Starting phenix.real_space_refine on Sat Jul 4 20:07:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2w_50165/07_2026/9f2w_50165_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2w_50165/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9f2w_50165/07_2026/9f2w_50165_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2w_50165/07_2026/9f2w_50165_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f2w_50165/07_2026/9f2w_50165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2w_50165/07_2026/9f2w_50165.map" } 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-dev-6108/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: 16.56, per 1000 atoms: 0.71 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: 2.40 Conformation dependent library (CDL) restraints added in 528.2 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: 4.06 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: 5.54 Time building geometry restraints manager: 3.21 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: 41402 1.32 - 2.65: 1377 2.65 - 3.97: 169 3.97 - 5.29: 16 5.29 - 6.62: 8 Bond angle restraints: 42972 Sorted by residual: angle pdb=" O4 U Y 4 " pdb=" C4 U Y 4 " pdb=" C5 U Y 4 " ideal model delta sigma weight residual 125.90 124.29 1.61 6.00e-01 2.78e+00 7.21e+00 angle pdb=" C3' ATP A1102 " pdb=" C4' ATP A1102 " pdb=" C5' ATP A1102 " ideal model delta sigma weight residual 115.19 110.57 4.62 1.76e+00 3.23e-01 6.88e+00 angle pdb=" C3' ATP B1102 " pdb=" C4' ATP B1102 " pdb=" C5' ATP B1102 " ideal model delta sigma weight residual 115.19 110.59 4.60 1.76e+00 3.23e-01 6.84e+00 angle pdb=" O4 U D 4 " pdb=" C4 U D 4 " pdb=" C5 U D 4 " ideal model delta sigma weight residual 125.90 124.34 1.56 6.00e-01 2.78e+00 6.76e+00 angle pdb=" C LYS A 772 " pdb=" N GLU A 773 " pdb=" CA GLU A 773 " ideal model delta sigma weight residual 120.31 116.57 3.74 1.52e+00 4.33e-01 6.05e+00 ... (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: 1714 0.055 - 0.110: 193 0.110 - 0.165: 41 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 44.000 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.590 ------------------------------------------------------------------------------- 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= 0.190 Angle : 0.574 6.618 16816 Z= 0.346 Chirality : 0.041 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 0.00331 / 0.19 (12270) covalent geometry : angle 0.56729 / 0.35 (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 : 0.659 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: 0.8118 (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: 0.8478 (pp20) REVERT: A 918 GLU cc_start: 0.7680 (pm20) cc_final: 0.7072 (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: 0.2535 time to fit residues: 86.1776 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 : 0.645 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.092893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.069769 restraints weight = 119906.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.073438 restraints weight = 50646.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.075747 restraints weight = 30662.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.077207 restraints weight = 22562.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.078012 restraints weight = 18575.672| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 12278 Z= 0.330 Angle : 0.734 6.137 16816 Z= 0.407 Chirality : 0.044 0.232 1954 Planarity : 0.005 0.057 1924 Dihedral : 14.442 83.193 2374 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.99 (0.22), residues: 1330 helix: 0.84 (0.19), residues: 700 sheet: -1.78 (0.37), residues: 174 loop : -2.58 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 843 TYR 0.014 0.002 TYR B 408 PHE 0.020 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 0.00661 / 0.33 (12270) covalent geometry : angle 0.73148 / 0.41 (16804) hydrogen bonds : bond 0.05617 / 3.66 ( 656) hydrogen bonds : angle 5.17566 / 3.67 ( 1818) metal coordination : bond 0.01332 / 0.66 ( 8) metal coordination : angle 2.54450 / 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 187 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.516 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: A 377 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7437 (mt-10) REVERT: B 520 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8358 (mmmm) REVERT: B 807 TYR cc_start: 0.7932 (t80) cc_final: 0.7594 (t80) outliers start: 2 outliers final: 0 residues processed: 187 average time/residue: 0.1888 time to fit residues: 53.2820 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 : 0.557 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 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 = 0.3839 r_free = 0.3839 target = 0.095668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.072538 restraints weight = 117864.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.076231 restraints weight = 52108.