Starting phenix.real_space_refine on Thu Jul 2 20:08:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dnz_30791/07_2026/7dnz_30791.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dnz_30791/07_2026/7dnz_30791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dnz_30791/07_2026/7dnz_30791.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dnz_30791/07_2026/7dnz_30791.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dnz_30791/07_2026/7dnz_30791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dnz_30791/07_2026/7dnz_30791.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dnz_30791/07_2026/7dnz_30791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dnz_30791/07_2026/7dnz_30791.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 38 5.16 5 C 6256 2.51 5 N 1634 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9671 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4669 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 577} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4669 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 577} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 145 Unusual residues: {'GSH': 2, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 188 Unusual residues: {'GSH': 2, 'HEM': 1, 'Y01': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 1.66, per 1000 atoms: 0.17 Number of scatterers: 9671 At special positions: 0 Unit cell: (80.51, 98.77, 137.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 38 16.00 O 1742 8.00 N 1634 7.00 C 6256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 354.6 milliseconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 8 sheets defined 70.7% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 239 through 254 removed outlier: 3.610A pdb=" N GLY A 243 " --> pdb=" O TRP A 239 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 295 removed outlier: 4.006A pdb=" N VAL A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Proline residue: A 283 - end of helix removed outlier: 3.656A pdb=" N GLU A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 316 removed outlier: 3.637A pdb=" N LEU A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 355 removed outlier: 3.512A pdb=" N ARG A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 338 " --> pdb=" O TRP A 334 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.946A pdb=" N HIS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 390 removed outlier: 3.806A pdb=" N VAL A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ARG A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 409 Processing helix chain 'A' and resid 410 through 459 removed outlier: 3.700A pdb=" N GLY A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 removed outlier: 3.513A pdb=" N ASN A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 522 removed outlier: 4.276A pdb=" N LYS A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 545 removed outlier: 4.327A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Proline residue: A 543 - end of helix Processing helix chain 'A' and resid 546 through 570 removed outlier: 3.699A pdb=" N TYR A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'A' and resid 680 through 685 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 705 through 712 Processing helix chain 'A' and resid 728 through 744 Processing helix chain 'A' and resid 758 through 773 Processing helix chain 'A' and resid 784 through 790 Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.672A pdb=" N ASP A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.610A pdb=" N GLY B 243 " --> pdb=" O TRP B 239 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 295 removed outlier: 4.006A pdb=" N VAL B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 3.656A pdb=" N GLU B 295 " --> pdb=" O ASN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 316 removed outlier: 3.638A pdb=" N LEU B 302 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 355 removed outlier: 4.887A pdb=" N ARG B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 338 " --> pdb=" O TRP B 334 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 364 removed outlier: 3.946A pdb=" N HIS B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 390 removed outlier: 3.805A pdb=" N VAL B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ARG B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 410 through 459 removed outlier: 3.700A pdb=" N GLY B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 467 removed outlier: 3.513A pdb=" N ASN B 467 " --> pdb=" O VAL B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 522 removed outlier: 4.276A pdb=" N LYS B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 545 removed outlier: 4.327A