Starting phenix.real_space_refine on Thu Aug 6 06:57:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vjh_65113/08_2026/9vjh_65113.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vjh_65113/08_2026/9vjh_65113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vjh_65113/08_2026/9vjh_65113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vjh_65113/08_2026/9vjh_65113.map" model { file = "/net/cci-nas-00/data/ceres_data/9vjh_65113/08_2026/9vjh_65113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vjh_65113/08_2026/9vjh_65113.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 92 5.49 5 S 86 5.16 5 C 8570 2.51 5 N 2492 2.21 5 O 2718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13958 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6034 Classifications: {'peptide': 770} Link IDs: {'PTRANS': 38, 'TRANS': 731} Chain breaks: 4 Chain: "B" Number of atoms: 6034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6034 Classifications: {'peptide': 770} Link IDs: {'PTRANS': 38, 'TRANS': 731} Chain breaks: 4 Chain: "C" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 466 Classifications: {'DNA': 23} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 22} Chain: "E" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 466 Classifications: {'DNA': 23} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 479 Classifications: {'DNA': 23} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 479 Classifications: {'DNA': 23} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 22} Time building chain proxies: 3.22, per 1000 atoms: 0.23 Number of scatterers: 13958 At special positions: 0 Unit cell: (113.98, 113.98, 104.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 92 15.00 O 2718 8.00 N 2492 7.00 C 8570 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: 1.06 Conformation dependent library (CDL) restraints added in 565.7 milliseconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 10 sheets defined 54.5% alpha, 8.1% beta 41 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 19 through 38 removed outlier: 3.727A pdb=" N GLU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 Proline residue: A 47 - end of helix Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 190 through 205 Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.720A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 285 through 296 removed outlier: 3.531A pdb=" N GLU A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 319 removed outlier: 3.820A pdb=" N GLN A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 4.043A pdb=" N GLN A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 removed outlier: 4.247A pdb=" N VAL A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'A' and resid 459 through 475 removed outlier: 4.552A pdb=" N TYR A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 506 through 532 removed outlier: 4.546A pdb=" N ARG A 529 " --> pdb=" O GLN A 525 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU A 530 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.760A pdb=" N GLU A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 557 Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 576 through 595 Processing helix chain 'A' and resid 595 through 601 removed outlier: 3.884A pdb=" N THR A 599 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 600 " --> pdb=" O PRO A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 613 Processing helix chain 'A' and resid 637 through 654 Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 702 through 714 removed outlier: 3.757A pdb=" N SER A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 761 through 772 removed outlier: 3.596A pdb=" N HIS A 772 " --> pdb=" O LEU A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 792 removed outlier: 3.552A pdb=" N HIS A 792 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 812 removed outlier: 3.628A pdb=" N CYS A 811 " --> pdb=" O TRP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 834 Processing helix chain 'B' and resid 20 through 38 Processing helix chain 'B' and resid 41 through 50 Proline residue: B 47 - end of helix Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 190 through 205 Processing helix chain 'B' and resid 216 through 227 removed outlier: 3.600A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 256 through 264 Processing helix chain 'B' and resid 285 through 296 removed outlier: 3.699A pdb=" N GLY B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 319 removed outlier: 3.795A pdb=" N GLN B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.548A pdb=" N GLY B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN B 341 " --> pdb=" O THR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 removed outlier: 4.272A pdb=" N VAL B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 412 through 422 removed outlier: 3.544A pdb=" N LEU B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 464 through 475 removed outlier: 4.082A pdb=" N HIS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.623A pdb=" N ARG B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 527 " --> pdb=" O ARG B 523 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG B 529 " --> pdb=" O GLN B 525 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU B 530 " --> pdb=" O ARG B 526 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.891A