Starting phenix.real_space_refine on Fri Sep 19 04:45:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2w_50165/09_2025/9f2w_50165_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2w_50165/09_2025/9f2w_50165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f2w_50165/09_2025/9f2w_50165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2w_50165/09_2025/9f2w_50165.map" model { file = "/net/cci-nas-00/data/ceres_data/9f2w_50165/09_2025/9f2w_50165_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2w_50165/09_2025/9f2w_50165_trim.cif" } resolution = 4.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 62 5.49 5 S 66 5.16 5 C 7338 2.51 5 N 2092 2.21 5 O 2402 1.98 5 H 11450 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 12.96, per 1000 atoms: 0.55 Number of scatterers: 23412 At special positions: 0 Unit cell: (102.424, 94.99, 118.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 66 16.00 P 62 15.00 O 2402 8.00 N 2092 7.00 C 7338 6.00 H 11450 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 646.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 3.49 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: 5.26 Time building geometry restraints manager: 2.81 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=" 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=" 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 angle pdb=" C LYS B 772 " pdb=" N GLU B 773 " pdb=" CA GLU B 773 " ideal model delta sigma weight residual 120.31 116.59 3.72 1.52e+00 4.33e-01 6.00e+00 angle pdb=" C1' ATP A1102 " pdb=" C2' ATP A1102 " pdb=" O2' ATP A1102 " ideal model delta sigma weight residual 110.58 103.96 6.62 2.79e+00 1.28e-01 5.61e+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: 1.340 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: 0.140 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 37.440 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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= 0.167 Angle : 0.574 6.618 16816 Z= 0.306 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 aren 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 covalent geometry : bond 0.00330 (12270) covalent geometry : angle 0.56728 (16804) hydrogen bonds : bond 0.13111 ( 656) hydrogen bonds : angle 5.56894 ( 1818) metal coordination : bond 0.00595 ( 8) metal coordination : angle 3.21944 ( 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 : 0.691 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: 0.6724 (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: 0.2456 time to fit residues: 82.9057 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 : 0.619 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 416 GLN A 475 GLN A 484 GLN ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN B 525 ASN B 678 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.089544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.066969 restraints weight = 117423.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.070398 restraints weight = 50372.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.072441 restraints weight = 30857.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.073816 restraints weight = 23188.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.074672 restraints weight = 19216.358| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 12278 Z= 0.327 Angle : 0.780 8.313 16816 Z= 0.426 Chirality : 0.045 0.181 1954 Planarity : 0.005 0.063 1924 Dihedral : 14.991 76.343 2374 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.43 % Allowed : 4.69 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -1.15 (0.22), residues: 1330 helix: 0.70 (0.19), residues: 714 sheet: -1.70 (0.39), residues: 164 loop : -2.81 (0.24), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 468 TYR 0.030 0.003 TYR B 408 PHE 0.019 0.003 PHE B 744 TRP 0.012 0.002 TRP A 582 HIS 0.012 0.003 HIS B 974 Details of bonding type rmsd covalent geometry : bond 0.00662 (12270) covalent geometry : angle 0.77537 (16804) hydrogen bonds : bond 0.05712 ( 656) hydrogen bonds : angle 5.15984 ( 1818) metal coordination : bond 0.01480 ( 8) metal coordination : angle 3.18942 ( 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 192 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 0.532 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: B 499 LYS cc_start: 0.8955 (mptt) cc_final: 0.8627 (mptt) REVERT: B 520 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8351 (mmmm) REVERT: B 807 TYR cc_start: 0.7815 (t80) cc_final: 0.7466 (t80) REVERT: B 886 MET cc_start: 0.8594 (mtm) cc_final: 0.8305 (mtm) outliers start: 5 outliers final: 2 residues processed: 191 average time/residue: 0.2041 time to fit residues: 58.2191 Evaluate side-chains 149 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN A 525 ASN ** 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 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 = 0.3783 r_free = 0.3783 target = 0.093275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.070588 restraints weight = 114528.