pdb=" N VAL B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Proline residue: B 543 - end of helix Processing helix chain 'B' and resid 546 through 570 removed outlier: 3.699A pdb=" N TYR B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 Processing helix chain 'B' and resid 658 through 665 Processing helix chain 'B' and resid 680 through 685 Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 705 through 712 Processing helix chain 'B' and resid 728 through 744 Processing helix chain 'B' and resid 758 through 773 Processing helix chain 'B' and resid 784 through 790 Processing helix chain 'B' and resid 807 through 815 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.671A pdb=" N ASP B 820 " --> pdb=" O GLY B 816 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 590 through 596 removed outlier: 3.524A pdb=" N GLU A 591 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 648 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 593 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A 646 " --> pdb=" O GLU A 593 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 595 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER A 644 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 618 through 621 removed outlier: 3.652A pdb=" N ILE A 779 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 781 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 679 Processing sheet with id=AA4, first strand: chain 'A' and resid 794 through 798 removed outlier: 3.839A pdb=" N GLY A 806 " --> pdb=" O ILE A 794 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 804 " --> pdb=" O VAL A 796 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 798 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 590 through 596 removed outlier: 3.525A pdb=" N GLU B 591 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 648 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 593 " --> pdb=" O CYS B 646 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 646 " --> pdb=" O GLU B 593 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 595 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER B 644 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 618 through 621 removed outlier: 3.652A pdb=" N ILE B 779 " --> pdb=" O ILE B 748 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 781 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 678 through 679 Processing sheet with id=AA8, first strand: chain 'B' and resid 794 through 798 removed outlier: 3.839A pdb=" N GLY B 806 " --> pdb=" O ILE B 794 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 804 " --> pdb=" O VAL B 796 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS B 798 " --> pdb=" O ILE B 802 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE B 802 " --> pdb=" O LYS B 798 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 3768 1.38 - 1.56: 6038 1.56 - 1.74: 4 1.74 - 1.92: 61 1.92 - 2.10: 3 Bond restraints: 9874 Sorted by residual: bond pdb=" C3C HEM B 901 " pdb=" CAC HEM B 901 " ideal model delta sigma weight residual 1.544 1.471 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C3B HEM B 901 " pdb=" CAB HEM B 901 " ideal model delta sigma weight residual 1.544 1.475 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 GSH B 903 " pdb=" O12 GSH B 903 " ideal model delta sigma weight residual 1.307 1.244 0.063 1.90e-02 2.77e+03 1.09e+01 bond pdb=" C1 GSH A 902 " pdb=" O12 GSH A 902 " ideal model delta sigma weight residual 1.307 1.245 0.062 1.90e-02 2.77e+03 1.07e+01 bond pdb=" C1 GSH B 902 " pdb=" O11 GSH B 902 " ideal model delta sigma weight residual 1.213 1.246 -0.033 1.00e-02 1.00e+04 1.06e+01 ... (remaining 9869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 12524 1.99 - 3.97: 724 3.97 - 5.96: 132 5.96 - 7.94: 34 7.94 - 9.93: 18 Bond angle restraints: 13432 Sorted by residual: angle pdb=" C PHE B 325 " pdb=" N VAL B 326 " pdb=" CA VAL B 326 " ideal model delta sigma weight residual 122.63 113.76 8.87 1.19e+00 7.06e-01 5.56e+01 angle pdb=" C THR A 320 " pdb=" CA THR A 320 " pdb=" CB THR A 320 " ideal model delta sigma weight residual 109.72 119.03 -9.31 1.66e+00 3.63e-01 3.15e+01 angle pdb=" N GLY A 318 " pdb=" CA GLY A 318 " pdb=" C GLY A 318 " ideal model delta sigma weight residual 112.73 106.03 6.70 1.20e+00 6.94e-01 3.12e+01 angle pdb=" N VAL A 280 " pdb=" CA VAL A 280 " pdb=" C VAL A 280 " ideal model delta sigma weight residual 112.96 108.41 4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" N SER B 322 " pdb=" CA SER B 322 " pdb=" C SER B 322 " ideal model delta sigma weight residual 108.24 102.24 6.00 1.32e+00 5.74e-01 2.07e+01 ... (remaining 13427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5049 17.94 - 35.88: 543 35.88 - 53.82: 