pdb=" N GLU B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 557 Processing helix chain 'B' and resid 563 through 575 Processing helix chain 'B' and resid 576 through 595 Processing helix chain 'B' and resid 595 through 601 removed outlier: 3.872A pdb=" N THR B 599 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 600 " --> pdb=" O PRO B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 613 Processing helix chain 'B' and resid 637 through 654 removed outlier: 3.520A pdb=" N LEU B 654 " --> pdb=" O MET B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 677 Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 702 through 714 removed outlier: 3.748A pdb=" N SER B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 739 Processing helix chain 'B' and resid 756 through 760 removed outlier: 3.586A pdb=" N LEU B 760 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 772 removed outlier: 3.633A pdb=" N HIS B 772 " --> pdb=" O LEU B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 792 removed outlier: 3.626A pdb=" N HIS B 792 " --> pdb=" O LEU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 812 removed outlier: 3.641A pdb=" N CYS B 811 " --> pdb=" O TRP B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 834 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 58 removed outlier: 6.033A pdb=" N THR A 77 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASP A 212 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A 79 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 171 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU A 107 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP A 174 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL A 109 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.689A pdb=" N VAL A 345 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 304 " --> pdb=" O TYR A 347 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ARG A 248 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE A 398 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU A 250 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N MET A 400 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS A 249 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 615 through 620 removed outlier: 4.039A pdb=" N GLY A 615 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 656 through 657 Processing sheet with id=AA5, first strand: chain 'A' and resid 744 through 745 Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 58 removed outlier: 6.029A pdb=" N THR B 77 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ASP B 212 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL B 79 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 171 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU B 107 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP B 174 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL B 109 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL B 152 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL B 108 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 326 removed outlier: 3.835A pdb=" N VAL B 345 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 304 " --> pdb=" O TYR B 347 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ARG B 248 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE B 398 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU B 250 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N MET B 400 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS B 249 " --> pdb=" O ARG B 497 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 615 through 620 removed outlier: 3.992A pdb=" N GLY B 615 " --> pdb=" O LEU B 631 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 656 through 657 Processing sheet with id=AB1, first strand: chain 'B' and resid 744 through 745 582 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4250 1.34 - 1.46: 2944 1.46 - 1.58: 6948 1.58 - 1.70: 180 1.70 - 1.82: 130 Bond restraints: 14452 Sorted by residual: bond pdb=" C3' DG C 2 " pdb=" C2' DG C 2 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG E 2 " pdb=" C2' DG E 2 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG D 13 " pdb=" C2' DG D 13 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DG F 13 " pdb=" C2' DG F 13 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.96e+00 bond pdb=" C3' DG E 15 " pdb=" C2' DG E 15 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.02e+00 ... (remaining 14447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 19898 2.61 - 5.23: 97 5.23 - 7.84: 10 7.84 - 10.46: 3 10.46 - 13.07: 2 Bond angle restraints: 20010 Sorted by residual: angle pdb=" CB MET B 842 " pdb=" CG MET B 842 " pdb=" SD MET B 842 " ideal model delta sigma weight residual 112.70 125.77 -13.07 3.00e+00 1.11e-01 1.90e+01 angle pdb=" N3 DT C 13 " pdb=" C4 DT C 13 " pdb=" O4 DT C 13 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT C 6 " pdb=" C4 DT C 6 " pdb=" O4 DT C 6 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT E 16 " pdb=" C4 DT E 16 " pdb=" O4 DT E 16 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT F 4 " pdb=" C4 DT F 4 " pdb=" O4 DT F 4 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 20005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.59: 6424 14.59 - 29.17: 1086 29.17 - 