Starting phenix.real_space_refine on Fri Aug 7 18:04:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2w_50165/08_2026/9f2w_50165_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2w_50165/08_2026/9f2w_50165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f2w_50165/08_2026/9f2w_50165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2w_50165/08_2026/9f2w_50165.map" model { file = "/net/cci-nas-00/data/ceres_data/9f2w_50165/08_2026/9f2w_50165_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2w_50165/08_2026/9f2w_50165_trim.cif" } resolution = 4.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 62 5.49 5 S 66 5.16 5 C 7338 2.51 5 N 2092 2.21 5 O 2402 1.98 5 H 11450 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 23412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 10774 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 21, 'TRANS': 653} Chain breaks: 4 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "X" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 459 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna3p_pur': 10, 'rna3p_pyr': 4} Link IDs: {'rna3p': 13} Chain: "Y" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 441 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 10} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9106 SG CYS A 907 78.024 41.491 84.218 1.00169.40 S ATOM 9152 SG CYS A 910 81.747 41.327 84.273 1.00177.05 S ATOM 9797 SG CYS A 962 79.858 42.092 87.525 1.00171.25 S ATOM 9829 SG CYS A 964 80.088 44.703 84.968 1.00176.38 S Restraints were copied for chains: B, C, D Time building chain proxies: 15.09, per 1000 atoms: 0.64 Number of scatterers: 23412 At special positions: 0 Unit cell: (102.424, 94.99, 118.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 66 16.00 P 62 15.00 O 2402 8.00 N 2092 7.00 C 7338 6.00 H 11450 1.00 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: 1.90 Conformation dependent library (CDL) restraints added in 716.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " pdb=" ZN B1101 " pdb="ZN ZN B1101 " - pdb=" SG CYS B 962 " pdb="ZN ZN B1101 " - pdb=" SG CYS B 964 " pdb="ZN ZN B1101 " - pdb=" SG CYS B 910 " pdb="ZN ZN B1101 " - pdb=" SG CYS B 907 " Number of angles added : 12 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 10 sheets defined 57.0% alpha, 11.0% beta 28 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 335 through 354 Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.933A pdb=" N ALA A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 Processing helix chain 'A' and resid 400 through 409 removed outlier: 3.774A pdb=" N VAL A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 406 " --> pdb=" O PRO A 402 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 525 through 533 Processing helix chain 'A' and resid 548 through 567 Processing helix chain 'A' and resid 576 through 594 Processing helix chain 'A' and resid 599 through 616 Processing helix chain 'A' and resid 619 through 645 removed outlier: 3.791A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 693 removed outlier: 4.529A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 716 Processing helix chain 'A' and resid 727 through 741 Processing helix chain 'A' and resid 741 through 748 removed outlier: 3.893A pdb=" N ALA A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.776A pdb=" N GLU A 793 " --> pdb=" O THR A 789 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 794 " --> pdb=" O THR A 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 789 through 794' Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 840 through 863 removed outlier: 3.696A pdb=" N ARG A 860 " --> pdb=" O LYS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 895 removed outlier: 3.742A pdb=" N GLN A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.518A pdb=" N LYS A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 987 Processing helix chain 'A' and resid 1014 through 1019 Processing helix chain 'B' and resid 310 through 318 Processing helix chain 'B' and resid 319 through 322 Processing helix chain 'B' and resid 335 through 354 Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.933A pdb=" N ALA B 370 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'B' and resid 400 through 409 removed outlier: 3.774A pdb=" N VAL B 404 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP B 409 " --> pdb=" O VAL B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 428 Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 446 through 449 