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.078592 restraints weight = 32012.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.080069 restraints weight = 23610.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.080924 restraints weight = 19456.760| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12278 Z= 0.137 Angle : 0.568 8.299 16816 Z= 0.304 Chirality : 0.040 0.190 1954 Planarity : 0.005 0.118 1924 Dihedral : 14.567 85.241 2374 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: -0.54 (0.22), residues: 1330 helix: 1.20 (0.19), residues: 700 sheet: -1.26 (0.41), residues: 162 loop : -2.48 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 822 TYR 0.020 0.001 TYR A 624 PHE 0.012 0.001 PHE A 680 TRP 0.005 0.001 TRP B 582 HIS 0.004 0.001 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (12270) covalent geometry : angle 0.55363 / 0.30 (16804) hydrogen bonds : bond 0.04901 / 3.22 ( 656) hydrogen bonds : angle 4.75796 / 3.37 ( 1818) metal coordination : bond 0.00538 / 0.26 ( 8) metal coordination : angle 4.83519 / 2.37 ( 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 190 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.651 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: A 377 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7307 (mt-10) REVERT: A 586 MET cc_start: 0.8491 (tpp) cc_final: 0.8287 (tpp) REVERT: A 882 LEU cc_start: 0.9273 (tp) cc_final: 0.8759 (tp) REVERT: B 520 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8380 (mmmm) REVERT: B 807 TYR cc_start: 0.7757 (t80) cc_final: 0.7438 (t80) REVERT: B 1015 TYR cc_start: 0.7346 (m-80) cc_final: 0.7057 (m-80) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2330 time to fit residues: 63.8965 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 : 0.633 ------------------------------------------------------------------------------- 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: 5.9990 chunk 94 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 525 ASN ** 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 = 0.3774 r_free = 0.3774 target = 0.092390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.069399 restraints weight = 118915.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.072901 restraints weight = 52237.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.075106 restraints weight = 32391.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.076495 restraints weight = 24198.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.077360 restraints weight = 20084.160| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12278 Z= 0.277 Angle : 0.631 5.961 16816 Z= 0.349 Chirality : 0.040 0.158 1954 Planarity : 0.004 0.061 1924 Dihedral : 14.452 85.332 2374 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.83 (0.22), residues: 1330 helix: 1.07 (0.19), residues: 700 sheet: -1.86 (0.37), residues: 174 loop : -2.64 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 843 TYR 0.018 0.002 TYR A 624 PHE 0.017 0.002 PHE A 680 TRP 0.007 0.001 TRP A 582 HIS 0.008 0.002 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.28 (12270) covalent geometry : angle 0.62950 / 0.35 (16804) hydrogen bonds : bond 0.05057 / 3.29 ( 656) hydrogen bonds : angle 4.90716 / 3.49 ( 1818) metal coordination : bond 0.01144 / 0.56 ( 8) metal coordination : angle 1.72155 / 0.88 ( 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: 0 poor density : 185 time to evaluate : 0.548 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: 0.7255 (mt-10) REVERT: A 635 LYS cc_start: 0.8694 (tppt) cc_final: 0.8357 (tmtt) REVERT: B 371 GLU cc_start: 0.8753 (tt0) cc_final: 0.8228 (tp30) REVERT: B 520 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8288 (mmmm) REVERT: B 676 LEU cc_start: 0.8533 (mt) cc_final: 0.8310 (mt) REVERT: B 807 TYR cc_start: 0.7760 (t80) cc_final: 0.7464 (t80) REVERT: B 1015 TYR cc_start: 0.7609 (m-80) cc_final: 0.7320 (m-80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2076 time to fit residues: 57.7206 Evaluate side-chains 144 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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: 3.9990 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 470 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 = 0.3769 r_free = 0.3769 target = 0.092193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069193 restraints weight = 117826.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.072710 restraints weight = 51030.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.074934 restraints weight = 31607.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.076282 restraints weight = 23511.