43.76: 522 43.76 - 58.35: 306 58.35 - 72.94: 32 Dihedral angle restraints: 8370 sinusoidal: 3924 harmonic: 4446 Sorted by residual: dihedral pdb=" CA ASN A 299 " pdb=" CB ASN A 299 " pdb=" CG ASN A 299 " pdb=" OD1 ASN A 299 " ideal model delta sinusoidal sigma weight residual 120.00 -167.06 -72.94 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASN B 299 " pdb=" CB ASN B 299 " pdb=" CG ASN B 299 " pdb=" OD1 ASN B 299 " ideal model delta sinusoidal sigma weight residual 120.00 -167.83 -72.17 2 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA MET A 744 " pdb=" C MET A 744 " pdb=" N ALA A 745 " pdb=" CA ALA A 745 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 8367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1338 0.027 - 0.054: 608 0.054 - 0.082: 190 0.082 - 0.109: 122 0.109 - 0.136: 24 Chirality restraints: 2282 Sorted by residual: chirality pdb=" CA VAL B 46 " pdb=" N VAL B 46 " pdb=" C VAL B 46 " pdb=" CB VAL B 46 " both_signs ideal model delta sigma weight residual False 2.44 2.31 0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" P DA E 1 " pdb=" OP1 DA E 1 " pdb=" OP2 DA E 1 " pdb=" O5' DA E 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.47 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" P DT F 1 " pdb=" OP1 DT F 1 " pdb=" OP2 DT F 1 " pdb=" O5' DT F 1 " both_signs ideal model delta sigma weight residual True 2.34 2.47 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 2279 not shown) Planarity restraints: 2238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 408 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO B 409 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 842 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C MET A 842 " 0.029 2.00e-02 2.50e+03 pdb=" O MET A 842 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN A 843 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 842 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C MET B 842 " 0.028 2.00e-02 2.50e+03 pdb=" O MET B 842 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN B 843 " -0.010 2.00e-02 2.50e+03 ... (remaining 2235 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1371 2.75 - 3.29: 13378 3.29 - 3.82: 24851 3.82 - 4.36: 27203 4.36 - 4.90: 44714 Nonbonded interactions: 111517 Sorted by model distance: nonbonded pdb=" OG1 THR B 349 " pdb=" OG SER B 384 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR A 349 " pdb=" OG SER A 384 " model vdw 2.212 3.040 nonbonded pdb=" O ASP B 610 " pdb=" OG1 THR B 614 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR B 609 " pdb=" OG1 THR B 634 " model vdw 2.223 3.040 nonbonded pdb=" O ASP A 610 " pdb=" OG1 THR A 614 " model vdw 2.226 3.040 ... (remaining 111512 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.860 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14452 Z= 0.271 Angle : 0.571 13.070 20010 Z= 0.384 Chirality : 0.039 0.136 2282 Planarity : 0.003 0.044 2238 Dihedral : 19.980 72.937 5498 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 27.64 % Favored : 72.36 % 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: 1.45 (0.22), residues: 1520 helix: 1.76 (0.19), residues: 768 sheet: 1.74 (0.39), residues: 180 loop : -0.37 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 472 TYR 0.015 0.001 TYR A 342 PHE 0.019 0.001 PHE A 309 TRP 0.006 0.001 TRP A 339 HIS 0.001 0.000 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.27 (14452) covalent geometry : angle 0.57057 / 0.38 (20010) hydrogen bonds : bond 0.21239 / 14.86 ( 680) hydrogen bonds : angle 7.11432 / 5.16 ( 1899) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1168 time to fit residues: 29.2825 Evaluate side-chains 164 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 HIS A 216 ASN A 299 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.233258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.186726 restraints weight = 18067.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.185166 restraints weight = 22420.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.186689 restraints weight = 24313.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.187485 restraints weight = 15366.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.188386 restraints weight = 13390.566| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14452 Z= 0.141 Angle : 0.571 8.618 20010 Z= 0.305 Chirality : 0.042 0.279 2282 Planarity : 0.004 0.038 2238 Dihedral : 19.518 59.967 2694 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.22 % Allowed : 26.26 % Favored : 71.52 % 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: 1.36 (0.22), residues: 1520 helix: 1.70 (0.19), residues: 782 sheet: 1.67 (0.38), residues: 178 loop : -0.47 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 810 TYR 0.016 0.002 TYR A 342 PHE 0.018 0.002 PHE A 222 TRP 0.010 0.001 TRP A 339 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (14452) covalent geometry : angle 0.57064 / 0.31 (20010) hydrogen bonds : bond 0.06142 / 4.40 ( 680) hydrogen bonds : angle 4.37629 / 3.07 ( 1899) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.4482 (ttt180) cc_final: 0.3501 (mtp85) REVERT: A 510 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.6311 (m-80) REVERT: B 561 ASP cc_start: 0.6800 (m-30) cc_final: 0.6373 (t0) outliers start: 29 outliers final: 17 residues processed: 205 average time/residue: 0.1056 time to fit residues: 33.5048 Evaluate side-chains 191 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 742 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 101 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 43 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 GLN A 373 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.231698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.185276 restraints weight = 18050.