91 53.82 - 71.76: 26 71.76 - 89.69: 7 Dihedral angle restraints: 5716 sinusoidal: 2316 harmonic: 3400 Sorted by residual: dihedral pdb=" C2B HEM B 901 " pdb=" C3B HEM B 901 " pdb=" CAB HEM B 901 " pdb=" CBB HEM B 901 " ideal model delta sinusoidal sigma weight residual 0.00 71.87 -71.87 2 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" C2C HEM B 901 " pdb=" C3C HEM B 901 " pdb=" CAC HEM B 901 " pdb=" CBC HEM B 901 " ideal model delta sinusoidal sigma weight residual -0.00 -65.50 65.50 2 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" C THR A 320 " pdb=" N THR A 320 " pdb=" CA THR A 320 " pdb=" CB THR A 320 " ideal model delta harmonic sigma weight residual -122.00 -136.24 14.24 0 2.50e+00 1.60e-01 3.24e+01 ... (remaining 5713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1360 0.094 - 0.187: 178 0.187 - 0.281: 9 0.281 - 0.375: 0 0.375 - 0.468: 1 Chirality restraints: 1548 Sorted by residual: chirality pdb=" CA THR A 320 " pdb=" N THR A 320 " pdb=" C THR A 320 " pdb=" CB THR A 320 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" CA PHE B 408 " pdb=" N PHE B 408 " pdb=" C PHE B 408 " pdb=" CB PHE B 408 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA THR B 320 " pdb=" N THR B 320 " pdb=" C THR B 320 " pdb=" CB THR B 320 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1545 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG1 GSH A 901 " 0.162 2.00e-02 2.50e+03 1.94e-01 4.71e+02 pdb=" CD1 GSH A 901 " -0.064 2.00e-02 2.50e+03 pdb=" OE1 GSH A 901 " -0.009 2.00e-02 2.50e+03 pdb=" CA2 GSH A 901 " 0.233 2.00e-02 2.50e+03 pdb=" N2 GSH A 901 " -0.322 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG1 GSH B 902 " 0.136 2.00e-02 2.50e+03 1.56e-01 3.05e+02 pdb=" CD1 GSH B 902 " -0.051 2.00e-02 2.50e+03 pdb=" OE1 GSH B 902 " -0.018 2.00e-02 2.50e+03 pdb=" CA2 GSH B 902 " 0.188 2.00e-02 2.50e+03 pdb=" N2 GSH B 902 " -0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 GSH B 902 " -0.043 2.00e-02 2.50e+03 1.26e-01 1.97e+02 pdb=" CA2 GSH B 902 " 0.113 2.00e-02 2.50e+03 pdb=" CA3 GSH B 902 " 0.153 2.00e-02 2.50e+03 pdb=" N3 GSH B 902 " -0.201 2.00e-02 2.50e+03 pdb=" O2 GSH B 902 " -0.022 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2824 2.82 - 3.34: 9776 3.34 - 3.86: 15815 3.86 - 4.38: 16675 4.38 - 4.90: 28224 Nonbonded interactions: 73314 Sorted by model distance: nonbonded pdb=" ND1 HIS B 808 " pdb=" OH TYR B 818 " model vdw 2.295 3.120 nonbonded pdb=" ND1 HIS A 808 " pdb=" OH TYR A 818 " model vdw 2.295 3.120 nonbonded pdb=" NH1 ARG B 638 " pdb=" O ILE B 654 " model vdw 2.303 3.120 nonbonded pdb=" NH1 ARG A 638 " pdb=" O ILE A 654 " model vdw 2.303 3.120 nonbonded pdb=" OH TYR A 424 " pdb=" OE1 GLN A 501 " model vdw 2.312 3.040 ... (remaining 73309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 236 through 826 or resid 902 or resid 904 through 905)) selection = (chain 'B' and (resid 236 through 826 or resid 902 or resid 904 through 905)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.010 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.009 0.219 9874 Z= 0.442 Angle : 1.121 9.926 13432 Z= 0.636 Chirality : 0.061 0.468 1548 Planarity : 0.010 0.194 1668 Dihedral : 15.152 89.694 3540 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.60 % Allowed : 1.10 % Favored : 98.29 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.23), residues: 1178 helix: 0.53 (0.18), residues: 780 sheet: -2.29 (0.65), residues: 50 loop : -2.39 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 663 TYR 0.032 0.003 TYR B 466 PHE 0.050 0.004 PHE B 460 TRP 0.008 0.001 TRP A 304 HIS 0.007 0.002 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00942 / 0.44 ( 9874) covalent geometry : angle 1.12080 / 0.64 (13432) hydrogen bonds : bond 0.14736 / 9.75 ( 625) hydrogen bonds : angle 5.57330 / 4.06 ( 1857) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8517 (tm-30) REVERT: A 408 PHE cc_start: 0.7597 (m-80) cc_final: 0.7083 (m-10) REVERT: A 452 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7864 (tpp80) REVERT: A 614 MET cc_start: 0.8929 (mpp) cc_final: 0.8299 (mpp) REVERT: A 748 ILE cc_start: 0.8701 (mt) cc_final: 0.8475 (mt) REVERT: B 275 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 408 PHE cc_start: 0.7738 (m-80) cc_final: 0.7112 (m-10) REVERT: B 452 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7951 (tpp80) REVERT: B 614 MET cc_start: 0.8889 (mpp) cc_final: 0.8231 (mpp) REVERT: B 748 ILE cc_start: 0.8667 (mt) cc_final: 0.8430 (mt) outliers start: 6 outliers final: 3 residues processed: 147 average time/residue: 0.0686 time to fit residues: 15.6721 Evaluate side-chains 95 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 455 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.0170 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN A 316 GLN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS A 539 GLN A 557 ASN B 279 ASN B 316 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS B 539 GLN B 557 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.147237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.102325 restraints weight = 16455.