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.077179 restraints weight = 19628.027| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3272 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= 0.208 Angle : 0.575 5.723 16816 Z= 0.317 Chirality : 0.040 0.152 1954 Planarity : 0.004 0.037 1924 Dihedral : 14.590 79.298 2374 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.09 % Allowed : 1.19 % Favored : 98.72 % 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: -0.75 (0.22), residues: 1330 helix: 1.15 (0.19), residues: 700 sheet: -1.80 (0.38), residues: 162 loop : -2.63 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 468 TYR 0.013 0.002 TYR B 408 PHE 0.015 0.002 PHE A 680 TRP 0.006 0.001 TRP A 582 HIS 0.006 0.001 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (12270) covalent geometry : angle 0.57199 / 0.32 (16804) hydrogen bonds : bond 0.04785 / 3.06 ( 656) hydrogen bonds : angle 4.75371 / 3.38 ( 1818) metal coordination : bond 0.00916 / 0.44 ( 8) metal coordination : angle 2.10805 / 1.10 ( 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 187 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.682 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: 0.7687 (mm-30) cc_final: 0.7104 (mt-10) REVERT: A 882 LEU cc_start: 0.9309 (tp) cc_final: 0.8750 (tp) REVERT: A 886 MET cc_start: 0.8699 (mmt) cc_final: 0.8482 (mmm) REVERT: B 371 GLU cc_start: 0.8738 (tt0) cc_final: 0.8241 (tp30) REVERT: B 499 LYS cc_start: 0.8876 (mptt) cc_final: 0.8499 (mptt) REVERT: B 520 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8276 (mmmm) REVERT: B 676 LEU cc_start: 0.8539 (mt) cc_final: 0.8271 (mt) REVERT: B 807 TYR cc_start: 0.7733 (t80) cc_final: 0.7454 (t80) REVERT: B 1015 TYR cc_start: 0.7657 (m-80) cc_final: 0.7329 (m-80) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.2113 time to fit residues: 59.6312 Evaluate side-chains 146 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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: 0.0670 chunk 66 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN ** 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 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 = 0.3782 r_free = 0.3782 target = 0.092952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.070203 restraints weight = 115815.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073823 restraints weight = 48678.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.076114 restraints weight = 29351.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.077523 restraints weight = 21500.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.078397 restraints weight = 17737.487| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3419 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= 0.138 Angle : 0.539 4.945 16816 Z= 0.296 Chirality : 0.039 0.162 1954 Planarity : 0.003 0.033 1924 Dihedral : 14.558 76.610 2374 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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: -0.55 (0.22), residues: 1330 helix: 1.29 (0.19), residues: 700 sheet: -1.67 (0.38), residues: 162 loop : -2.52 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 822 TYR 0.022 0.001 TYR A 565 PHE 0.015 0.001 PHE A 675 TRP 0.005 0.001 TRP B 968 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (12270) covalent geometry : angle 0.53625 / 0.30 (16804) hydrogen bonds : bond 0.04598 / 2.99 ( 656) hydrogen bonds : angle 4.57009 / 3.25 ( 1818) metal coordination : bond 0.00634 / 0.31 ( 8) metal coordination : angle 2.17138 / 1.15 ( 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 180 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.499 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 377 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7021 (mt-10) REVERT: A 882 LEU cc_start: 0.9341 (tp) cc_final: 0.8719 (tp) REVERT: A 886 MET cc_start: 0.8676 (mmt) cc_final: 0.8472 (mmm) REVERT: B 336 LYS cc_start: 0.9012 (mtpt) cc_final: 0.8528 (mtpt) REVERT: B 371 GLU cc_start: 0.8725 (tt0) cc_final: 0.8196 (tp30) REVERT: B 520 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8229 (mmmm) REVERT: B 676 LEU cc_start: 0.8531 (mt) cc_final: 0.8274 (mt) REVERT: B 807 TYR cc_start: 0.7725 (t80) cc_final: 0.7468 (t80) REVERT: B 1015 TYR cc_start: 0.7649 (m-80) cc_final: 0.7333 (m-80) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1915 time to fit residues: 52.7774 Evaluate side-chains 144 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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: 4.9990 chunk 58 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 = 0.3768 r_free = 0.3768 target = 0.092404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.070104 restraints weight = 116747.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.073735 restraints weight = 49310.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.076006 restraints weight = 29765.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.077442 restraints weight = 21846.