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.184664 restraints weight = 24618.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.186370 restraints weight = 24390.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.187508 restraints weight = 15475.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.188619 restraints weight = 13378.318| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14452 Z= 0.127 Angle : 0.538 8.704 20010 Z= 0.284 Chirality : 0.039 0.149 2282 Planarity : 0.003 0.038 2238 Dihedral : 19.597 59.897 2694 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.68 % Allowed : 25.88 % Favored : 71.44 % 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: 1.37 (0.22), residues: 1520 helix: 1.83 (0.19), residues: 772 sheet: 1.41 (0.36), residues: 192 loop : -0.57 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 35 TYR 0.017 0.001 TYR A 342 PHE 0.019 0.001 PHE B 115 TRP 0.005 0.001 TRP B 94 HIS 0.013 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (14452) covalent geometry : angle 0.53774 / 0.28 (20010) hydrogen bonds : bond 0.05260 / 3.73 ( 680) hydrogen bonds : angle 4.10548 / 2.86 ( 1899) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.4478 (ttt180) cc_final: 0.3581 (mtp85) REVERT: A 510 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: A 561 ASP cc_start: 0.7050 (m-30) cc_final: 0.6695 (t0) REVERT: B 561 ASP cc_start: 0.6875 (m-30) cc_final: 0.6309 (t0) outliers start: 35 outliers final: 21 residues processed: 215 average time/residue: 0.1086 time to fit residues: 35.6863 Evaluate side-chains 196 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 772 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 70 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 159 optimal weight: 50.0000 chunk 30 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 157 optimal weight: 40.0000 chunk 132 optimal weight: 2.9990 chunk 158 optimal weight: 50.0000 chunk 95 optimal weight: 8.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN A 492 ASN A 573 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 ASN B 573 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.216114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.167579 restraints weight = 17937.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.171958 restraints weight = 33977.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.172601 restraints weight = 17998.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.174908 restraints weight = 11281.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175580 restraints weight = 9185.770| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 14452 Z= 0.319 Angle : 0.812 10.375 20010 Z= 0.414 Chirality : 0.050 0.251 2282 Planarity : 0.006 0.062 2238 Dihedral : 20.047 59.985 2694 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.82 % Allowed : 24.50 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.01 (0.21), residues: 1520 helix: 0.56 (0.18), residues: 784 sheet: 0.28 (0.36), residues: 194 loop : -0.81 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG B 532 TYR 0.024 0.004 TYR B 168 PHE 0.029 0.004 PHE A 222 TRP 0.017 0.002 TRP A 641 HIS 0.036 0.002 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.32 (14452) covalent geometry : angle 0.81201 / 0.41 (20010) hydrogen bonds : bond 0.05990 / 4.20 ( 680) hydrogen bonds : angle 4.45949 / 3.09 ( 1899) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 189 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.4564 (ttt180) cc_final: 0.3860 (mtp85) REVERT: A 211 MET cc_start: 0.8269 (ppp) cc_final: 0.8037 (ppp) REVERT: A 414 MET cc_start: 0.7921 (ppp) cc_final: 0.7666 (ppp) REVERT: A 485 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8308 (tt) REVERT: A 575 ASN cc_start: 0.8608 (t0) cc_final: 0.8387 (t0) REVERT: A 636 ASN cc_start: 0.8079 (t0) cc_final: 0.7865 (t0) REVERT: A 733 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8432 (ttpp) REVERT: B 485 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8382 (tt) REVERT: B 561 ASP cc_start: 0.7378 (m-30) cc_final: 0.6965 (t0) REVERT: B 699 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7473 (pt) outliers start: 76 outliers final: 48 residues processed: 253 average time/residue: 0.1139 time to fit residues: 43.3376 Evaluate side-chains 229 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 177 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain B residue 24 CYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 772 HIS Chi-restraints excluded: chain B residue 839 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 158 optimal weight: 50.0000 chunk 72 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN B 462 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.220474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.171647 restraints weight = 18042.