Starting phenix.real_space_refine on Thu May 22 18:36:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2w_50165/05_2025/9f2w_50165_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2w_50165/05_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_50165/05_2025/9f2w_50165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2w_50165/05_2025/9f2w_50165.map" model { file = "/net/cci-nas-00/data/ceres_data/9f2w_50165/05_2025/9f2w_50165_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2w_50165/05_2025/9f2w_50165_trim.cif" } resolution = 4.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 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} Chain: "C" 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: "D" 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} 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: Y, X, B Time building chain proxies: 35.24, per 1000 atoms: 1.51 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: 6.33 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 10.36 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: 8.58 Time building geometry restraints manager: 7.50 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: 0.07 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'Y' } ncs_group { reference = chain 'C' selection = chain 'X' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.510 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: 0.400 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 91.630 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.680 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP B 385 HIS 0.007 0.001 HIS B 974 PHE 0.014 0.001 PHE A 680 TYR 0.007 0.001 TYR A 342 ARG 0.005 0.001 ARG B 705 Details of bonding type rmsd hydrogen bonds : bond 0.13111 ( 656) hydrogen bonds : angle 5.56894 ( 1818) metal coordination : bond 0.00595 ( 8) metal coordination : angle 3.21944 ( 12) covalent geometry : bond 0.00330 (12270) covalent geometry : angle 0.56728 (16804) *********************** 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 : 1.719 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: symmetry clash REVERT: A 377 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6726 (mm-30) REVERT: A 586 MET cc_start: 0.8496 (tpp) cc_final: 0.8163 (tpp) REVERT: A 599 ARG cc_start: 0.6701 (ptp-170) cc_final: 0.5717 (mtm110) REVERT: A 610 GLU cc_start: 0.8702 (pp20) cc_final: 0.8478 (pp20) REVERT: A 677 MET cc_start: 0.6584 (ptm) cc_final: 0.6329 (ptm) 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: 0.5485 (t70) REVERT: B 999 GLN cc_start: 0.8213 (tt0) cc_final: 0.7457 (mm-40) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.5413 time to fit residues: 181.5300 Evaluate side-chains 160 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN A 416 GLN ** 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 B 974 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.093706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.071126 restraints weight = 115288.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.074761 restraints weight = 49625.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.077036 restraints weight = 30027.503| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12278 Z= 0.202 Angle : 0.606 5.404 16816 Z= 0.327 Chirality : 0.040 0.153 1954 Planarity : 0.004 0.062 1924 Dihedral : 14.388 81.841 2374 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.34 % Allowed : 2.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1330 helix: 1.36 (0.19), residues: 700 sheet: -1.24 (0.40), residues: 174 loop : -2.36 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.009 0.002 HIS A 531 PHE 0.012 0.002 PHE A 680 TYR 0.019 0.002 TYR B 408 ARG 0.005 0.001 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 656) hydrogen bonds : angle 4.70561 ( 1818) metal coordination : bond 0.00841 ( 8) metal coordination : angle 2.64271 ( 12) covalent geometry : bond 0.00407 (12270) covalent geometry : angle 0.60232 (16804) *********************** 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 194 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 918 GLU cc_start: 0.7749 (pm20) cc_final: 0.7546 (pm20) REVERT: B 520 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8438 (mmmm) REVERT: B 807 TYR cc_start: 0.7837 (t80) cc_final: 0.7483 (t80) REVERT: B 886 MET cc_start: 0.8496 (mtm) cc_final: 0.8216 (mtm) REVERT: B 926 MET cc_start: 0.8790 (ptp) cc_final: 0.8468 (ptp) outliers start: 4 outliers final: 2 residues processed: 193 average time/residue: 0.4772 time to fit residues: 136.4643 Evaluate side-chains 145 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 38 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 525 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN B 447 HIS B 470 ASN B 475 GLN B 525 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.088871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066118 restraints weight = 119629.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.069578 restraints weight = 50553.