Starting phenix.real_space_refine on Wed Feb 12 11:14:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yaj_33714/02_2025/7yaj_33714.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yaj_33714/02_2025/7yaj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yaj_33714/02_2025/7yaj_33714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yaj_33714/02_2025/7yaj_33714.map" model { file = "/net/cci-nas-00/data/ceres_data/7yaj_33714/02_2025/7yaj_33714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yaj_33714/02_2025/7yaj_33714.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: 4.85, per 1000 atoms: 0.63 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: 2.16 Conformation dependent library (CDL) restraints added in 996.0 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: 0.97 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: 2.81 Time building geometry restraints manager: 2.43 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: 4221 24.80 - 49.60: 437 49.60 - 74.40: 56 74.40 - 99.20: 7 99.20 - 124.00: 2 Dihedral angle restraints: 4723 sinusoidal: 1863 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 4720 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.640 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 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 7776 Z= 0.339 Angle : 0.947 13.944 10532 Z= 0.542 Chirality : 0.054 0.306 1243 Planarity : 0.009 0.149 1327 Dihedral : 18.800 124.004 2878 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (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 TRP 0.042 0.002 TRP C 149 HIS 0.008 0.001 HIS A 467 PHE 0.020 0.002 PHE A 383 TYR 0.027 0.003 TYR C 143 ARG 0.005 0.001 ARG C 99 *********************** 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 : 0.918 Fit side-chains 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: 0.2694 (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: 0.2261 time to fit residues: 57.9867 Evaluate side-chains 141 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 83 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.122177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.095367 restraints weight = 22444.664| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 4.35 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7776 Z= 0.266 Angle : 0.689 9.463 10532 Z= 0.356 Chirality : 0.043 0.156 1243 Planarity : 0.006 0.067 1327 Dihedral : 9.563 125.131 1096 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 5.10 % Allowed : 30.13 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 987 helix: 0.52 (0.23), residues: 482 sheet: -0.83 (0.45), residues: 130 loop : -0.63 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 766 HIS 0.009 0.002 HIS A 53 PHE 0.028 0.002 PHE C 100 TYR 0.025 0.002 TYR A 618 ARG 0.006 0.001 ARG C 99 *********************** 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 187 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 1.506 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 85 MET cc_start: 0.7532 (mpp) cc_final: 0.7092 (mpp) REVERT: A 129 GLU cc_start: 0.8924 (tp30) cc_final: 0.8691 (tm-30) REVERT: A 131 LEU cc_start: 0.7934 (tp) cc_final: 0.7721 (tp) REVERT: A 167 ASP cc_start: 0.5468 (OUTLIER) cc_final: 0.5126 (m-30) REVERT: A 320 LEU cc_start: 0.8460 (tt) cc_final: 0.8065 (pp) REVERT: A 339 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: A 412 ASN cc_start: 0.7142 (m-40) cc_final: 0.6773 (m110) REVERT: A 444 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8968 (pm20) REVERT: A 677 LEU cc_start: 0.7821 (pt) cc_final: 0.7251 (tp) REVERT: A 681 ASP cc_start: 0.7488 (p0) cc_final: 0.7216 (p0) REVERT: A 803 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6432 (tp) REVERT: C 51 LEU cc_start: 0.7720 (tt) cc_final: 0.7233 (mp) REVERT: C 99 ARG cc_start: 0.7812 (ptt-90) cc_final: 0.5745 (ttp80) outliers start: 43 outliers final: 20 residues processed: 178 average time/residue: 0.2008 time to fit residues: 48.1008 Evaluate side-chains 150 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 444 GLN 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 533 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 740 ILE 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 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 19 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 140 HIS ** 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 = 0.4285 r_free = 0.4285 target = 0.122863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.096229 restraints weight = 22713.938| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 4.41 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7776 Z= 0.200 Angle : 0.612 7.394 10532 Z= 0.319 Chirality : 0.042 0.152 1243 Planarity : 0.005 0.062 1327 Dihedral : 9.031 123.096 1091 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 5.34 % Allowed : 30.25 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 987 helix: 0.93 (0.23), residues: 483 sheet: -0.75 (0.45), residues: 128 loop : -0.61 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 766 HIS 0.005 0.001 HIS C 86 PHE 0.020 0.002 PHE A 818 TYR 0.018 0.002 TYR C 148 ARG 0.008 0.001 ARG C 78 *********************** 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 187 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 