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.177121 restraints weight = 28070.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.176751 restraints weight = 18705.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.177453 restraints weight = 12217.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.181850 restraints weight = 10166.258| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14452 Z= 0.136 Angle : 0.589 8.330 20010 Z= 0.304 Chirality : 0.041 0.147 2282 Planarity : 0.004 0.035 2238 Dihedral : 19.973 59.939 2694 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.68 % Allowed : 26.26 % Favored : 70.06 % 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: 0.61 (0.22), residues: 1520 helix: 1.19 (0.19), residues: 772 sheet: 0.55 (0.37), residues: 190 loop : -0.70 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 607 TYR 0.026 0.002 TYR B 168 PHE 0.018 0.002 PHE B 732 TRP 0.007 0.001 TRP A 808 HIS 0.005 0.001 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (14452) covalent geometry : angle 0.58884 / 0.30 (20010) hydrogen bonds : bond 0.04714 / 3.27 ( 680) hydrogen bonds : angle 4.08535 / 2.83 ( 1899) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.4378 (ttt180) cc_final: 0.3644 (mtp85) REVERT: A 733 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8387 (ttpp) REVERT: B 561 ASP cc_start: 0.7330 (m-30) cc_final: 0.6966 (t0) REVERT: B 841 MET cc_start: 0.5955 (OUTLIER) cc_final: 0.5478 (mpp) outliers start: 48 outliers final: 33 residues processed: 225 average time/residue: 0.1101 time to fit residues: 37.4364 Evaluate side-chains 212 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 772 HIS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 837 GLU Chi-restraints excluded: chain B residue 839 TRP Chi-restraints excluded: chain B residue 841 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 42 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 156 optimal weight: 50.0000 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 158 optimal weight: 50.0000 chunk 161 optimal weight: 40.0000 chunk 137 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 HIS ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.219213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.170634 restraints weight = 17888.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176047 restraints weight = 29387.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.175863 restraints weight = 18752.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.176185 restraints weight = 13338.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.179214 restraints weight = 10826.375| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14452 Z= 0.161 Angle : 0.604 8.979 20010 Z= 0.308 Chirality : 0.043 0.444 2282 Planarity : 0.004 0.042 2238 Dihedral : 19.958 59.980 2694 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.05 % Allowed : 25.04 % Favored : 69.91 % 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: 0.63 (0.22), residues: 1520 helix: 1.28 (0.19), residues: 768 sheet: 0.37 (0.37), residues: 188 loop : -0.69 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 532 TYR 0.015 0.002 TYR A 347 PHE 0.017 0.002 PHE A 309 TRP 0.007 0.001 TRP B 839 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (14452) covalent geometry : angle 0.60403 / 0.31 (20010) hydrogen bonds : bond 0.04625 / 3.24 ( 680) hydrogen bonds : angle 4.09509 / 2.82 ( 1899) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 184 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.4318 (ttt180) cc_final: 0.3658 (mtp85) REVERT: A 485 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8554 (tt) REVERT: A 506 THR cc_start: 0.7185 (OUTLIER) cc_final: 0.6940 (p) REVERT: A 683 TYR cc_start: 0.7516 (t80) cc_final: 0.6849 (t80) REVERT: A 841 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.5321 (mpp) REVERT: B 485 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8472 (tt) REVERT: B 491 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8332 (mp) REVERT: B 561 ASP cc_start: 0.7358 (m-30) cc_final: 0.6921 (t0) REVERT: B 733 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8635 (ttpp) outliers start: 66 outliers final: 46 residues processed: 232 average time/residue: 0.1158 time to fit residues: 40.1300 Evaluate side-chains 230 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 772 HIS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 837 GLU Chi-restraints excluded: chain B residue 839 TRP Chi-restraints excluded: chain B residue 841 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 37 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.221042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172466 restraints weight = 18014.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.174185 restraints weight = 29123.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175275 restraints weight = 25131.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.176869 restraints weight = 14804.