Processing helix chain 'B' and resid 453 through 476 Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 525 through 533 Processing helix chain 'B' and resid 548 through 567 Processing helix chain 'B' and resid 576 through 594 Processing helix chain 'B' and resid 599 through 616 Processing helix chain 'B' and resid 619 through 645 removed outlier: 3.791A pdb=" N ALA B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 693 removed outlier: 4.530A pdb=" N LYS B 685 " --> pdb=" O PHE B 681 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N MET B 686 " --> pdb=" O ASP B 682 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 693 " --> pdb=" O LYS B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 716 Processing helix chain 'B' and resid 727 through 741 Processing helix chain 'B' and resid 741 through 748 removed outlier: 3.893A pdb=" N ALA B 745 " --> pdb=" O ASN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 781 Processing helix chain 'B' and resid 789 through 794 removed outlier: 3.776A pdb=" N GLU B 793 " --> pdb=" O THR B 789 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 794 " --> pdb=" O THR B 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 789 through 794' Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 840 through 863 removed outlier: 3.697A pdb=" N ARG B 860 " --> pdb=" O LYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 895 removed outlier: 3.742A pdb=" N GLN B 895 " --> pdb=" O SER B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 937 removed outlier: 3.518A pdb=" N LYS B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 987 Processing helix chain 'B' and resid 1014 through 1019 Processing sheet with id=1, first strand: chain 'A' and resid 327 through 329 removed outlier: 5.943A pdb=" N ILE A 328 " --> pdb=" O THR A 489 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 361 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASP A 444 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 363 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 360 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N SER A 413 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL A 362 " --> pdb=" O SER A 413 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 537 through 541 removed outlier: 5.584A pdb=" N CYS A 537 " --> pdb=" O TYR A 830 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU A 832 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 539 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASN A 802 " --> pdb=" O GLU A 827 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE A 722 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR A 807 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHE A 724 " --> pdb=" O TYR A 807 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY A 721 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA A 788 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A 723 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS A 752 " --> pdb=" O ILE A 787 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 913 through 915 Processing sheet with id=4, first strand: chain 'A' and resid 920 through 923 Processing sheet with id=5, first strand: chain 'A' and resid 940 through 942 removed outlier: 3.892A pdb=" N GLY A 969 " --> pdb=" O ILE A 960 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 327 through 329 removed outlier: 5.942A pdb=" N ILE B 328 " --> pdb=" O THR B 489 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE B 361 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASP B 444 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU B 363 " --> pdb=" O ASP B 444 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 360 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER B 413 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL B 362 " --> pdb=" O SER B 413 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 537 through 541 removed outlier: 5.584A pdb=" N CYS B 537 " --> pdb=" O TYR B 830 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU B 832 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS B 539 " --> pdb=" O LEU B 832 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASN B 802 " --> pdb=" O GLU B 827 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE B 722 " --> pdb=" O ILE B 805 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR B 807 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHE B 724 " --> pdb=" O TYR B 807 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY B 721 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA B 788 " --> pdb=" O GLY B 721 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE B 723 " --> pdb=" O ALA B 788 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS B 752 " --> pdb=" O ILE B 787 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 913 through 915 Processing sheet with id=9, first strand: chain 'B' and resid 920 through 923 Processing sheet with id=10, first strand: chain 'B' and resid 940 through 942 removed outlier: 3.891A pdb=" N GLY B 969 " --> pdb=" O ILE B 960 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11430 1.03 - 1.23: 36 1.23 - 1.42: 5106 1.42 - 1.62: 7044 1.62 - 1.81: 104 Bond restraints: 23720 Sorted by residual: bond pdb=" CA HIS B 974 " pdb=" CB HIS B 974 " ideal model delta sigma weight residual 1.532 1.495 0.037 1.58e-02 4.01e+03 5.53e+00 bond pdb=" CA HIS A 974 " pdb=" CB HIS A 974 " ideal model delta sigma weight residual 1.532 1.495 0.037 1.58e-02 4.01e+03 5.40e+00 bond pdb=" CB HIS A 974 " pdb=" CG HIS A 974 " ideal model delta sigma weight residual 1.497 1.468 0.029 1.40e-02 5.10e+03 4.19e+00 bond pdb=" CB HIS B 974 " pdb=" CG HIS B 974 " ideal model delta sigma weight residual 1.497 1.469 0.028 1.40e-02 5.10e+03 4.02e+00 bond pdb=" N HIS A 974 " pdb=" CA HIS A 974 " ideal model delta sigma weight residual 1.458 1.439 0.019 1.19e-02 7.06e+03 2.56e+00 ... (remaining 23715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 41234 1.32 - 2.65: 1539 2.65 - 3.97: 175 3.97 - 5.29: 16 5.29 - 6.62: 8 Bond angle restraints: 42972 Sorted by residual: angle pdb=" O5' C Y 11 " pdb=" C5' C Y 11 " pdb=" C4' C Y 11 " ideal model delta sigma weight residual 109.40 112.14 -2.74 8.00e-01 1.56e+00 1.17e+01 angle pdb=" O5' C D 11 " pdb=" C5' C D 11 " pdb=" C4' C D 11 " ideal model delta sigma weight residual 109.40 112.12 -2.72 8.00e-01 1.56e+00 1.16e+01 angle pdb=" O5' U D 4 " pdb=" C5' U D 4 " pdb=" C4' U D 4 " ideal model delta sigma weight residual 109.40 112.12 -2.72 8.00e-01 1.56e+00 1.16e+01 angle pdb=" O5' U Y 4 " pdb=" C5' U Y 4 " pdb=" C4' U Y 4 " ideal model delta sigma weight residual 109.40 112.06 -2.66 8.00e-01 1.56e+00 1.11e+01 angle pdb=" O5' A X 11 " pdb=" C5' A X 11 " pdb=" C4' A X 11 " ideal model delta sigma weight residual 109.40 112.05 -2.65 8.00e-01 1.56e+00 1.10e+01 ... (remaining 42967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 10102 17.88 - 35.75: 712 35.75 - 53.63: 230 53.63 - 71.50: 98 71.50 - 89.38: 26 Dihedral angle restraints: 11168 sinusoidal: 6662 harmonic: 4506 Sorted by residual: dihedral pdb=" CA LEU A 397 " pdb=" C LEU A 397 " pdb=" N LYS A 398 " pdb=" CA LYS A 398 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA LEU B 397 " pdb=" C LEU B 397 " pdb=" N LYS B 398 " pdb=" CA LYS B 398 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CB GLU B 356 " pdb=" CG GLU B 356 " pdb=" CD GLU B 356 " pdb=" OE1 GLU B 356 " ideal model delta sinusoidal sigma weight residual 0.00 89.38 -89.38 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 11165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1655 0.055 - 0.110: 247 0.110 - 0.165: 46 0.165 - 0.220: 0 0.220 - 0.276: 6 Chirality restraints: 1954 Sorted by residual: chirality pdb=" C3' ATP B1102 " pdb=" C2' ATP B1102 " pdb=" C4' ATP B1102 " pdb=" O3' ATP B1102 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' ATP A1102 " pdb=" C2' ATP A1102 " pdb=" C4' ATP A1102 " pdb=" O3' ATP A1102 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2' ATP B1102 " pdb=" C1' ATP B1102 " pdb=" C3' ATP B1102 " pdb=" O2' ATP B1102 " both_signs ideal model delta sigma weight residual False -2.68 -2.95 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1951 not shown) Planarity restraints: 3266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 569 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 570 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 570 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 570 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 569 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO B 570 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 974 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C HIS B 974 " 0.026 2.00e-02 2.50e+03 pdb=" O HIS B 974 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS B 975 " -0.009 2.00e-02 2.50e+03 ... (remaining 3263 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.88: 111 1.88 - 2.56: 22059 2.56 - 3.24: 72880 3.24 - 3.92: 88841 3.92 - 4.60: 