0.968 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: 0.2655 (m-30) cc_final: 0.2400 (m-30) REVERT: A 129 GLU cc_start: 0.8951 (tp30) cc_final: 0.8731 (tm-30) REVERT: A 167 ASP cc_start: 0.5439 (OUTLIER) cc_final: 0.5136 (m-30) REVERT: A 320 LEU cc_start: 0.8453 (tt) cc_final: 0.8070 (pp) REVERT: A 339 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: A 359 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 412 ASN cc_start: 0.7345 (m-40) cc_final: 0.6988 (m110) REVERT: A 437 MET cc_start: 0.8245 (tpt) cc_final: 0.7997 (tpt) REVERT: A 803 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6400 (tp) REVERT: A 871 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: C 51 LEU cc_start: 0.7867 (tt) cc_final: 0.7150 (mp) outliers start: 45 outliers final: 19 residues processed: 177 average time/residue: 0.2174 time to fit residues: 51.2421 Evaluate side-chains 148 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 188 LEU 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 426 THR Chi-restraints excluded: chain A residue 430 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 533 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE 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 765 ASN Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 871 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 28 optimal weight: 0.0050 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 140 HIS ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.120558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.094321 restraints weight = 22531.538| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 4.26 r_work: 0.3609 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 7776 Z= 0.254 Angle : 0.649 8.163 10532 Z= 0.337 Chirality : 0.043 0.199 1243 Planarity : 0.005 0.073 1327 Dihedral : 8.870 126.133 1088 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 6.52 % Allowed : 30.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 987 helix: 1.03 (0.23), residues: 481 sheet: -0.74 (0.45), residues: 124 loop : -0.58 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 766 HIS 0.005 0.001 HIS C 86 PHE 0.014 0.002 PHE C 80 TYR 0.016 0.002 TYR A 618 ARG 0.009 0.001 ARG C 99 *********************** 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 181 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.9078 (tp30) cc_final: 0.8742 (tm-30) REVERT: A 167 ASP cc_start: 0.5735 (OUTLIER) cc_final: 0.5436 (m-30) REVERT: A 320 LEU cc_start: 0.8606 (tt) cc_final: 0.8212 (pp) REVERT: A 339 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: A 359 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 458 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: A 570 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7522 (p) REVERT: A 631 SER cc_start: 0.7938 (OUTLIER) cc_final: 0.7725 (t) REVERT: A 677 LEU cc_start: 0.8264 (pt) cc_final: 0.7781 (pt) REVERT: A 779 ILE cc_start: 0.8401 (mt) cc_final: 0.8140 (mt) REVERT: A 803 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6555 (tp) REVERT: A 871 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: C 115 MET cc_start: 0.8622 (mmp) cc_final: 0.7789 (tmm) outliers start: 55 outliers final: 31 residues processed: 172 average time/residue: 0.1995 time to fit residues: 46.6130 Evaluate side-chains 159 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 631 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 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 803 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 848 VAL 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 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 140 HIS ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN A 730 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4215 r_free = 0.4215 target = 0.118237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.093495 restraints weight = 22453.044| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 4.32 r_work: 0.3546 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7776 Z= 0.277 Angle : 0.656 9.697 10532 Z= 0.340 Chirality : 0.044 0.292 1243 Planarity : 0.005 0.061 1327 Dihedral : 8.882 127.580 1088 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 7.12 % Allowed : 29.89 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 987 helix: 1.04 (0.23), residues: 482 sheet: -0.88 (0.45), residues: 129 loop : -0.55 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 766 HIS 0.004 0.001 HIS C 86 PHE 0.034 0.002 PHE C 100 TYR 0.015 0.002 TYR C 148 ARG 0.006 0.001 ARG A 796 *********************** 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 178 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 118 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.9104 (tp30) cc_final: 0.8782 (tm-30) REVERT: A 167 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5724 (m-30) REVERT: A 320 LEU cc_start: 0.8625 (tt) cc_final: 0.8232 (pp) REVERT: A 339 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8174 (pt0) REVERT: A 359 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7932 (tm-30) REVERT: A 458 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: A 685 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8127 (tp) REVERT: A 779 ILE cc_start: 0.8416 (mt) cc_final: 