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.178866 restraints weight = 11900.951| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14452 Z= 0.138 Angle : 0.587 8.188 20010 Z= 0.299 Chirality : 0.040 0.207 2282 Planarity : 0.004 0.063 2238 Dihedral : 19.967 59.953 2694 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.98 % Allowed : 26.72 % Favored : 69.30 % 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: 0.71 (0.22), residues: 1520 helix: 1.33 (0.19), residues: 770 sheet: 0.40 (0.38), residues: 188 loop : -0.65 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 532 TYR 0.014 0.002 TYR B 347 PHE 0.018 0.002 PHE B 309 TRP 0.007 0.001 TRP B 808 HIS 0.016 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14452) covalent geometry : angle 0.58678 / 0.30 (20010) hydrogen bonds : bond 0.04442 / 3.11 ( 680) hydrogen bonds : angle 4.05295 / 2.80 ( 1899) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.4274 (tpt170) cc_final: 0.3591 (mtp85) REVERT: A 506 THR cc_start: 0.7225 (OUTLIER) cc_final: 0.6982 (p) REVERT: A 683 TYR cc_start: 0.7420 (t80) cc_final: 0.6465 (t80) REVERT: A 684 MET cc_start: 0.8531 (mmm) cc_final: 0.8269 (mmm) REVERT: A 841 MET cc_start: 0.5805 (OUTLIER) cc_final: 0.5237 (mpp) REVERT: B 112 ARG cc_start: 0.4765 (mmt180) cc_final: 0.3999 (mtp85) REVERT: B 561 ASP cc_start: 0.7379 (m-30) cc_final: 0.6957 (t0) REVERT: B 733 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8612 (ttpp) REVERT: B 841 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.5443 (mpp) outliers start: 52 outliers final: 43 residues processed: 222 average time/residue: 0.1050 time to fit residues: 35.4580 Evaluate side-chains 222 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 772 HIS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 837 GLU Chi-restraints excluded: chain B residue 839 TRP Chi-restraints excluded: chain B residue 841 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 148 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 102 optimal weight: 0.0670 chunk 18 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.222715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.174582 restraints weight = 18015.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.180476 restraints weight = 28994.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.179800 restraints weight = 19686.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.180639 restraints weight = 13193.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.183135 restraints weight = 10477.804| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14452 Z= 0.121 Angle : 0.576 7.848 20010 Z= 0.293 Chirality : 0.040 0.218 2282 Planarity : 0.004 0.057 2238 Dihedral : 19.950 59.769 2694 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.52 % Allowed : 27.11 % Favored : 69.37 % 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: 0.85 (0.22), residues: 1520 helix: 1.44 (0.19), residues: 764 sheet: 0.47 (0.38), residues: 188 loop : -0.54 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 708 TYR 0.013 0.001 TYR A 347 PHE 0.018 0.002 PHE B 309 TRP 0.008 0.001 TRP A 808 HIS 0.005 0.001 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (14452) covalent geometry : angle 0.57616 / 0.29 (20010) hydrogen bonds : bond 0.04263 / 2.99 ( 680) hydrogen bonds : angle 4.01569 / 2.76 ( 1899) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.4238 (tpt170) cc_final: 0.3553 (mtp85) REVERT: A 485 LEU cc_start: 0.8860 (mt) cc_final: 0.8561 (tt) REVERT: A 506 THR cc_start: 0.7259 (OUTLIER) cc_final: 0.7023 (p) REVERT: A 683 TYR cc_start: 0.7400 (t80) cc_final: 0.6384 (t80) REVERT: A 733 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8374 (ttpp) REVERT: A 841 MET cc_start: 0.5691 (OUTLIER) cc_final: 0.5167 (mpp) REVERT: A 842 MET cc_start: 0.5276 (ppp) cc_final: 0.4485 (ppp) REVERT: B 112 ARG cc_start: 0.4827 (mmt180) cc_final: 0.3938 (mtp85) REVERT: B 561 ASP cc_start: 0.7355 (m-30) cc_final: 0.6903 (t0) REVERT: B 733 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8584 (ttpp) REVERT: B 841 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5383 (mpp) outliers start: 46 outliers final: 37 residues processed: 216 average time/residue: 0.1119 time to fit residues: 36.6678 Evaluate side-chains 216 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 772 HIS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 837 GLU Chi-restraints excluded: chain B residue 839 TRP Chi-restraints excluded: chain B residue 841 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 50 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 154 optimal weight: 50.0000 chunk 120 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 160 optimal weight: 50.0000 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.221642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.173788 restraints weight = 18097.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.178209 restraints weight = 32868.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.179240 restraints weight = 17531.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.181547 restraints weight = 11234.