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.074331 restraints weight = 49317.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.076626 restraints weight = 29616.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.078094 restraints weight = 21664.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.079039 restraints weight = 17755.389| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12278 Z= 0.120 Angle : 0.540 5.698 16816 Z= 0.287 Chirality : 0.039 0.162 1954 Planarity : 0.003 0.031 1924 Dihedral : 14.474 83.575 2374 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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 aren not related in a simple way. whole: -0.28 (0.23), residues: 1330 helix: 1.45 (0.19), residues: 700 sheet: -1.35 (0.40), residues: 164 loop : -2.35 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 890 TYR 0.021 0.001 TYR A 624 PHE 0.012 0.001 PHE B 551 TRP 0.005 0.001 TRP A1003 HIS 0.007 0.001 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00251 (12270) covalent geometry : angle 0.53689 (16804) hydrogen bonds : bond 0.04258 ( 656) hydrogen bonds : angle 4.45836 ( 1818) metal coordination : bond 0.00572 ( 8) metal coordination : angle 2.23457 ( 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 192 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.538 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 377 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7081 (mm-30) REVERT: A 882 LEU cc_start: 0.9267 (tp) cc_final: 0.8663 (tp) REVERT: A 886 MET cc_start: 0.8707 (mmt) cc_final: 0.8460 (mmm) REVERT: A 966 GLN cc_start: 0.5940 (tp40) cc_final: 0.5633 (tp-100) REVERT: B 371 GLU cc_start: 0.8691 (tt0) cc_final: 0.8159 (tp30) REVERT: B 398 LYS cc_start: 0.6616 (ttpp) cc_final: 0.6365 (tttt) REVERT: B 499 LYS cc_start: 0.8873 (mptt) cc_final: 0.8577 (mptt) REVERT: B 515 ASP cc_start: 0.8828 (t0) cc_final: 0.8438 (t0) REVERT: B 520 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8283 (mmmm) REVERT: B 676 LEU cc_start: 0.8489 (mt) cc_final: 0.8281 (mt) REVERT: B 807 TYR cc_start: 0.7718 (t80) cc_final: 0.7438 (t80) REVERT: B 886 MET cc_start: 0.8580 (mtm) cc_final: 0.8361 (mtm) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2023 time to fit residues: 58.2998 Evaluate side-chains 153 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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: 0.7980 chunk 94 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS 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 = 0.3704 r_free = 0.3704 target = 0.089264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066916 restraints weight = 118254.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070315 restraints weight = 51179.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.072487 restraints weight = 31473.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073833 restraints weight = 23348.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.074634 restraints weight = 19379.096| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12278 Z= 0.245 Angle : 0.622 6.815 16816 Z= 0.337 Chirality : 0.040 0.168 1954 Planarity : 0.004 0.036 1924 Dihedral : 14.801 82.460 2374 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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 aren not related in a simple way. whole: -0.81 (0.22), residues: 1330 helix: 1.06 (0.19), residues: 714 sheet: -1.94 (0.37), residues: 164 loop : -2.64 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 843 TYR 0.016 0.002 TYR A 624 PHE 0.017 0.002 PHE A 680 TRP 0.007 0.001 TRP B 968 HIS 0.009 0.002 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00502 (12270) covalent geometry : angle 0.62045 (16804) hydrogen bonds : bond 0.04861 ( 656) hydrogen bonds : angle 4.66978 ( 1818) metal coordination : bond 0.01070 ( 8) metal coordination : angle 1.97668 ( 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 171 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.589 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: A 844 GLU cc_start: 0.8335 (tp30) cc_final: 0.8122 (tm-30) REVERT: A 882 LEU cc_start: 0.9334 (tp) cc_final: 0.8672 (tp) REVERT: A 926 MET cc_start: 0.8390 (ptp) cc_final: 0.8068 (ptp) REVERT: B 371 GLU cc_start: 0.8705 (tt0) cc_final: 0.8193 (tp30) REVERT: B 403 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8326 (mm-30) REVERT: B 499 LYS cc_start: 0.8987 (mptt) cc_final: 0.8711 (mptt) REVERT: B 520 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8244 (mmmm) REVERT: B 807 TYR cc_start: 0.7658 (t80) cc_final: 0.7398 (t80) REVERT: B 886 MET cc_start: 0.8589 (mtm) cc_final: 0.8297 (mtm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1908 time to fit residues: 49.0215 Evaluate side-chains 138 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 5.9990 chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 313 GLN B 450 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B 928 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.088627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.065761 restraints weight = 119358.