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105571 restraints weight = 7328.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107745 restraints weight = 4416.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.109103 restraints weight = 3213.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.109744 restraints weight = 2653.832| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9874 Z= 0.146 Angle : 0.595 9.086 13432 Z= 0.303 Chirality : 0.039 0.138 1548 Planarity : 0.004 0.039 1668 Dihedral : 7.659 89.140 1415 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.21 % Allowed : 11.35 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1178 helix: 1.42 (0.18), residues: 806 sheet: -0.07 (0.73), residues: 30 loop : -2.33 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 685 TYR 0.013 0.001 TYR B 466 PHE 0.017 0.001 PHE A 519 TRP 0.007 0.001 TRP A 334 HIS 0.003 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 9874) covalent geometry : angle 0.59528 / 0.30 (13432) hydrogen bonds : bond 0.06648 / 4.46 ( 625) hydrogen bonds : angle 4.42114 / 3.26 ( 1857) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8384 (tm-30) REVERT: A 407 MET cc_start: 0.8181 (tmm) cc_final: 0.7915 (tmm) REVERT: A 539 GLN cc_start: 0.8365 (tt0) cc_final: 0.7870 (tt0) REVERT: A 614 MET cc_start: 0.8970 (mpp) cc_final: 0.8282 (mpp) REVERT: A 666 ILE cc_start: 0.8838 (tp) cc_final: 0.8605 (tp) REVERT: A 671 GLN cc_start: 0.7291 (tp-100) cc_final: 0.6782 (tp-100) REVERT: A 748 ILE cc_start: 0.8359 (mt) cc_final: 0.8139 (mt) REVERT: A 821 MET cc_start: 0.7976 (tmm) cc_final: 0.7774 (tmm) REVERT: B 275 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8374 (tm-30) REVERT: B 407 MET cc_start: 0.8140 (tmm) cc_final: 0.7900 (tmm) REVERT: B 614 MET cc_start: 0.8992 (mpp) cc_final: 0.8311 (mpp) REVERT: B 671 GLN cc_start: 0.7268 (tp-100) cc_final: 0.6799 (tp-100) REVERT: B 748 ILE cc_start: 0.8415 (mt) cc_final: 0.8196 (mt) REVERT: B 750 LEU cc_start: 0.8483 (tt) cc_final: 0.8282 (tt) outliers start: 22 outliers final: 19 residues processed: 135 average time/residue: 0.0654 time to fit residues: 13.7857 Evaluate side-chains 120 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 725 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 77 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.143903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.098015 restraints weight = 16695.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.101102 restraints weight = 7644.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.103161 restraints weight = 4676.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104484 restraints weight = 3443.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.105235 restraints weight = 2865.212| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9874 Z= 0.203 Angle : 0.627 7.721 13432 Z= 0.316 Chirality : 0.040 0.153 1548 Planarity : 0.003 0.034 1668 Dihedral : 7.226 78.707 1415 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.31 % Allowed : 16.27 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1178 helix: 1.78 (0.19), residues: 806 sheet: 0.01 (0.64), residues: 34 loop : -2.22 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 330 TYR 0.013 0.001 TYR A 466 PHE 0.014 0.001 PHE B 408 TRP 0.011 0.001 TRP A 334 HIS 0.004 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 9874) covalent geometry : angle 0.62720 / 0.32 (13432) hydrogen bonds : bond 0.06616 / 4.44 ( 625) hydrogen bonds : angle 4.35878 / 3.20 ( 1857) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8407 (tm-30) REVERT: A 442 MET cc_start: 0.8637 (ttt) cc_final: 0.8413 (ttm) REVERT: A 614 MET cc_start: 0.8903 (mpp) cc_final: 0.8212 (mpp) REVERT: A 637 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8327 (t80) REVERT: A 705 ILE cc_start: 0.6547 (OUTLIER) cc_final: 0.6273 (mp) REVERT: A 748 ILE cc_start: 0.8457 (mt) cc_final: 0.8218 (mt) REVERT: A 750 LEU cc_start: 0.8810 (tt) cc_final: 0.8531 (tt) REVERT: B 275 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8406 (tm-30) REVERT: B 407 MET cc_start: 0.8400 (tmm) cc_final: 0.8142 (tmm) REVERT: B 614 MET cc_start: 0.8953 (mpp) cc_final: 0.8286 (mpp) REVERT: B 637 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8413 (t80) REVERT: B 671 GLN cc_start: 0.7305 (tp-100) cc_final: 0.6932 (tp40) REVERT: B 705 