138947 Nonbonded interactions: 322838 Sorted by model distance: nonbonded pdb="HH22 ARG A 890 " pdb=" O GLY B 976 " model vdw 1.196 2.450 nonbonded pdb=" HE2 HIS B 927 " pdb=" O2' G C 4 " model vdw 1.517 2.450 nonbonded pdb=" HE2 HIS A 927 " pdb=" O2' G X 4 " model vdw 1.517 2.450 nonbonded pdb=" HZ1 LYS A1001 " pdb=" OP1 U Y 4 " model vdw 1.541 2.450 nonbonded pdb=" HZ1 LYS B1001 " pdb=" OP1 U D 4 " model vdw 1.541 2.450 ... (remaining 322833 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 'X' selection = chain 'C' } ncs_group { reference = chain 'Y' selection = chain 'D' } 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: 1.810 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: 0.140 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 42.690 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 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 0.042 12278 Z= 0.199 Angle : 0.608 6.618 16816 Z= 0.388 Chirality : 0.044 0.276 1954 Planarity : 0.003 0.042 1924 Dihedral : 15.378 89.380 5092 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: -0.24 (0.23), residues: 1330 helix: 1.47 (0.20), residues: 670 sheet: -1.13 (0.42), residues: 164 loop : -2.16 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 705 TYR 0.007 0.001 TYR A 342 PHE 0.014 0.001 PHE A 680 TRP 0.005 0.001 TRP B 385 HIS 0.007 0.001 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.20 (12270) covalent geometry : angle 0.60248 / 0.39 (16804) hydrogen bonds : bond 0.13111 / 8.41 ( 656) hydrogen bonds : angle 5.56894 / 3.86 ( 1818) metal coordination : bond 0.00595 / 0.28 ( 8) metal coordination : angle 3.21944 / 1.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6725 (mm-30) REVERT: A 586 MET cc_start: 0.8496 (tpp) cc_final: 0.8119 (tpp) REVERT: A 599 ARG cc_start: 0.6701 (ptp-170) cc_final: 0.5723 (mtm110) REVERT: A 610 GLU cc_start: 0.8702 (pp20) cc_final: 0.8477 (pp20) REVERT: A 918 GLU cc_start: 0.7680 (pm20) cc_final: 0.7073 (pm20) REVERT: B 759 HIS cc_start: 0.5698 (p-80) cc_final: 0.5482 (t70) REVERT: B 999 GLN cc_start: 0.8213 (tt0) cc_final: 0.7458 (mm-40) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2333 time to fit residues: 79.7155 Evaluate side-chains 161 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN B 416 GLN B 563 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.093214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.070322 restraints weight = 120689.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.073986 restraints weight = 52449.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076270 restraints weight = 32023.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.077680 restraints weight = 23669.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.078607 restraints weight = 19601.803| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12278 Z= 0.324 Angle : 0.727 5.880 16816 Z= 0.402 Chirality : 0.045 0.190 1954 Planarity : 0.005 0.057 1924 Dihedral : 14.423 84.275 2374 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.17 % Allowed : 3.75 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.22), residues: 1330 helix: 0.86 (0.19), residues: 700 sheet: -1.75 (0.37), residues: 174 loop : -2.59 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 468 TYR 0.014 0.002 TYR B 408 PHE 0.019 0.002 PHE A 680 TRP 0.008 0.001 TRP A 582 HIS 0.010 0.002 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.32 (12270) covalent geometry : angle 0.72378 / 0.40 (16804) hydrogen bonds : bond 0.05526 / 3.62 ( 656) hydrogen bonds : angle 5.21112 / 3.69 ( 1818) metal coordination : bond 0.01236 / 0.61 ( 8) metal coordination : angle 2.56457 / 1.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7448 (mt-10) REVERT: A 926 MET cc_start: 0.8277 (ptp) cc_final: 0.7815 (ptp) REVERT: B 465 GLN cc_start: 0.8579 (tp40) cc_final: 0.7910 (tp-100) REVERT: B 520 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8389 (mmmm) REVERT: B 807 TYR cc_start: 0.7832 (t80) cc_final: 0.7489 (t80) outliers start: 2 outliers final: 0 residues processed: 190 average time/residue: 0.2060 time to fit residues: 59.0979 Evaluate side-chains 141 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 95 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 23 optimal weight: 0.0170 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 overall best weight: 2.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN B 563 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.095352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.071949 restraints weight = 117829.