0.8145 (mt) REVERT: A 803 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6701 (tp) REVERT: A 871 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: C 115 MET cc_start: 0.8366 (mmp) cc_final: 0.7422 (tmm) outliers start: 60 outliers final: 39 residues processed: 166 average time/residue: 0.1904 time to fit residues: 43.7274 Evaluate side-chains 155 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU 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 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 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 458 GLN Chi-restraints excluded: chain A residue 514 LYS 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 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 631 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 715 THR 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 803 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 848 VAL 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 111 VAL 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 53 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 54 optimal weight: 0.0030 chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 53 HIS A 140 HIS ** C 114 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 = 0.4234 r_free = 0.4234 target = 0.119479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.093001 restraints weight = 22651.363| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 4.23 r_work: 0.3586 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7776 Z= 0.198 Angle : 0.640 10.263 10532 Z= 0.326 Chirality : 0.042 0.149 1243 Planarity : 0.005 0.056 1327 Dihedral : 8.742 123.824 1088 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 6.52 % Allowed : 30.49 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 987 helix: 1.21 (0.23), residues: 483 sheet: -0.73 (0.44), residues: 126 loop : -0.63 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 766 HIS 0.004 0.001 HIS A 53 PHE 0.027 0.002 PHE C 100 TYR 0.015 0.001 TYR C 143 ARG 0.009 0.001 ARG C 78 *********************** 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 184 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8627 (mm110) cc_final: 0.8194 (tm-30) REVERT: A 63 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.5589 (p90) REVERT: A 85 MET cc_start: 0.8064 (mpp) cc_final: 0.7836 (mpp) REVERT: A 167 ASP cc_start: 0.5951 (OUTLIER) cc_final: 0.5718 (m-30) REVERT: A 243 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: A 281 MET cc_start: 0.8169 (ppp) cc_final: 0.7916 (tpt) REVERT: A 320 LEU cc_start: 0.8585 (tt) cc_final: 0.8234 (pp) REVERT: A 339 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: A 458 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: A 461 MET cc_start: 0.6077 (ptt) cc_final: 0.5867 (ptt) REVERT: A 496 LYS cc_start: 0.9474 (mmmt) cc_final: 0.9248 (tppt) REVERT: A 538 PHE cc_start: 0.7808 (t80) cc_final: 0.7550 (t80) REVERT: A 687 SER cc_start: 0.9106 (m) cc_final: 0.8868 (p) REVERT: A 779 ILE cc_start: 0.8366 (mt) cc_final: 0.8093 (mt) REVERT: A 803 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6557 (tp) REVERT: A 871 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: C 78 ARG cc_start: 0.8661 (tpt90) cc_final: 0.8251 (tpt170) REVERT: C 97 LYS cc_start: 0.9401 (mmmm) cc_final: 0.9196 (mmmm) REVERT: C 113 LEU cc_start: 0.8087 (mt) cc_final: 0.7835 (mt) REVERT: C 115 MET cc_start: 0.8283 (mmp) cc_final: 0.7312 (tmm) outliers start: 55 outliers final: 32 residues processed: 171 average time/residue: 0.2329 time to fit residues: 53.4865 Evaluate side-chains 159 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 243 GLU 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 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 458 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU 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 740 ILE Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 788 CYS 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 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 112 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.117043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.092147 restraints weight = 22708.661| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 4.29 r_work: 0.3532 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7776 Z= 0.280 Angle : 0.689 10.567 10532 Z= 0.353 Chirality : 0.044 0.191 1243 Planarity : 0.005 0.055 1327 Dihedral : 8.849 126.089 1088 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 6.76 % Allowed : 31.55 % Favored : 61.