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6682 (mp) REVERT: B 748 ILE cc_start: 0.8484 (mt) cc_final: 0.8246 (mt) REVERT: B 750 LEU cc_start: 0.8729 (tt) cc_final: 0.8462 (tt) REVERT: B 751 ASP cc_start: 0.6445 (t0) cc_final: 0.6141 (t0) outliers start: 33 outliers final: 19 residues processed: 123 average time/residue: 0.0642 time to fit residues: 12.7902 Evaluate side-chains 112 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 0.0270 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 30.0000 chunk 103 optimal weight: 0.3980 chunk 2 optimal weight: 0.0060 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 HIS B 354 HIS B 557 ASN B 652 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.145492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.100333 restraints weight = 18164.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.103794 restraints weight = 7591.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106093 restraints weight = 4460.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.107485 restraints weight = 3240.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.108206 restraints weight = 2699.674| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9874 Z= 0.121 Angle : 0.541 10.327 13432 Z= 0.265 Chirality : 0.037 0.145 1548 Planarity : 0.003 0.028 1668 Dihedral : 6.545 67.244 1414 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.51 % Allowed : 18.88 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1178 helix: 2.11 (0.19), residues: 810 sheet: 0.50 (0.72), residues: 34 loop : -2.17 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 685 TYR 0.009 0.001 TYR B 465 PHE 0.010 0.001 PHE A 712 TRP 0.006 0.001 TRP A 434 HIS 0.003 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 ( 9874) covalent geometry : angle 0.54124 / 0.26 (13432) hydrogen bonds : bond 0.05288 / 3.55 ( 625) hydrogen bonds : angle 3.93921 / 2.90 ( 1857) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8353 (tm-30) REVERT: A 338 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8209 (tm-30) REVERT: A 407 MET cc_start: 0.8449 (tmm) cc_final: 0.8224 (tmm) REVERT: A 539 GLN cc_start: 0.8403 (tt0) cc_final: 0.7936 (tt0) REVERT: A 553 MET cc_start: 0.8472 (mtm) cc_final: 0.8173 (mtp) REVERT: A 671 GLN cc_start: 0.7074 (tp-100) cc_final: 0.6869 (tp-100) REVERT: A 750 LEU cc_start: 0.8701 (tt) cc_final: 0.8373 (tt) REVERT: B 275 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8318 (tm-30) REVERT: B 315 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8395 (mp) REVERT: B 338 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8189 (tm-30) REVERT: B 389 PHE cc_start: 0.8930 (m-10) cc_final: 0.8709 (m-10) REVERT: B 539 GLN cc_start: 0.8438 (tt0) cc_final: 0.8112 (tt0) REVERT: B 614 MET cc_start: 0.8958 (mpp) cc_final: 0.8242 (mpp) REVERT: B 671 GLN cc_start: 0.7114 (tp-100) cc_final: 0.6808 (tp-100) REVERT: B 750 LEU cc_start: 0.8609 (tt) cc_final: 0.8327 (tt) outliers start: 25 outliers final: 17 residues processed: 142 average time/residue: 0.0644 time to fit residues: 14.8301 Evaluate side-chains 128 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 47 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS B 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.148235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.102678 restraints weight = 16649.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.105855 restraints weight = 7477.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.108044 restraints weight = 4550.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.109425 restraints weight = 3327.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.110132 restraints weight = 2763.259| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9874 Z= 0.129 Angle : 0.569 8.947 13432 Z= 0.275 Chirality : 0.037 0.145 1548 Planarity : 0.003 0.028 1668 Dihedral : 6.275 65.793 1414 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.91 % Allowed : 19.68 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.25), residues: 1178 helix: 2.16 (0.19), residues: 812 sheet: 0.74 (0.76), residues: 34 loop : -2.07 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 330 TYR 0.011 0.001 TYR A 466 PHE 0.009 0.001 PHE A 460 TRP 0.007 0.001 TRP B 334 HIS 0.009 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9874) covalent geometry : angle 0.56929 / 0.27 (13432) hydrogen bonds : bond 0.05339 / 3.59 ( 625) hydrogen bonds : angle 3.87332 / 2.84 ( 1857) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8385 (tm-30) REVERT: A 315 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8558 (mp) REVERT: A 338 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 539 GLN cc_start: 0.8387 (tt0) cc_final: 0.7958 (tt0) REVERT: A 