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.075723 restraints weight = 50007.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.078139 restraints weight = 30185.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.079636 restraints weight = 22082.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.080365 restraints weight = 18153.554| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12278 Z= 0.148 Angle : 0.574 8.380 16816 Z= 0.308 Chirality : 0.039 0.185 1954 Planarity : 0.005 0.127 1924 Dihedral : 14.452 84.246 2374 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1330 helix: 1.16 (0.19), residues: 700 sheet: -1.29 (0.40), residues: 162 loop : -2.52 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 822 TYR 0.011 0.001 TYR B 408 PHE 0.014 0.001 PHE A 680 TRP 0.005 0.001 TRP A 582 HIS 0.004 0.001 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (12270) covalent geometry : angle 0.55901 / 0.31 (16804) hydrogen bonds : bond 0.04981 / 3.28 ( 656) hydrogen bonds : angle 4.81051 / 3.41 ( 1818) metal coordination : bond 0.00593 / 0.29 ( 8) metal coordination : angle 4.98199 / 2.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7359 (mt-10) REVERT: A 882 LEU cc_start: 0.9333 (tp) cc_final: 0.8817 (tp) REVERT: A 886 MET cc_start: 0.8789 (mmt) cc_final: 0.8537 (mmm) REVERT: B 520 LYS cc_start: 0.8585 (mmmt) cc_final: 0.8324 (mmmm) REVERT: B 807 TYR cc_start: 0.7912 (t80) cc_final: 0.7583 (t80) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2287 time to fit residues: 63.2121 Evaluate side-chains 142 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 37 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 GLN A 484 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN B 470 ASN B 525 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.092457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.069734 restraints weight = 120996.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.073320 restraints weight = 52081.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.075574 restraints weight = 32194.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.076961 restraints weight = 23972.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.077740 restraints weight = 19941.160| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12278 Z= 0.243 Angle : 0.625 5.933 16816 Z= 0.342 Chirality : 0.040 0.157 1954 Planarity : 0.004 0.052 1924 Dihedral : 14.418 83.354 2374 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.78 % 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: -0.82 (0.22), residues: 1330 helix: 1.10 (0.19), residues: 700 sheet: -1.87 (0.37), residues: 174 loop : -2.65 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 942 TYR 0.016 0.002 TYR B 408 PHE 0.016 0.002 PHE A 680 TRP 0.006 0.001 TRP A 582 HIS 0.009 0.002 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.24 (12270) covalent geometry : angle 0.62304 / 0.34 (16804) hydrogen bonds : bond 0.04939 / 3.23 ( 656) hydrogen bonds : angle 4.82250 / 3.43 ( 1818) metal coordination : bond 0.00914 / 0.44 ( 8) metal coordination : angle 1.92851 / 0.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7234 (mt-10) REVERT: B 336 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8606 (mttt) REVERT: B 371 GLU cc_start: 0.8744 (tt0) cc_final: 0.8229 (tp30) REVERT: B 520 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8278 (mmmm) REVERT: B 676 LEU cc_start: 0.8558 (mt) cc_final: 0.8343 (mt) REVERT: B 807 TYR cc_start: 0.7784 (t80) cc_final: 0.7488 (t80) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.2090 time to fit residues: 58.6605 Evaluate side-chains 142 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 2 optimal weight: 0.4980 chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.092268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.069427 restraints weight = 120123.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.073053 restraints weight = 50916.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.075329 restraints weight = 31148.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.076729 restraints weight = 23108.