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 987 helix: 1.14 (0.23), residues: 482 sheet: -0.77 (0.43), residues: 134 loop : -0.60 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 766 HIS 0.004 0.001 HIS C 86 PHE 0.030 0.002 PHE C 100 TYR 0.026 0.002 TYR C 143 ARG 0.013 0.001 ARG A 760 *********************** 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 179 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8631 (mm110) cc_final: 0.8318 (tm-30) REVERT: A 85 MET cc_start: 0.8079 (mpp) cc_final: 0.7624 (mpp) REVERT: A 281 MET cc_start: 0.8165 (ppp) cc_final: 0.7958 (tpt) REVERT: A 320 LEU cc_start: 0.8637 (tt) cc_final: 0.8297 (pp) REVERT: A 339 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8226 (pt0) REVERT: A 412 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7312 (m110) REVERT: A 458 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: A 496 LYS cc_start: 0.9488 (mmmt) cc_final: 0.9258 (tppt) REVERT: A 514 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8576 (ttpt) REVERT: A 779 ILE cc_start: 0.8484 (mt) cc_final: 0.8212 (mt) REVERT: A 803 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6680 (tp) REVERT: A 871 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7610 (pm20) outliers start: 57 outliers final: 40 residues processed: 167 average time/residue: 0.2191 time to fit residues: 48.9277 Evaluate side-chains 160 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 188 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 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 559 LEU 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 631 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 871 GLU 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 112 TYR 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 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 140 HIS C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.118897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.093876 restraints weight = 22569.617| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 4.31 r_work: 0.3570 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7776 Z= 0.210 Angle : 0.694 11.659 10532 Z= 0.350 Chirality : 0.043 0.178 1243 Planarity : 0.005 0.055 1327 Dihedral : 8.774 121.872 1088 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 6.52 % Allowed : 32.03 % Favored : 61.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.27), residues: 987 helix: 1.26 (0.23), residues: 483 sheet: -0.65 (0.43), residues: 132 loop : -0.59 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 766 HIS 0.004 0.001 HIS A 53 PHE 0.045 0.002 PHE C 80 TYR 0.028 0.002 TYR C 143 ARG 0.011 0.001 ARG A 760 *********************** 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 179 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 124 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8705 (mm110) cc_final: 0.8280 (tm-30) REVERT: A 63 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.5615 (p90) REVERT: A 85 MET cc_start: 0.8052 (mpp) cc_final: 0.7588 (mpp) REVERT: A 243 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: A 320 LEU cc_start: 0.8590 (tt) cc_final: 0.8250 (pp) REVERT: A 339 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8215 (pt0) REVERT: A 412 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7266 (m110) REVERT: A 496 LYS cc_start: 0.9472 (mmmt) cc_final: 0.9246 (tppt) REVERT: A 687 SER cc_start: 0.9205 (m) cc_final: 0.8997 (p) REVERT: A 778 LYS cc_start: 0.8457 (tppp) cc_final: 0.7888 (mtmm) REVERT: A 779 ILE cc_start: 0.8410 (mt) cc_final: 0.8116 (mt) REVERT: A 803 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6577 (tp) REVERT: A 871 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: C 53 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7553 (mm) REVERT: C 78 ARG cc_start: 0.8492 (tpt90) cc_final: 0.8217 (tpt170) REVERT: C 99 ARG cc_start: 0.8694 (tmm-80) cc_final: 0.7801 (ttp80) REVERT: C 115 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.7248 (tmm) REVERT: C 118 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7028 (pt) REVERT: C 119 LYS cc_start: 0.9248 (mmtt) cc_final: 0.9003 (mmtt) outliers start: 55 outliers final: 35 residues processed: 167 average time/residue: 0.2141 time to fit residues: 48.0224 Evaluate side-chains 163 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 86 LEU Chi-restraints excluded: chain A residue 98 HIS 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 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 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 412 ASN 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 533 LEU Chi-restraints excluded: chain A residue 559 LEU 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 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 740 ILE 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 803 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.119005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.093721 restraints weight = 22783.329| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 4.38 r_work: 0.3575 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7776 Z= 0.211 Angle : 0.694 10.696 10532 Z= 0.347 Chirality : 0.043 0.149 1243 Planarity : 0.005 0.055 1327 Dihedral : 8.701 119.662 1088 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.46 % Allowed : 32.74 % Favored : 61.