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069153 restraints weight = 52080.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071278 restraints weight = 32419.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.072614 restraints weight = 24349.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.073463 restraints weight = 20348.939| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12278 Z= 0.244 Angle : 0.624 6.098 16816 Z= 0.338 Chirality : 0.041 0.173 1954 Planarity : 0.004 0.044 1924 Dihedral : 14.938 85.158 2374 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % 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 aren not related in a simple way. whole: -1.08 (0.22), residues: 1330 helix: 0.93 (0.19), residues: 714 sheet: -2.23 (0.36), residues: 160 loop : -2.86 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 890 TYR 0.016 0.002 TYR A1015 PHE 0.017 0.002 PHE A 680 TRP 0.010 0.001 TRP B1003 HIS 0.013 0.002 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00492 (12270) covalent geometry : angle 0.62200 (16804) hydrogen bonds : bond 0.04637 ( 656) hydrogen bonds : angle 4.75352 ( 1818) metal coordination : bond 0.01063 ( 8) metal coordination : angle 1.98191 ( 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 181 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.549 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 882 LEU cc_start: 0.9284 (tp) cc_final: 0.8768 (tp) REVERT: A 966 GLN cc_start: 0.6537 (tp40) cc_final: 0.6295 (tp-100) REVERT: B 371 GLU cc_start: 0.8700 (tt0) cc_final: 0.8190 (tp30) REVERT: B 403 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8227 (mm-30) REVERT: B 499 LYS cc_start: 0.9055 (mptt) cc_final: 0.8775 (mptt) REVERT: B 520 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8216 (mmmm) REVERT: B 604 HIS cc_start: 0.8405 (m90) cc_final: 0.8197 (m170) REVERT: B 807 TYR cc_start: 0.7640 (t80) cc_final: 0.7428 (t80) REVERT: B 886 MET cc_start: 0.8594 (mtm) cc_final: 0.8337 (mtm) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.1940 time to fit residues: 53.2001 Evaluate side-chains 143 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 0.9980 chunk 66 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** B 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.089341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.066547 restraints weight = 117489.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.070000 restraints weight = 50590.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.072160 restraints weight = 31068.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.073565 restraints weight = 23152.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.074440 restraints weight = 19138.009| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12278 Z= 0.174 Angle : 0.562 5.823 16816 Z= 0.303 Chirality : 0.039 0.184 1954 Planarity : 0.003 0.034 1924 Dihedral : 14.788 80.953 2374 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.22), residues: 1330 helix: 1.15 (0.19), residues: 712 sheet: -2.20 (0.36), residues: 160 loop : -2.83 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 890 TYR 0.011 0.001 TYR A 462 PHE 0.016 0.001 PHE A 680 TRP 0.006 0.001 TRP B 385 HIS 0.005 0.001 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00350 (12270) covalent geometry : angle 0.56057 (16804) hydrogen bonds : bond 0.04314 ( 656) hydrogen bonds : angle 4.52420 ( 1818) metal coordination : bond 0.00735 ( 8) metal coordination : angle 1.56053 ( 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 179 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.627 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 882 LEU cc_start: 0.9335 (tp) cc_final: 0.8754 (tp) REVERT: A 966 GLN cc_start: 0.6565 (tp40) cc_final: 0.6320 (tp-100) REVERT: B 371 GLU cc_start: 0.8704 (tt0) cc_final: 0.8184 (tp30) REVERT: B 499 LYS cc_start: 0.9101 (mptt) cc_final: 0.8785 (mptt) REVERT: B 520 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8143 (mmmm) REVERT: B 807 TYR cc_start: 0.7650 (t80) cc_final: 0.7440 (t80) REVERT: B 886 MET cc_start: 0.8648 (mtm) cc_final: 0.8418 (mtm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1919 time to fit residues: 52.2156 Evaluate side-chains 148 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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: 10.0000 chunk 58 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.088473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066119 restraints weight = 117186.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069517 restraints weight = 50379.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.071668 restraints weight = 30771.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.072984 restraints weight = 22827.