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.077559 restraints weight = 19189.627| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12278 Z= 0.198 Angle : 0.576 6.749 16816 Z= 0.316 Chirality : 0.040 0.165 1954 Planarity : 0.004 0.051 1924 Dihedral : 14.566 86.610 2374 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -0.74 (0.22), residues: 1330 helix: 1.15 (0.19), residues: 700 sheet: -1.75 (0.38), residues: 162 loop : -2.63 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 822 TYR 0.029 0.002 TYR A 624 PHE 0.015 0.002 PHE A 680 TRP 0.005 0.001 TRP B 968 HIS 0.006 0.001 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 (12270) covalent geometry : angle 0.57407 / 0.32 (16804) hydrogen bonds : bond 0.04718 / 3.05 ( 656) hydrogen bonds : angle 4.72104 / 3.35 ( 1818) metal coordination : bond 0.00876 / 0.43 ( 8) metal coordination : angle 1.93224 / 1.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7078 (mt-10) REVERT: A 882 LEU cc_start: 0.9320 (tp) cc_final: 0.8780 (tp) REVERT: A 886 MET cc_start: 0.8754 (mmt) cc_final: 0.8507 (mmm) REVERT: B 336 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8606 (mtpt) REVERT: B 371 GLU cc_start: 0.8737 (tt0) cc_final: 0.8218 (tp30) REVERT: B 520 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8237 (mmmm) REVERT: B 676 LEU cc_start: 0.8550 (mt) cc_final: 0.8281 (mt) REVERT: B 807 TYR cc_start: 0.7787 (t80) cc_final: 0.7500 (t80) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2060 time to fit residues: 57.6060 Evaluate side-chains 140 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 134 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.092714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.070252 restraints weight = 117286.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073915 restraints weight = 49340.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.076193 restraints weight = 29758.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.077627 restraints weight = 21831.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.078351 restraints weight = 17934.160| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12278 Z= 0.139 Angle : 0.534 4.841 16816 Z= 0.291 Chirality : 0.039 0.173 1954 Planarity : 0.003 0.039 1924 Dihedral : 14.543 87.952 2374 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -0.53 (0.22), residues: 1330 helix: 1.32 (0.19), residues: 700 sheet: -1.66 (0.38), residues: 162 loop : -2.53 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 890 TYR 0.014 0.001 TYR B 408 PHE 0.013 0.001 PHE A 680 TRP 0.005 0.001 TRP B 968 HIS 0.005 0.001 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (12270) covalent geometry : angle 0.53129 / 0.29 (16804) hydrogen bonds : bond 0.04447 / 2.87 ( 656) hydrogen bonds : angle 4.52402 / 3.21 ( 1818) metal coordination : bond 0.00610 / 0.29 ( 8) metal coordination : angle 1.92932 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7006 (mt-10) REVERT: A 635 LYS cc_start: 0.8765 (tppt) cc_final: 0.8414 (tmtt) REVERT: A 882 LEU cc_start: 0.9345 (tp) cc_final: 0.8719 (tp) REVERT: A 886 MET cc_start: 0.8695 (mmt) cc_final: 0.8475 (mmm) REVERT: B 336 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8537 (mtpt) REVERT: B 371 GLU cc_start: 0.8743 (tt0) cc_final: 0.8209 (tp30) REVERT: B 520 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8246 (mmmm) REVERT: B 676 LEU cc_start: 0.8541 (mt) cc_final: 0.8266 (mt) REVERT: B 807 TYR cc_start: 0.7760 (t80) cc_final: 0.7496 (t80) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2056 time to fit residues: 57.9107 Evaluate side-chains 147 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 131 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN B 509 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.091707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069541 restraints weight = 117968.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.073077 restraints weight = 50449.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.075261 restraints weight = 30729.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.076691 restraints weight = 22755.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.077550 restraints weight = 18672.980| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12278 Z= 0.196 Angle : 0.564 5.499 16816 Z= 0.311 Chirality : 0.039 0.154 1954 Planarity : 0.004 0.037 1924 Dihedral : 14.543 85.814 2374 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -0.66 (0.22), residues: 1330 helix: 1.25 (0.19), residues: 700 sheet: -1.81 (0.38), residues: 162 loop : -2.59 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 468 TYR 0.029 0.002 TYR A 565 PHE 0.025 0.002 PHE A 675 TRP 0.005 0.001 TRP A 582 HIS 0.006 0.001 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.20 (12270) covalent geometry : angle 0.56159 / 0.31 (16804) hydrogen bonds : bond 0.04600 / 2.98 ( 656) hydrogen bonds : angle 4.60721 / 3.27 ( 1818) metal coordination : bond 0.00828 / 0.40 ( 8) metal coordination : angle 1.93329 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7006 (mt-10) REVERT: A 635 LYS cc_start: 0.8718 (tppt) cc_final: 0.8329 (tmtt) REVERT: A 882 LEU cc_start: 0.9284 (tp) cc_final: 0.8725 (tp) REVERT: B 336 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8608 (mtpt) REVERT: B 371 GLU cc_start: 0.8724 (tt0) cc_final: 0.8232 (tp30) REVERT: B 520 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8255 (mmmm) REVERT: B 676 LEU cc_start: 0.8524 (mt) cc_final: 0.8247 (mt) REVERT: B 807 TYR cc_start: 0.7661 (t80) cc_final: 0.7437 (t80) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2059 time to fit residues: 57.5235 Evaluate side-chains 145 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 102 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 525 ASN ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 HIS B 919 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.090770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068782 restraints weight = 117175.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072232 restraints weight = 50790.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.074376 restraints weight = 31295.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.075668 restraints weight = 23254.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.076562 restraints weight = 19424.810| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12278 Z= 0.220 Angle : 0.605 6.126 16816 Z= 0.330 Chirality : 0.040 0.195 1954 Planarity : 0.004 0.039 1924 Dihedral : 14.681 82.219 2374 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: 1330 helix: 1.06 (0.19), residues: 714 sheet: -2.10 (0.37), residues: 164 loop : -2.85 (0.24), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 728 TYR 0.019 0.002 TYR B 408 PHE 0.018 0.002 PHE A 680 TRP 0.006 0.001 TRP A 582 HIS 0.007 0.002 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.22 (12270) covalent geometry : angle 0.60361 / 0.33 (16804) hydrogen bonds : bond 0.04730 / 3.03 ( 656) hydrogen bonds : angle 4.66146 / 3.30 ( 1818) metal coordination : bond 0.00921 / 0.45 ( 8) metal coordination : angle 1.75932 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 LYS cc_start: 0.8706 (tppt) cc_final: 0.8324 (tmtt) REVERT: A 882 LEU cc_start: 0.9282 (tp) cc_final: 0.8660 (tp) REVERT: B 371 GLU cc_start: 0.8668 (tt0) cc_final: 0.8219 (tp30) REVERT: B 520 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8267 (mmmm) REVERT: B 807 TYR cc_start: 0.7584 (t80) cc_final: 0.7380 (t80) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2074 time to fit residues: 55.7227 Evaluate side-chains 148 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 95 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN A 944 ASN B 416 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.091248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068650 restraints weight = 119639.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072254 restraints weight = 50771.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.074485 restraints weight = 30873.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.075915 restraints weight = 22921.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.076830 restraints weight = 18884.042| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12278 Z= 0.155 Angle : 0.552 7.130 16816 Z= 0.301 Chirality : 0.040 0.186 1954 Planarity : 0.003 0.036 1924 Dihedral : 14.708 80.996 2374 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.22), residues: 1330 helix: 1.22 (0.19), residues: 714 sheet: -1.94 (0.37), residues: 160 loop : -2.79 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 890 TYR 0.015 0.002 TYR B 408 PHE 0.015 0.002 PHE A1010 TRP 0.005 0.001 TRP B 968 HIS 0.007 0.001 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (12270) covalent geometry : angle 0.55027 / 0.30 (16804) hydrogen bonds : bond 0.04390 / 2.83 ( 656) hydrogen bonds : angle 4.50812 / 3.20 ( 1818) metal coordination : bond 0.00665 / 0.32 ( 8) metal coordination : angle 1.90561 / 0.