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 987 helix: 1.29 (0.23), residues: 483 sheet: -0.58 (0.44), residues: 129 loop : -0.64 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 766 HIS 0.003 0.001 HIS C 86 PHE 0.034 0.002 PHE A 218 TYR 0.026 0.002 TYR C 143 ARG 0.011 0.000 ARG A 760 *********************** 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 169 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 123 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8709 (mm110) cc_final: 0.8270 (tm-30) REVERT: A 63 PHE cc_start: 0.7101 (OUTLIER) cc_final: 0.5515 (p90) REVERT: A 84 ILE cc_start: 0.8018 (mm) cc_final: 0.7799 (mm) REVERT: A 85 MET cc_start: 0.8068 (mpp) cc_final: 0.7589 (mpp) REVERT: A 320 LEU cc_start: 0.8594 (tt) cc_final: 0.8284 (pp) REVERT: A 339 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8215 (pt0) REVERT: A 417 ARG cc_start: 0.8949 (ttt-90) cc_final: 0.8561 (ttp80) REVERT: A 496 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9247 (tppt) REVERT: A 687 SER cc_start: 0.9197 (m) cc_final: 0.8962 (p) REVERT: A 778 LYS cc_start: 0.8465 (tppp) cc_final: 0.7906 (mtmm) REVERT: A 779 ILE cc_start: 0.8430 (mt) cc_final: 0.8136 (mt) REVERT: A 803 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6524 (tp) REVERT: A 871 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: C 53 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7255 (mm) REVERT: C 99 ARG cc_start: 0.8662 (tmm-80) cc_final: 0.8144 (tmm-80) REVERT: C 112 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8946 (m-80) REVERT: C 115 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.6921 (tmm) REVERT: C 118 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7116 (pt) REVERT: C 119 LYS cc_start: 0.9244 (mmtt) cc_final: 0.8984 (mmtt) outliers start: 46 outliers final: 34 residues processed: 159 average time/residue: 0.2252 time to fit residues: 47.7832 Evaluate side-chains 160 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 86 LEU Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 249 GLN 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 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 559 LEU 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 740 ILE Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 62 optimal weight: 0.0040 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.119636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.094799 restraints weight = 22385.969| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 4.28 r_work: 0.3590 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7776 Z= 0.198 Angle : 0.712 12.052 10532 Z= 0.353 Chirality : 0.043 0.156 1243 Planarity : 0.005 0.054 1327 Dihedral : 8.655 118.104 1088 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.98 % Allowed : 33.21 % Favored : 61.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.27), residues: 987 helix: 1.31 (0.23), residues: 483 sheet: -0.54 (0.45), residues: 129 loop : -0.61 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 766 HIS 0.004 0.001 HIS A 53 PHE 0.033 0.002 PHE C 100 TYR 0.024 0.002 TYR C 143 ARG 0.013 0.000 ARG A 760 ********************** 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 164 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.5483 (p90) REVERT: A 84 ILE cc_start: 0.8024 (mm) cc_final: 0.7792 (mm) REVERT: A 85 MET cc_start: 0.8054 (mpp) cc_final: 0.7570 (mpp) REVERT: A 320 LEU cc_start: 0.8559 (tt) cc_final: 0.8275 (pp) REVERT: A 339 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: A 417 ARG cc_start: 0.8927 (ttt-90) cc_final: 0.8545 (ttp80) REVERT: A 496 LYS cc_start: 0.9480 (mmmt) cc_final: 0.9244 (tppt) REVERT: A 570 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7301 (p) REVERT: A 687 SER cc_start: 0.9173 (m) cc_final: 0.8973 (p) REVERT: A 691 GLU cc_start: 0.7751 (pp20) cc_final: 0.7422 (pp20) REVERT: A 778 LYS cc_start: 0.8458 (tppp) cc_final: 0.7907 (mtmm) REVERT: A 779 ILE cc_start: 0.8407 (mt) cc_final: 0.8105 (mt) REVERT: A 871 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: C 53 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7253 (mm) REVERT: C 99 ARG cc_start: 0.8656 (tmm-80) cc_final: 0.8214 (tmm-80) REVERT: C 112 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8911 (m-80) REVERT: C 115 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.6969 (tmm) REVERT: C 118 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.7019 (pt) REVERT: C 119 LYS cc_start: 0.9266 (mmtt) cc_final: 0.8997 (mmtt) outliers start: 42 outliers final: 30 residues processed: 153 average time/residue: 0.2158 time to fit residues: 44.1328 Evaluate side-chains 155 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 86 LEU Chi-restraints excluded: chain A residue 175 LEU 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 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 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 559 LEU 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 740 ILE Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.119645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.094766 restraints weight = 22320.556| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 4.30 r_work: 0.3592 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7776 Z= 0.206 Angle : 0.703 10.354 10532 Z= 0.350 Chirality : 0.043 0.139 1243 Planarity : 0.005 0.056 1327 Dihedral : 8.500 117.452 1088 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.22 % Allowed : 32.74 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.27), residues: 987 helix: 1.33 (0.23), residues: 483 sheet: -0.50 (0.45), residues: 129 loop : -0.62 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 766 HIS 0.003 0.001 HIS C 86 PHE 0.031 0.002 PHE C 100 TYR 0.022 0.002 TYR C 143 ARG 0.012 0.001 ARG A 760 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4220.31 seconds wall clock time: 75 minutes 50.40 seconds (4550.40 seconds total)