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.073768 restraints weight = 18958.929| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12278 Z= 0.216 Angle : 0.599 5.944 16816 Z= 0.326 Chirality : 0.040 0.183 1954 Planarity : 0.004 0.036 1924 Dihedral : 14.917 86.659 2374 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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 aren not related in a simple way. whole: -1.03 (0.22), residues: 1330 helix: 1.12 (0.19), residues: 710 sheet: -2.45 (0.36), residues: 160 loop : -2.97 (0.23), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 890 TYR 0.013 0.002 TYR A 462 PHE 0.019 0.002 PHE A 680 TRP 0.009 0.001 TRP B 582 HIS 0.005 0.001 HIS B 974 Details of bonding type rmsd covalent geometry : bond 0.00438 (12270) covalent geometry : angle 0.59810 (16804) hydrogen bonds : bond 0.04595 ( 656) hydrogen bonds : angle 4.63390 ( 1818) metal coordination : bond 0.00893 ( 8) metal coordination : angle 1.51473 ( 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 170 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.571 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: A 377 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 499 LYS cc_start: 0.9190 (mptt) cc_final: 0.8921 (mmmm) REVERT: A 882 LEU cc_start: 0.9282 (tp) cc_final: 0.8770 (tp) REVERT: B 371 GLU cc_start: 0.8689 (tt0) cc_final: 0.8158 (tp30) REVERT: B 499 LYS cc_start: 0.9142 (mptt) cc_final: 0.8836 (mptt) REVERT: B 520 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8134 (mmmm) REVERT: B 886 MET cc_start: 0.8672 (mtm) cc_final: 0.8455 (mtm) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1975 time to fit residues: 51.0087 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 : 0.665 ------------------------------------------------------------------------------- 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: 9.9990 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 ASN B 416 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.087991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065195 restraints weight = 118710.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.068640 restraints weight = 49803.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.070820 restraints weight = 30309.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.072153 restraints weight = 22462.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.072970 restraints weight = 18750.879| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12278 Z= 0.259 Angle : 0.642 6.540 16816 Z= 0.350 Chirality : 0.041 0.182 1954 Planarity : 0.004 0.045 1924 Dihedral : 15.086 86.626 2374 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.09 % Allowed : 2.22 % Favored : 97.70 % 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 aren not related in a simple way. whole: -1.31 (0.22), residues: 1330 helix: 0.90 (0.19), residues: 714 sheet: -2.85 (0.34), residues: 172 loop : -3.01 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 890 TYR 0.013 0.002 TYR A 807 PHE 0.019 0.002 PHE A 680 TRP 0.009 0.001 TRP B 582 HIS 0.007 0.002 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00522 (12270) covalent geometry : angle 0.63743 (16804) hydrogen bonds : bond 0.04913 ( 656) hydrogen bonds : angle 4.77988 ( 1818) metal coordination : bond 0.01364 ( 8) metal coordination : angle 2.82913 ( 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 167 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 499 LYS cc_start: 0.9266 (mptt) cc_final: 0.8945 (mmmm) REVERT: A 559 MET cc_start: 0.8257 (mtp) cc_final: 0.8040 (mtp) REVERT: A 926 MET cc_start: 0.8505 (ptp) cc_final: 0.8157 (ptm) REVERT: B 371 GLU cc_start: 0.8767 (tt0) cc_final: 0.8227 (tp30) REVERT: B 499 LYS cc_start: 0.9214 (mptt) cc_final: 0.8895 (mptt) REVERT: B 520 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8190 (mmmm) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.1893 time to fit residues: 48.6095 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 : 0.500 ------------------------------------------------------------------------------- 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: 20.0000 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 HIS ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B 944 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.090056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.067568 restraints weight = 117091.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071054 restraints weight = 49847.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.073304 restraints weight = 30359.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.074727 restraints weight = 22343.