637 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8243 (t80) REVERT: A 671 GLN cc_start: 0.7182 (tp-100) cc_final: 0.6982 (tp-100) REVERT: A 705 ILE cc_start: 0.6556 (OUTLIER) cc_final: 0.6279 (mp) REVERT: A 750 LEU cc_start: 0.8761 (tt) cc_final: 0.8406 (tt) REVERT: B 275 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 315 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8498 (mp) REVERT: B 389 PHE cc_start: 0.8991 (m-10) cc_final: 0.8749 (m-10) REVERT: B 539 GLN cc_start: 0.8387 (tt0) cc_final: 0.7910 (tt0) REVERT: B 614 MET cc_start: 0.8858 (mpp) cc_final: 0.8657 (mmm) REVERT: B 637 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8285 (t80) REVERT: B 705 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6816 (mp) REVERT: B 750 LEU cc_start: 0.8700 (tt) cc_final: 0.8396 (tt) outliers start: 29 outliers final: 19 residues processed: 129 average time/residue: 0.0557 time to fit residues: 11.8783 Evaluate side-chains 128 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 62 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 HIS B 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.148224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.103568 restraints weight = 16668.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106866 restraints weight = 7242.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.109044 restraints weight = 4305.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.110435 restraints weight = 3117.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.111185 restraints weight = 2572.829| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9874 Z= 0.120 Angle : 0.572 9.037 13432 Z= 0.270 Chirality : 0.037 0.144 1548 Planarity : 0.003 0.024 1668 Dihedral : 6.132 63.832 1414 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.41 % Allowed : 21.08 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.25), residues: 1178 helix: 2.24 (0.19), residues: 812 sheet: 0.89 (0.78), residues: 34 loop : -2.03 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 330 TYR 0.009 0.001 TYR A 465 PHE 0.008 0.001 PHE A 533 TRP 0.006 0.000 TRP B 334 HIS 0.007 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 9874) covalent geometry : angle 0.57173 / 0.27 (13432) hydrogen bonds : bond 0.05159 / 3.47 ( 625) hydrogen bonds : angle 3.78223 / 2.78 ( 1857) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 279 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8591 (t0) REVERT: A 338 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 539 GLN cc_start: 0.8388 (tt0) cc_final: 0.8135 (tt0) REVERT: A 637 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8255 (t80) REVERT: A 705 ILE cc_start: 0.6579 (OUTLIER) cc_final: 0.6311 (mp) REVERT: A 750 LEU cc_start: 0.8749 (tt) cc_final: 0.8383 (tt) REVERT: B 275 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8434 (tm-30) REVERT: B 389 PHE cc_start: 0.8982 (m-10) cc_final: 0.8728 (m-10) REVERT: B 539 GLN cc_start: 0.8404 (tt0) cc_final: 0.7926 (tt0) REVERT: B 637 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8223 (t80) REVERT: B 671 GLN cc_start: 0.7064 (tp-100) cc_final: 0.6805 (tp-100) REVERT: B 705 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6811 (mp) REVERT: B 750 LEU cc_start: 0.8682 (tt) cc_final: 0.8335 (tt) outliers start: 34 outliers final: 23 residues processed: 133 average time/residue: 0.0538 time to fit residues: 11.5365 Evaluate side-chains 136 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 115 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.146556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.102073 restraints weight = 16654.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.105200 restraints weight = 7398.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107284 restraints weight = 4446.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.108602 restraints weight = 3242.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.109391 restraints weight = 2689.637| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9874 Z= 0.151 Angle : 0.617 10.334 13432 Z= 0.289 Chirality : 0.037 0.147 1548 Planarity : 0.003 0.023 1668 Dihedral : 6.082 63.421 1414 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.71 % Allowed : 21.08 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1178 helix: 2.26 (0.19), residues: 812 sheet: 0.77 (0.78), residues: 34 loop : -1.93 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 638 TYR 0.013 0.001 TYR B 465 PHE 0.008 0.001 PHE A 533 TRP 0.007 0.001 TRP B 334 HIS 0.006 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9874) covalent geometry : angle 0.61719 / 0.29 (13432) hydrogen bonds : bond 0.05507 / 3.70 ( 625) hydrogen bonds : angle 3.85613 / 2.83 ( 