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.071755 restraints weight = 31147.337| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12278 Z= 0.297 Angle : 0.709 7.384 16816 Z= 0.382 Chirality : 0.043 0.202 1954 Planarity : 0.005 0.048 1924 Dihedral : 15.143 82.861 2374 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.26 % Allowed : 5.12 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1330 helix: 0.83 (0.19), residues: 714 sheet: -1.91 (0.37), residues: 164 loop : -2.87 (0.24), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1003 HIS 0.010 0.002 HIS A 927 PHE 0.020 0.002 PHE A 675 TYR 0.025 0.003 TYR B 408 ARG 0.012 0.001 ARG A 890 Details of bonding type rmsd hydrogen bonds : bond 0.05496 ( 656) hydrogen bonds : angle 4.92838 ( 1818) metal coordination : bond 0.01511 ( 8) metal coordination : angle 2.86233 ( 12) covalent geometry : bond 0.00607 (12270) covalent geometry : angle 0.70500 (16804) *********************** 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 176 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 173 time to evaluate : 1.657 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: A 844 GLU cc_start: 0.8300 (tp30) cc_final: 0.8098 (tm-30) REVERT: B 371 GLU cc_start: 0.8749 (tt0) cc_final: 0.8265 (tp30) REVERT: B 499 LYS cc_start: 0.9013 (mptt) cc_final: 0.8734 (mptt) REVERT: B 504 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8853 (mt-10) REVERT: B 520 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8161 (mmmm) REVERT: B 677 MET cc_start: 0.8818 (tpt) cc_final: 0.8528 (tmm) REVERT: B 734 LEU cc_start: 0.9132 (mm) cc_final: 0.8890 (mm) REVERT: B 807 TYR cc_start: 0.7833 (t80) cc_final: 0.7596 (t80) REVERT: B 886 MET cc_start: 0.8571 (mtm) cc_final: 0.8271 (mtm) outliers start: 3 outliers final: 2 residues processed: 176 average time/residue: 0.4594 time to fit residues: 120.4333 Evaluate side-chains 140 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.088375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.065875 restraints weight = 117287.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069263 restraints weight = 49920.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071410 restraints weight = 30717.071| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12278 Z= 0.265 Angle : 0.649 5.910 16816 Z= 0.354 Chirality : 0.041 0.194 1954 Planarity : 0.004 0.039 1924 Dihedral : 14.975 79.007 2374 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.22), residues: 1330 helix: 0.77 (0.19), residues: 714 sheet: -2.45 (0.34), residues: 172 loop : -2.90 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 737 HIS 0.007 0.002 HIS A 927 PHE 0.018 0.002 PHE A 680 TYR 0.022 0.002 TYR A 624 ARG 0.013 0.001 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 656) hydrogen bonds : angle 4.80715 ( 1818) metal coordination : bond 0.01218 ( 8) metal coordination : angle 2.10766 ( 12) covalent geometry : bond 0.00533 (12270) covalent geometry : angle 0.64649 (16804) *********************** 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 172 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 926 MET cc_start: 0.8421 (ptp) cc_final: 0.8207 (ptp) REVERT: B 371 GLU cc_start: 0.8729 (tt0) cc_final: 0.8280 (tp30) REVERT: B 499 LYS cc_start: 0.9112 (mptt) cc_final: 0.8796 (mptt) REVERT: B 520 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8237 (mmmm) REVERT: B 807 TYR cc_start: 0.7799 (t80) cc_final: 0.7563 (t80) REVERT: B 886 MET cc_start: 0.8612 (mtm) cc_final: 0.8300 (mtm) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.4355 time to fit residues: 113.1123 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 : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B 919 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.090472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067419 restraints weight = 117288.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070932 restraints weight = 50546.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.073162 restraints weight = 31098.799| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12278 Z= 0.150 Angle : 0.540 5.666 16816 Z= 0.294 Chirality : 0.039 0.187 1954 Planarity : 0.003 0.045 1924 Dihedral : 14.787 82.617 2374 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.22), residues: 1330 helix: 1.17 (0.19), residues: 714 sheet: -2.09 (0.36), residues: 160 loop : -2.82 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1003 HIS 0.006 0.001 HIS A 927 PHE 0.016 0.001 PHE A 680 TYR 0.017 0.001 TYR A 624 ARG 0.004 0.000 ARG A 890 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 656) hydrogen bonds : angle 4.47741 ( 1818) metal coordination : bond 0.00680 ( 8) metal coordination : angle 1.36217 ( 12) covalent geometry : bond 0.00306 (12270) covalent geometry : angle 0.53859 (16804) *********************** 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 174 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.729 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 470 ASN cc_start: 0.7391 (m110) cc_final: 0.7187 (m110) REVERT: A 926 MET cc_start: 0.8425 (ptp) cc_final: 0.8087 (ptp) REVERT: B 371 GLU cc_start: 0.8739 (tt0) cc_final: 0.8223 (tp30) REVERT: B 399 ILE cc_start: 0.6769 (mt) cc_final: 0.6381 (mt) REVERT: B 499 LYS cc_start: 0.9141 (mptt) cc_final: 0.8791 (mptt) REVERT: B 520 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8155 (mmmm) REVERT: B 807 TYR cc_start: 0.7759 (t80) cc_final: 0.7544 (t80) REVERT: B 886 MET cc_start: 0.8629 (mtm) cc_final: 0.8406 (mtm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.4270 time to fit residues: 112.8174 Evaluate side-chains 142 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 43 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 986 ASN B 450 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.088454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066177 restraints weight = 115903.