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.078171 restraints weight = 17929.652| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12278 Z= 0.144 Angle : 0.530 5.070 16816 Z= 0.290 Chirality : 0.039 0.161 1954 Planarity : 0.003 0.035 1924 Dihedral : 14.499 75.186 2374 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % 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: -0.43 (0.23), residues: 1330 helix: 1.42 (0.19), residues: 700 sheet: -1.67 (0.38), residues: 162 loop : -2.49 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 822 TYR 0.018 0.001 TYR A1015 PHE 0.015 0.001 PHE A 675 TRP 0.004 0.001 TRP B 968 HIS 0.005 0.001 HIS B 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (12270) covalent geometry : angle 0.52791 / 0.29 (16804) hydrogen bonds : bond 0.04340 / 2.80 ( 656) hydrogen bonds : angle 4.48434 / 3.20 ( 1818) metal coordination : bond 0.00564 / 0.27 ( 8) metal coordination : angle 1.99794 / 1.06 ( 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 181 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.597 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: 0.7632 (mm-30) cc_final: 0.7018 (mt-10) REVERT: A 882 LEU cc_start: 0.9295 (tp) cc_final: 0.8722 (tp) REVERT: A 886 MET cc_start: 0.8697 (mmt) cc_final: 0.8467 (mmm) REVERT: B 336 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8517 (mttt) REVERT: B 371 GLU cc_start: 0.8733 (tt0) cc_final: 0.8209 (tp30) REVERT: B 520 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8234 (mmmm) REVERT: B 676 LEU cc_start: 0.8539 (mt) cc_final: 0.8259 (mt) REVERT: B 807 TYR cc_start: 0.7745 (t80) cc_final: 0.7494 (t80) REVERT: B 1015 TYR cc_start: 0.7666 (m-80) cc_final: 0.7355 (m-80) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2083 time to fit residues: 57.6770 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 : 0.594 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.091752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068983 restraints weight = 119317.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072572 restraints weight = 51171.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.074776 restraints weight = 31424.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.076173 restraints weight = 23434.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.076900 restraints weight = 19450.318| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3776 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= 0.194 Angle : 0.563 5.823 16816 Z= 0.312 Chirality : 0.040 0.177 1954 Planarity : 0.004 0.036 1924 Dihedral : 14.525 74.200 2374 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % 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: -0.56 (0.22), residues: 1330 helix: 1.35 (0.19), residues: 700 sheet: -1.81 (0.37), residues: 162 loop : -2.57 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 468 TYR 0.048 0.002 TYR A 565 PHE 0.021 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 0.00388 / 0.19 (12270) covalent geometry : angle 0.56094 / 0.31 (16804) hydrogen bonds : bond 0.04588 / 2.98 ( 656) hydrogen bonds : angle 4.62616 / 3.29 ( 1818) metal coordination : bond 0.00754 / 0.36 ( 8) metal coordination : angle 1.91101 / 1.00 ( 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 178 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 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: A 882 LEU cc_start: 0.9345 (tp) cc_final: 0.8726 (tp) REVERT: B 336 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8473 (mttt) REVERT: B 371 GLU cc_start: 0.8740 (tt0) cc_final: 0.8227 (tp30) REVERT: B 465 GLN cc_start: 0.8643 (tp40) cc_final: 0.7917 (tp-100) REVERT: B 520 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8240 (mmmm) REVERT: B 676 LEU cc_start: 0.8567 (mt) cc_final: 0.8297 (mt) REVERT: B 807 TYR cc_start: 0.7752 (t80) cc_final: 0.7507 (t80) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2118 time to fit residues: 57.5422 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 : 0.709 ------------------------------------------------------------------------------- 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: 10.0000 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 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 = 0.3755 r_free = 0.3755 target = 0.091752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.069056 restraints weight = 119482.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.072677 restraints weight = 50648.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.074947 restraints weight = 30781.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.076374 restraints weight = 22748.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.077228 restraints weight = 18747.813| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12278 Z= 0.163 Angle : 0.545 5.986 16816 Z= 0.298 Chirality : 0.039 0.164 1954 Planarity : 0.003 0.036 1924 Dihedral : 14.593 74.816 2374 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -0.50 (0.22), residues: 1330 helix: 1.40 (0.19), residues: 700 sheet: -1.82 (0.37), residues: 162 loop : -2.54 (0.24), residues: 468 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 0.016 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 0.00329 / 0.16 (12270) covalent geometry : angle 0.54257 / 0.30 (16804) hydrogen bonds : bond 0.04367 / 2.81 ( 656) hydrogen bonds : angle 4.52088 / 3.21 ( 1818) metal coordination : bond 0.00655 / 0.31 ( 8) metal coordination : angle 1.85417 / 0.96 ( 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 175 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.603 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: A 589 LYS cc_start: 0.9056 (mtmt) cc_final: 0.8836 (mtpt) REVERT: A 882 LEU cc_start: 0.9283 (tp) cc_final: 0.8794 (tp) REVERT: A 886 MET cc_start: 0.8703 (mmt) cc_final: 0.8452 (mmm) REVERT: B 336 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8500 (mtpt) REVERT: B 371 GLU cc_start: 0.8742 (tt0) cc_final: 0.8248 (tp30) REVERT: B 465 GLN cc_start: 0.8646 (tp40) cc_final: 0.7910 (tp-100) REVERT: B 504 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8833 (mt-10) REVERT: B 520 LYS cc_start: 0.8525 (mmmt) cc_final: 0.8219 (mmmm) REVERT: B 676 LEU cc_start: 0.8538 (mt) cc_final: 0.8287 (mt) REVERT: B 807 TYR cc_start: 0.7730 (t80) cc_final: 0.7507 (t80) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2053 time to fit residues: 55.1785 Evaluate side-chains 146 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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: 7.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 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 = 0.3743 r_free = 0.3743 target = 0.091091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.068341 restraints weight = 119130.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.071977 restraints weight = 50070.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.074240 restraints weight = 30323.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.075625 restraints weight = 22369.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.076515 restraints weight = 18524.721| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4105 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= 0.188 Angle : 0.572 6.333 16816 Z= 0.316 Chirality : 0.040 0.196 1954 Planarity : 0.004 0.037 1924 Dihedral : 14.586 74.964 2374 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -0.77 (0.22), residues: 1330 helix: 1.18 (0.19), residues: 712 sheet: -1.88 (0.37), residues: 160 loop : -2.79 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 890 TYR 0.036 0.002 TYR A 565 PHE 0.024 0.002 PHE A 675 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 0.00378 / 0.19 (12270) covalent geometry : angle 0.56997 / 0.32 (16804) hydrogen bonds : bond 0.04547 / 2.94 ( 656) hydrogen bonds : angle 4.61060 / 3.27 ( 1818) metal coordination : bond 0.00775 / 0.37 ( 8) metal coordination : angle 1.78513 / 0.91 ( 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 173 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.717 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: A 589 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8842 (mtpt) REVERT: A 673 ASP cc_start: 0.8569 (t0) cc_final: 0.8166 (p0) REVERT: A 882 LEU cc_start: 0.9339 (tp) cc_final: 0.8783 (tp) REVERT: A 886 MET cc_start: 0.8714 (mmt) cc_final: 0.8477 (mmm) REVERT: B 371 GLU cc_start: 0.8757 (tt0) cc_final: 0.8260 (tp30) REVERT: B 520 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8192 (mmmm) REVERT: B 676 LEU cc_start: 0.8545 (mt) cc_final: 0.8327 (mt) REVERT: B 807 TYR cc_start: 0.7735 (t80) cc_final: 0.7511 (t80) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2085 time to fit residues: 55.4659 Evaluate side-chains 146 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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: 5.9990 chunk 47 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 447 HIS ** 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 = 0.3708 r_free = 0.3708 target = 0.089285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066791 restraints weight = 120977.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.070324 restraints weight = 51033.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.072545 restraints weight = 31124.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.073824 restraints weight = 23091.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.074723 restraints weight = 19358.890| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12278 Z= 0.277 Angle : 0.645 6.899 16816 Z= 0.356 Chirality : 0.042 0.165 1954 Planarity : 0.004 0.039 1924 Dihedral : 14.704 78.172 2374 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.22), residues: 1330 helix: 0.96 (0.19), residues: 700 sheet: -2.27 (0.36), residues: 160 loop : -2.92 (0.23), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 728 TYR 0.019 0.002 TYR B 408 PHE 0.021 0.002 PHE A 680 TRP 0.009 0.001 TRP B 582 HIS 0.011 0.002 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.28 (12270) covalent geometry : angle 0.64355 / 0.36 (16804) hydrogen bonds : bond 0.05068 / 3.20 ( 656) hydrogen bonds : angle 4.80999 / 3.41 ( 1818) metal coordination : bond 0.01205 / 0.59 ( 8) metal coordination : angle 1.85884 / 0.92 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.02 seconds wall clock time: 65 minutes 50.61 seconds (3950.61 seconds total)