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.182451 restraints weight = 9112.620| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14452 Z= 0.136 Angle : 0.587 8.152 20010 Z= 0.298 Chirality : 0.040 0.174 2282 Planarity : 0.004 0.055 2238 Dihedral : 19.963 59.962 2694 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.29 % Allowed : 27.41 % Favored : 69.30 % 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: 0.86 (0.22), residues: 1520 helix: 1.44 (0.19), residues: 768 sheet: 0.45 (0.38), residues: 188 loop : -0.54 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 526 TYR 0.031 0.002 TYR B 168 PHE 0.021 0.002 PHE B 309 TRP 0.007 0.001 TRP A 808 HIS 0.006 0.001 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (14452) covalent geometry : angle 0.58665 / 0.30 (20010) hydrogen bonds : bond 0.04263 / 3.00 ( 680) hydrogen bonds : angle 3.96972 / 2.73 ( 1899) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.4293 (tpt170) cc_final: 0.3581 (mtp85) REVERT: A 506 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6914 (p) REVERT: A 683 TYR cc_start: 0.7428 (t80) cc_final: 0.6596 (t80) REVERT: A 842 MET cc_start: 0.5336 (ppp) cc_final: 0.4468 (ppp) REVERT: B 543 GLN cc_start: 0.7775 (tp40) cc_final: 0.7512 (tp-100) REVERT: B 561 ASP cc_start: 0.7372 (m-30) cc_final: 0.6984 (t0) REVERT: B 683 TYR cc_start: 0.7236 (t80) cc_final: 0.6514 (t80) REVERT: B 733 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8604 (ttpp) REVERT: B 841 MET cc_start: 0.5819 (OUTLIER) cc_final: 0.5412 (mpp) outliers start: 43 outliers final: 35 residues processed: 213 average time/residue: 0.0995 time to fit residues: 32.2277 Evaluate side-chains 215 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 772 HIS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 839 TRP Chi-restraints excluded: chain B residue 841 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 31 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 111 optimal weight: 0.0470 chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 0.1980 chunk 74 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.223917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.175281 restraints weight = 17993.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.178234 restraints weight = 26297.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.178100 restraints weight = 24922.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.179654 restraints weight = 13643.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.180751 restraints weight = 11397.665| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14452 Z= 0.116 Angle : 0.581 10.035 20010 Z= 0.293 Chirality : 0.040 0.186 2282 Planarity : 0.004 0.052 2238 Dihedral : 19.960 59.797 2694 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.76 % Allowed : 27.79 % Favored : 69.45 % 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: 0.94 (0.22), residues: 1520 helix: 1.50 (0.19), residues: 764 sheet: 0.52 (0.38), residues: 188 loop : -0.48 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 526 TYR 0.014 0.001 TYR B 342 PHE 0.018 0.001 PHE B 309 TRP 0.011 0.001 TRP A 808 HIS 0.004 0.000 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (14452) covalent geometry : angle 0.58093 / 0.29 (20010) hydrogen bonds : bond 0.04094 / 2.88 ( 680) hydrogen bonds : angle 3.94251 / 2.71 ( 1899) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.4297 (tpt170) cc_final: 0.3366 (mtp85) REVERT: A 378 MET cc_start: 0.8621 (mmp) cc_final: 0.8391 (mmp) REVERT: A 506 THR cc_start: 0.7187 (OUTLIER) cc_final: 0.6964 (p) REVERT: A 683 TYR cc_start: 0.7366 (t80) cc_final: 0.6285 (t80) REVERT: A 684 MET cc_start: 0.8402 (mmm) cc_final: 0.8041 (mmm) REVERT: B 112 ARG cc_start: 0.4155 (mmt180) cc_final: 0.3627 (mmm160) REVERT: B 543 GLN cc_start: 0.7710 (tp40) cc_final: 0.7491 (tp-100) REVERT: B 561 ASP cc_start: 0.7429 (m-30) cc_final: 0.6945 (t0) REVERT: B 683 TYR cc_start: 0.7150 (t80) cc_final: 0.6536 (t80) REVERT: B 841 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.5484 (mpp) outliers start: 36 outliers final: 31 residues processed: 213 average time/residue: 0.0961 time to fit residues: 31.2917 Evaluate side-chains 206 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 772 HIS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 839 TRP Chi-restraints excluded: chain B residue 841 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 25 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 159 optimal weight: 50.0000 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.223229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.175227 restraints weight = 18144.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.178010 restraints weight = 29878.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.179047 restraints weight = 22430.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.180490 restraints weight = 13917.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.181585 restraints weight = 11579.557| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14452 Z= 0.125 Angle : 0.586 8.285 20010 Z= 0.295 Chirality : 0.040 0.175 2282 Planarity : 0.004 0.047 2238 Dihedral : 19.955 59.651 2694 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.76 % Allowed : 27.57 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.92 (0.22), residues: 1520 helix: 1.47 (0.19), residues: 768 sheet: 0.48 (0.38), residues: 188 loop : -0.49 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 526 TYR 0.016 0.001 TYR A 342 PHE 0.022 0.001 PHE B 309 TRP 0.007 0.001 TRP A 808 HIS 0.004 0.001 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (14452) covalent geometry : angle 0.58584 / 0.29 (20010) hydrogen bonds : bond 0.04106 / 2.89 ( 680) hydrogen bonds : angle 3.92090 / 2.69 ( 1899) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2007.84 seconds wall clock time: 35 minutes 32.32 seconds (2132.32 seconds total)