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.075600 restraints weight = 18392.149| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12278 Z= 0.129 Angle : 0.551 6.093 16816 Z= 0.296 Chirality : 0.039 0.192 1954 Planarity : 0.003 0.035 1924 Dihedral : 14.776 87.051 2374 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.66 % 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 aren not related in a simple way. whole: -0.77 (0.23), residues: 1330 helix: 1.27 (0.19), residues: 714 sheet: -2.38 (0.33), residues: 196 loop : -2.72 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 890 TYR 0.011 0.001 TYR A 408 PHE 0.015 0.001 PHE A 680 TRP 0.006 0.001 TRP A 385 HIS 0.003 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00270 (12270) covalent geometry : angle 0.54777 (16804) hydrogen bonds : bond 0.04102 ( 656) hydrogen bonds : angle 4.40812 ( 1818) metal coordination : bond 0.00421 ( 8) metal coordination : angle 2.35876 ( 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 173 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.457 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: A 377 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7686 (mm-30) REVERT: A 499 LYS cc_start: 0.9190 (mptt) cc_final: 0.8888 (mmmm) REVERT: A 559 MET cc_start: 0.8161 (mtp) cc_final: 0.7950 (mtp) REVERT: A 586 MET cc_start: 0.8661 (tpt) cc_final: 0.8451 (tpt) REVERT: A 589 LYS cc_start: 0.9145 (mtmt) cc_final: 0.8861 (mtpt) REVERT: B 371 GLU cc_start: 0.8708 (tt0) cc_final: 0.8174 (tp30) REVERT: B 499 LYS cc_start: 0.9048 (mptt) cc_final: 0.8662 (mptt) REVERT: B 520 LYS cc_start: 0.8394 (mmmt) cc_final: 0.8190 (mmmm) REVERT: B 807 TYR cc_start: 0.7499 (t80) cc_final: 0.7203 (t80) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1879 time to fit residues: 49.7101 Evaluate side-chains 148 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 54 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B 944 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.090367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068155 restraints weight = 115033.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.071685 restraints weight = 49020.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.073948 restraints weight = 29590.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.075364 restraints weight = 21606.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076247 restraints weight = 17736.569| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.6042 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= 0.120 Angle : 0.533 6.299 16816 Z= 0.284 Chirality : 0.038 0.180 1954 Planarity : 0.003 0.035 1924 Dihedral : 14.529 85.135 2374 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.23), residues: 1330 helix: 1.53 (0.19), residues: 712 sheet: -2.27 (0.33), residues: 196 loop : -2.63 (0.26), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 890 TYR 0.010 0.001 TYR A 462 PHE 0.015 0.001 PHE A 680 TRP 0.007 0.001 TRP B 582 HIS 0.004 0.001 HIS B 928 Details of bonding type rmsd covalent geometry : bond 0.00256 (12270) covalent geometry : angle 0.53014 (16804) hydrogen bonds : bond 0.03908 ( 656) hydrogen bonds : angle 4.24699 ( 1818) metal coordination : bond 0.00369 ( 8) metal coordination : angle 2.13273 ( 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: 1 poor density : 172 time to evaluate : 0.625 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: A 377 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7771 (mt-10) REVERT: A 462 TYR cc_start: 0.8905 (t80) cc_final: 0.8665 (t80) REVERT: A 499 LYS cc_start: 0.9193 (mptt) cc_final: 0.8949 (mmmm) REVERT: A 589 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8955 (mtpt) REVERT: B 371 GLU cc_start: 0.8713 (tt0) cc_final: 0.8161 (tp30) REVERT: B 499 LYS cc_start: 0.8999 (mptt) cc_final: 0.8622 (mptt) REVERT: B 807 TYR cc_start: 0.7386 (t80) cc_final: 0.7117 (t80) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1977 time to fit residues: 52.3331 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 : 0.614 ------------------------------------------------------------------------------- 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: 5.9990 chunk 84 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.089788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.067267 restraints weight = 117371.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070782 restraints weight = 50124.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.073015 restraints weight = 30587.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.074365 restraints weight = 22588.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.075270 restraints weight = 18738.618| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12278 Z= 0.159 Angle : 0.552 5.884 16816 Z= 0.296 Chirality : 0.039 0.178 1954 Planarity : 0.004 0.062 1924 Dihedral : 14.564 88.846 2374 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % 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 aren not related in a simple way. whole: -0.57 (0.23), residues: 1330 helix: 1.48 (0.19), residues: 712 sheet: -2.32 (0.33), residues: 196 loop : -2.71 (0.26), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 890 TYR 0.011 0.001 TYR A 939 PHE 0.017 0.001 PHE A 680 TRP 0.008 0.001 TRP B 582 HIS 0.005 0.001 HIS B 974 Details of bonding type rmsd covalent geometry : bond 0.00331 (12270) covalent geometry : angle 0.54977 (16804) hydrogen bonds : bond 0.04121 ( 656) hydrogen bonds : angle 4.34566 ( 1818) metal coordination : bond 0.00575 ( 8) metal coordination : angle 1.97350 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3692.36 seconds wall clock time: 63 minutes 52.63 seconds (3832.63 seconds total)