1857) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8371 (tm-30) REVERT: A 614 MET cc_start: 0.8811 (mmt) cc_final: 0.8545 (mmm) REVERT: A 637 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8225 (t80) REVERT: A 705 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6294 (mp) REVERT: A 750 LEU cc_start: 0.8824 (tt) cc_final: 0.8443 (tt) REVERT: B 275 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8389 (tm-30) REVERT: B 389 PHE cc_start: 0.9068 (m-10) cc_final: 0.8787 (m-10) REVERT: B 465 TYR cc_start: 0.8995 (m-80) cc_final: 0.8687 (m-80) REVERT: B 539 GLN cc_start: 0.8427 (tt0) cc_final: 0.7940 (tt0) REVERT: B 637 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8339 (t80) REVERT: B 671 GLN cc_start: 0.7062 (tp-100) cc_final: 0.6824 (tp-100) REVERT: B 705 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6760 (mp) REVERT: B 750 LEU cc_start: 0.8816 (tt) cc_final: 0.8434 (tt) outliers start: 37 outliers final: 25 residues processed: 130 average time/residue: 0.0623 time to fit residues: 13.1228 Evaluate side-chains 131 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS A 539 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.146839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.101976 restraints weight = 16455.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.105087 restraints weight = 7384.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.107171 restraints weight = 4461.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.108463 restraints weight = 3263.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.109245 restraints weight = 2719.977| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9874 Z= 0.146 Angle : 0.620 11.365 13432 Z= 0.290 Chirality : 0.037 0.147 1548 Planarity : 0.003 0.025 1668 Dihedral : 6.018 64.247 1414 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.21 % Allowed : 21.89 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.25), residues: 1178 helix: 2.26 (0.19), residues: 814 sheet: 0.59 (0.79), residues: 34 loop : -1.84 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 638 TYR 0.013 0.001 TYR B 465 PHE 0.008 0.001 PHE B 519 TRP 0.007 0.001 TRP B 334 HIS 0.004 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 9874) covalent geometry : angle 0.62001 / 0.29 (13432) hydrogen bonds : bond 0.05519 / 3.72 ( 625) hydrogen bonds : angle 3.82279 / 2.80 ( 1857) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8385 (tm-30) REVERT: A 614 MET cc_start: 0.8854 (mmt) cc_final: 0.8579 (mmm) REVERT: A 637 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8172 (t80) REVERT: A 705 ILE cc_start: 0.6605 (OUTLIER) cc_final: 0.6329 (mp) REVERT: A 750 LEU cc_start: 0.8835 (tt) cc_final: 0.8464 (tt) REVERT: B 275 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8393 (tm-30) REVERT: B 465 TYR cc_start: 0.8989 (m-80) cc_final: 0.8678 (m-80) REVERT: B 539 GLN cc_start: 0.8358 (tt0) cc_final: 0.7873 (tt0) REVERT: B 637 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8373 (t80) REVERT: B 671 GLN cc_start: 0.7030 (tp-100) cc_final: 0.6808 (tp-100) REVERT: B 705 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6808 (mp) REVERT: B 750 LEU cc_start: 0.8799 (tt) cc_final: 0.8415 (tt) outliers start: 32 outliers final: 24 residues processed: 122 average time/residue: 0.0523 time to fit residues: 10.4839 Evaluate side-chains 128 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 HIS B 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.144220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.099367 restraints weight = 16655.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102401 restraints weight = 7562.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.104435 restraints weight = 4614.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105805 restraints weight = 3388.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106499 restraints weight = 2807.638| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9874 Z= 0.169 Angle : 0.651 12.678 13432 Z= 0.304 Chirality : 0.038 0.146 1548 Planarity : 0.003 0.023 1668 Dihedral : 6.018 65.903 1414 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.51 % Allowed : 21.89 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.25), residues: 1178 helix: 2.19 (0.19), residues: 814 sheet: 0.44 (0.79), residues: 34 loop : -1.82 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 638 TYR 0.013 0.001 TYR B 476 PHE 0.009 0.001 PHE A 676 TRP 0.007 0.001 TRP B 334 HIS 0.005 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 9874) covalent geometry : angle 0.65094 / 0.30 (13432) hydrogen bonds : bond 0.05730 / 3.85 ( 625) hydrogen bonds : angle 3.88532 / 2.86 ( 1857) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 614 MET