (p) REVERT: A 661 MET cc_start: 0.8494 (mmm) cc_final: 0.8015 (mmm) REVERT: A 691 GLU cc_start: 0.7398 (pp20) cc_final: 0.7120 (pp20) REVERT: A 718 SER cc_start: 0.7772 (t) cc_final: 0.7503 (p) REVERT: A 803 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6503 (tp) REVERT: A 871 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: C 51 LEU cc_start: 0.7640 (mp) cc_final: 0.7309 (tt) REVERT: C 115 MET cc_start: 0.8755 (mmt) cc_final: 0.7573 (tmm) outliers start: 55 outliers final: 39 residues processed: 168 average time/residue: 0.0828 time to fit residues: 18.9610 Evaluate side-chains 165 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 148 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 55 optimal weight: 0.0970 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.119576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.095194 restraints weight = 22538.336| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 4.23 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7777 Z= 0.154 Angle : 0.696 17.604 10534 Z= 0.350 Chirality : 0.043 0.205 1243 Planarity : 0.005 0.054 1327 Dihedral : 6.240 101.260 1061 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 6.29 % Allowed : 31.08 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 987 helix: 1.26 (0.23), residues: 483 sheet: -0.60 (0.44), residues: 137 loop : -0.48 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 760 TYR 0.022 0.002 TYR C 143 PHE 0.025 0.002 PHE C 80 TRP 0.039 0.003 TRP A 766 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 7776) covalent geometry : angle 0.69565 / 0.35 (10532) SS BOND : bond 0.00189 / 0.10 ( 1) SS BOND : angle 0.50869 / 0.27 ( 2) hydrogen bonds : bond 0.03932 / 2.59 ( 423) hydrogen bonds : angle 4.70434 / 3.32 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8540 (mm110) cc_final: 0.8161 (tm-30) REVERT: A 63 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.5528 (p90) REVERT: A 85 MET cc_start: 0.7334 (mpp) cc_final: 0.7057 (mpp) REVERT: A 101 ASP cc_start: 0.2964 (m-30) cc_final: 0.2700 (m-30) REVERT: A 131 LEU cc_start: 0.8155 (tp) cc_final: 0.7909 (tp) REVERT: A 167 ASP cc_start: 0.5756 (OUTLIER) cc_final: 0.5403 (m-30) REVERT: A 219 MET cc_start: 0.5672 (mmm) cc_final: 0.5325 (mmm) REVERT: A 243 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: A 320 LEU cc_start: 0.8333 (tt) cc_final: 0.8077 (pp) REVERT: A 339 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: A 458 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: A 496 LYS cc_start: 0.9437 (mmmt) cc_final: 0.9195 (tppt) REVERT: A 570 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7501 (p) REVERT: A 641 MET cc_start: 0.6603 (ttp) cc_final: 0.6341 (ttp) REVERT: A 661 MET cc_start: 0.8396 (mmm) cc_final: 0.7971 (mmm) REVERT: A 718 SER cc_start: 0.7835 (t) cc_final: 0.7519 (p) REVERT: A 778 LYS cc_start: 0.8202 (tppp) cc_final: 0.7773 (mtmm) REVERT: A 779 ILE cc_start: 0.8316 (mt) cc_final: 0.8029 (mt) REVERT: A 803 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6520 (tp) REVERT: A 871 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: C 51 LEU cc_start: 0.7600 (mp) cc_final: 0.7270 (tt) REVERT: C 97 LYS cc_start: 0.8998 (mmtm) cc_final: 0.8796 (mmtm) REVERT: C 115 MET cc_start: 0.8748 (mmt) cc_final: 0.7381 (tmm) outliers start: 53 outliers final: 35 residues processed: 166 average time/residue: 0.0854 time to fit residues: 19.5092 Evaluate side-chains 160 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 84 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.120312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.093944 restraints weight = 22348.459| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 4.25 r_work: 0.3591 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7777 Z= 0.146 Angle : 0.720 17.708 10534 Z= 0.359 Chirality : 0.044 0.179 1243 Planarity : 0.005 0.054 1327 Dihedral : 6.129 97.794 1061 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.69 % Allowed : 31.67 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.27), residues: 987 helix: 1.32 (0.23), residues: 483 sheet: -0.56 (0.45), residues: 131 loop : -0.46 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 760 TYR 0.022 0.002 TYR C 143 PHE 0.024 0.002 PHE C 80 TRP 0.042 0.003 TRP A 766 HIS 0.003 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 7776) covalent geometry : angle 0.72046 / 0.36 (10532) SS BOND : bond 0.00197 / 0.10 ( 1) SS BOND : angle 0.35956 / 0.19 ( 2) hydrogen bonds : bond 0.03892 / 2.57 ( 423) hydrogen bonds : angle 4.65604 / 3.28 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8687 (mm110) cc_final: 0.8270 (tm-30) REVERT: A 63 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.5540 (p90) REVERT: A 85 MET cc_start: 0.7775 (mpp) cc_final: 0.7449 (mpp) REVERT: A 101 ASP cc_start: 0.3176 (m-30) cc_final: 0.2906 (m-30) REVERT: A 131 LEU cc_start: 0.8112 (tp) cc_final: 0.7857 (tp) REVERT: A 167 ASP cc_start: 0.5907 (OUTLIER) cc_final: 0.5632 (m-30) REVERT: A 243 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: A 320 LEU cc_start: 0.8557 (tt) cc_final: 0.8230 (pp) REVERT: A 339 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8246 (pt0) REVERT: A 458 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: A 496 LYS cc_start: 0.9441 (mmmt) cc_final: 0.9197 (tppt) REVERT: A 570 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7544 (p) REVERT: A 661 MET cc_start: 0.8448 (mmm) cc_final: 0.8065 (mmm) REVERT: A 718 SER cc_start: 0.8140 (t) cc_final: 0.7832 (p) REVERT: A 778 LYS cc_start: 0.8451 (tppp) cc_final: 0.8101 (mtmt) REVERT: A 779 ILE cc_start: 0.8404 (mt) cc_final: 0.8105 (mt) REVERT: A 803 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6386 (tp) REVERT: A 871 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: C 51 LEU cc_start: 0.7803 (mp) cc_final: 0.7519 (tt) REVERT: C 112 TYR cc_start: 0.9147 (m-80) cc_final: 0.8816 (m-80) REVERT: C 115 MET cc_start: 0.8890 (mmt) cc_final: 0.7433 (tmm) outliers start: 48 outliers final: 35 residues processed: 164 average time/residue: 0.0924 time to fit residues: 20.5711 Evaluate side-chains 161 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 42 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 HIS ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.121025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.096198 restraints weight = 22202.347| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 4.49 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7777 Z= 0.138 Angle : 0.732 18.282 10534 Z= 0.364 Chirality : 0.044 0.205 1243 Planarity : 0.005 0.055 1327 Dihedral : 6.067 95.749 1061 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.74 % Allowed : 32.74 % Favored : 62.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.27), residues: 987 helix: 1.39 (0.23), residues: 480 sheet: -0.51 (0.45), residues: 131 loop : -0.48 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 760 TYR 0.021 0.002 TYR C 143 PHE 0.035 0.002 PHE C 80 TRP 0.041 0.002 TRP A 766 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 7776) covalent geometry : angle 0.73179 / 0.36 (10532) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.41475 / 0.22 ( 2) hydrogen bonds : bond 0.03806 / 2.52 ( 423) hydrogen bonds : angle 4.61475 / 3.26 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8633 (mm110) cc_final: 0.8237 (tm-30) REVERT: A 63 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.5540 (p90) REVERT: A 85 MET cc_start: 0.7414 (mpp) cc_final: 0.7181 (mpp) REVERT: A 101 ASP cc_start: 0.3367 (m-30) cc_final: 0.3053 (m-30) REVERT: A 131 LEU cc_start: 0.8133 (tp) cc_final: 0.7889 (tp) REVERT: A 167 ASP cc_start: 0.5681 (OUTLIER) cc_final: 0.5370 (m-30) REVERT: A 243 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: A 339 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: A 496 LYS cc_start: 0.9461 (mmmt) cc_final: 0.9218 (tppt) REVERT: A 550 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.8871 (p) REVERT: A 570 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7348 (p) REVERT: A 661 MET cc_start: 0.8285 (mmm) cc_final: 0.7788 (mmm) REVERT: A 718 SER cc_start: 0.7785 (t) cc_final: 0.7450 (p) REVERT: A 779 ILE cc_start: 0.8309 (mt) cc_final: 0.8012 (mt) REVERT: A 871 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: C 51 LEU cc_start: 0.7721 (mp) cc_final: 0.7338 (tt) REVERT: C 94 ASP cc_start: 0.7691 (p0) cc_final: 0.6885 (t0) REVERT: C 112 TYR cc_start: 0.8904 (m-80) cc_final: 0.8684 (m-80) REVERT: C 115 MET cc_start: 0.8783 (mmt) cc_final: 0.7341 (tmm) outliers start: 40 outliers final: 27 residues processed: 156 average time/residue: 0.0868 time to fit residues: 18.6814 Evaluate side-chains 154 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 42 optimal weight: 0.0070 chunk 61 optimal weight: 5.9990 chunk 3 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 chunk 74 optimal weight: 0.0030 chunk 89 optimal weight: 30.0000 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 overall best weight: 1.0210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.120284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.095545 restraints weight = 22621.453| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 4.29 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7777 Z= 0.147 Angle : 0.749 18.281 10534 Z= 0.369 Chirality : 0.044 0.223 1243 Planarity : 0.005 0.053 1327 Dihedral : 6.013 94.480 1061 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.86 % Allowed : 32.62 % Favored : 62.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.27), residues: 987 helix: 1.30 (0.23), residues: 482 sheet: -0.40 (0.44), residues: 131 loop : -0.41 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 760 TYR 0.020 0.002 TYR C 143 PHE 0.032 0.002 PHE C 80 TRP 0.046 0.004 TRP C 69 HIS 0.002 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 7776) covalent geometry : angle 0.74886 / 0.37 (10532) SS BOND : bond 0.00218 / 0.11 ( 1) SS BOND : angle 0.66064 / 0.38 ( 2) hydrogen bonds : bond 0.03860 / 2.57 ( 423) hydrogen bonds : angle 4.65288 / 3.30 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.16 seconds wall clock time: 33 minutes 15.09 seconds (1995.09 seconds total)