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 LYS cc_start: 0.8742 (tppt) cc_final: 0.8356 (tmtt) REVERT: A 882 LEU cc_start: 0.9285 (tp) cc_final: 0.8703 (tp) REVERT: B 371 GLU cc_start: 0.8725 (tt0) cc_final: 0.8249 (tp30) REVERT: B 411 ILE cc_start: 0.9053 (mp) cc_final: 0.8782 (mt) REVERT: B 465 GLN cc_start: 0.8656 (tp40) cc_final: 0.7899 (tp-100) REVERT: B 504 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8829 (mt-10) REVERT: B 520 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8202 (mmmm) REVERT: B 807 TYR cc_start: 0.7726 (t80) cc_final: 0.7496 (t80) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1872 time to fit residues: 52.4996 Evaluate side-chains 155 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 54 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 0.0170 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 134 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.092099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069494 restraints weight = 118552.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.073131 restraints weight = 50058.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.075425 restraints weight = 30463.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.076872 restraints weight = 22479.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.077793 restraints weight = 18515.210| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12278 Z= 0.121 Angle : 0.544 7.306 16816 Z= 0.295 Chirality : 0.040 0.173 1954 Planarity : 0.003 0.036 1924 Dihedral : 14.618 78.831 2374 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.23), residues: 1330 helix: 1.53 (0.19), residues: 702 sheet: -1.64 (0.38), residues: 156 loop : -2.51 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 890 TYR 0.014 0.001 TYR A 462 PHE 0.018 0.001 PHE A 712 TRP 0.006 0.001 TRP A 385 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (12270) covalent geometry : angle 0.54125 / 0.29 (16804) hydrogen bonds : bond 0.04252 / 2.77 ( 656) hydrogen bonds : angle 4.38983 / 3.11 ( 1818) metal coordination : bond 0.00434 / 0.20 ( 8) metal coordination : angle 1.93080 / 1.01 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue THR 546 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue TYR 608 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 750 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue LYS 894 is missing expected H atoms. Skipping. Residue MET 931 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 LYS cc_start: 0.8734 (tppt) cc_final: 0.8356 (tmtt) REVERT: A 882 LEU cc_start: 0.9324 (tp) cc_final: 0.8768 (tp) REVERT: A 886 MET cc_start: 0.8697 (mmt) cc_final: 0.8495 (mmm) REVERT: B 371 GLU cc_start: 0.8710 (tt0) cc_final: 0.8239 (tp30) REVERT: B 411 ILE cc_start: 0.9032 (mp) cc_final: 0.8758 (mt) REVERT: B 465 GLN cc_start: 0.8636 (tp40) cc_final: 0.7908 (tp-100) REVERT: B 520 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8197 (mmmm) REVERT: B 807 TYR cc_start: 0.7712 (t80) cc_final: 0.7453 (t80) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.1863 time to fit residues: 51.5650 Evaluate side-chains 145 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 8 optimal weight: 0.2980 chunk 90 optimal weight: 0.0970 chunk 50 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 126 optimal weight: 0.3980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.092498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.069853 restraints weight = 118350.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.073558 restraints weight = 49742.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.075869 restraints weight = 30089.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.077287 restraints weight = 22095.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.078244 restraints weight = 18276.308| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12278 Z= 0.116 Angle : 0.529 6.479 16816 Z= 0.286 Chirality : 0.039 0.185 1954 Planarity : 0.003 0.035 1924 Dihedral : 14.520 76.267 2374 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.83 % 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: -0.26 (0.23), residues: 1330 helix: 1.56 (0.19), residues: 700 sheet: -1.47 (0.39), residues: 156 loop : -2.45 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 890 TYR 0.013 0.001 TYR A 462 PHE 0.014 0.001 PHE A 551 TRP 0.006 0.001 TRP A 385 HIS 0.004 0.001 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (12270) covalent geometry : angle 0.52631 / 0.29 (16804) hydrogen bonds : bond 0.04105 / 2.67 ( 656) hydrogen bonds : angle 4.35277 / 3.09 ( 1818) metal coordination : bond 0.00462 / 0.21 ( 8) metal coordination : angle 2.09084 / 1.10 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3840.86 seconds wall clock time: 66 minutes 35.82 seconds (3995.82 seconds total)