cc_start: 0.8789 (mmt) cc_final: 0.8528 (mmm) REVERT: A 637 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8233 (t80) REVERT: A 705 ILE cc_start: 0.6587 (OUTLIER) cc_final: 0.6300 (mp) REVERT: A 750 LEU cc_start: 0.8892 (tt) cc_final: 0.8555 (tt) REVERT: B 275 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 465 TYR cc_start: 0.8996 (m-80) cc_final: 0.8685 (m-80) REVERT: B 539 GLN cc_start: 0.8407 (tt0) cc_final: 0.7928 (tt0) REVERT: B 637 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8459 (t80) REVERT: B 671 GLN cc_start: 0.7047 (tp-100) cc_final: 0.6818 (tp-100) REVERT: B 705 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6774 (mp) REVERT: B 750 LEU cc_start: 0.8849 (tt) cc_final: 0.8484 (tt) outliers start: 35 outliers final: 25 residues processed: 124 average time/residue: 0.0547 time to fit residues: 10.9762 Evaluate side-chains 130 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 0.0170 chunk 95 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.150646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.106230 restraints weight = 16465.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.109471 restraints weight = 7346.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.111649 restraints weight = 4409.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.112992 restraints weight = 3208.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.113626 restraints weight = 2666.212| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.002 0.037 9874 Z= 0.118 Angle : 0.613 10.201 13432 Z= 0.284 Chirality : 0.037 0.143 1548 Planarity : 0.003 0.023 1668 Dihedral : 5.787 68.708 1414 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.31 % Allowed : 23.59 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.26), residues: 1178 helix: 2.36 (0.19), residues: 814 sheet: 0.43 (0.86), residues: 40 loop : -1.80 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 776 TYR 0.011 0.001 TYR B 465 PHE 0.013 0.001 PHE B 408 TRP 0.007 0.001 TRP B 334 HIS 0.003 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 9874) covalent geometry : angle 0.61270 / 0.28 (13432) hydrogen bonds : bond 0.04889 / 3.29 ( 625) hydrogen bonds : angle 3.69658 / 2.71 ( 1857) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8433 (tm-30) REVERT: A 408 PHE cc_start: 0.6948 (m-80) cc_final: 0.6699 (m-80) REVERT: A 614 MET cc_start: 0.8761 (mmt) cc_final: 0.8493 (mmm) REVERT: A 637 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8090 (t80) REVERT: A 705 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6533 (mp) REVERT: A 750 LEU cc_start: 0.8750 (tt) cc_final: 0.8394 (tt) REVERT: B 275 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8362 (tm-30) REVERT: B 389 PHE cc_start: 0.8974 (m-10) cc_final: 0.8692 (m-10) REVERT: B 465 TYR cc_start: 0.8880 (m-80) cc_final: 0.8613 (m-80) REVERT: B 637 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8213 (t80) REVERT: B 671 GLN cc_start: 0.6905 (tp-100) cc_final: 0.6687 (tp-100) REVERT: B 750 LEU cc_start: 0.8776 (tt) cc_final: 0.8405 (tt) outliers start: 23 outliers final: 19 residues processed: 132 average time/residue: 0.0636 time to fit residues: 13.7825 Evaluate side-chains 135 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 96 optimal weight: 30.0000 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 64 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.148117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.103808 restraints weight = 16548.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.106955 restraints weight = 7314.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.109096 restraints weight = 4392.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.110424 restraints weight = 3186.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.111168 restraints weight = 2632.147| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9874 Z= 0.141 Angle : 0.639 10.581 13432 Z= 0.298 Chirality : 0.038 0.125 1548 Planarity : 0.003 0.024 1668 Dihedral : 5.758 70.245 1414 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.71 % Allowed : 23.80 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.25), residues: 1178 helix: 2.32 (0.19), residues: 814 sheet: 0.58 (0.84), residues: 34 loop : -1.76 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 330 TYR 0.016 0.001 TYR A 466 PHE 0.021 0.001 PHE B 408 TRP 0.007 0.001 TRP B 334 HIS 0.008 0.002 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 9874) covalent geometry : angle 0.63882 / 0.30 (13432) hydrogen bonds : bond 0.05259 / 3.53 ( 625) hydrogen bonds : angle 3.75785 / 2.75 ( 1857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1575.70 seconds wall clock time: 27 minutes 51.14 seconds (1671.14 seconds total)