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.069570 restraints weight = 50028.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.071717 restraints weight = 30634.686| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12278 Z= 0.239 Angle : 0.614 6.355 16816 Z= 0.337 Chirality : 0.040 0.178 1954 Planarity : 0.004 0.038 1924 Dihedral : 14.950 82.778 2374 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.09 % Allowed : 1.88 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1330 helix: 1.01 (0.19), residues: 712 sheet: -2.43 (0.35), residues: 160 loop : -2.98 (0.23), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1003 HIS 0.008 0.001 HIS B 974 PHE 0.020 0.002 PHE A 680 TYR 0.016 0.002 TYR B 408 ARG 0.006 0.001 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 656) hydrogen bonds : angle 4.65719 ( 1818) metal coordination : bond 0.01090 ( 8) metal coordination : angle 1.70251 ( 12) covalent geometry : bond 0.00490 (12270) covalent geometry : angle 0.61237 (16804) *********************** 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 166 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 847 ASN cc_start: 0.8404 (m-40) cc_final: 0.8167 (m-40) REVERT: A 926 MET cc_start: 0.8330 (ptp) cc_final: 0.8023 (ptp) REVERT: B 371 GLU cc_start: 0.8669 (tt0) cc_final: 0.8202 (tp30) REVERT: B 499 LYS cc_start: 0.9131 (mptt) cc_final: 0.8831 (mptt) REVERT: B 520 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8213 (mmmm) REVERT: B 582 TRP cc_start: 0.8421 (t-100) cc_final: 0.8100 (t-100) REVERT: B 886 MET cc_start: 0.8657 (mtm) cc_final: 0.8425 (mtm) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.4488 time to fit residues: 112.7626 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 : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 119 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.089673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.066839 restraints weight = 116949.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070339 restraints weight = 50053.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.072569 restraints weight = 30654.608| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12278 Z= 0.165 Angle : 0.546 5.192 16816 Z= 0.299 Chirality : 0.039 0.168 1954 Planarity : 0.003 0.037 1924 Dihedral : 14.798 85.122 2374 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1330 helix: 1.30 (0.19), residues: 700 sheet: -2.44 (0.35), residues: 172 loop : -2.91 (0.23), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 737 HIS 0.008 0.001 HIS B 974 PHE 0.017 0.001 PHE A 680 TYR 0.012 0.001 TYR A 624 ARG 0.004 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 656) hydrogen bonds : angle 4.44964 ( 1818) metal coordination : bond 0.00708 ( 8) metal coordination : angle 1.20367 ( 12) covalent geometry : bond 0.00337 (12270) covalent geometry : angle 0.54534 (16804) *********************** 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 168 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 690 LEU cc_start: 0.8508 (tp) cc_final: 0.8279 (mt) REVERT: A 847 ASN cc_start: 0.8464 (m-40) cc_final: 0.8259 (m-40) REVERT: A 926 MET cc_start: 0.8429 (ptp) cc_final: 0.8103 (ptp) REVERT: B 371 GLU cc_start: 0.8729 (tt0) cc_final: 0.8212 (tp30) REVERT: B 499 LYS cc_start: 0.9183 (mptt) cc_final: 0.8870 (mptt) REVERT: B 520 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8189 (mmmm) REVERT: B 886 MET cc_start: 0.8693 (mtm) cc_final: 0.8464 (mtm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.4601 time to fit residues: 117.3783 Evaluate side-chains 147 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 68 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.088754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.066394 restraints weight = 115526.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.069796 restraints weight = 49198.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.071942 restraints weight = 30016.783| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5910 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= 0.207 Angle : 0.583 5.667 16816 Z= 0.318 Chirality : 0.040 0.171 1954 Planarity : 0.004 0.036 1924 Dihedral : 14.859 86.389 2374 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.22), residues: 1330 helix: 1.30 (0.19), residues: 696 sheet: -2.48 (0.32), residues: 196 loop : -2.94 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1003 HIS 0.009 0.001 HIS B 974 PHE 0.018 0.002 PHE A 680 TYR 0.014 0.002 TYR B 408 ARG 0.005 0.001 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 656) hydrogen bonds : angle 4.54061 ( 1818) metal coordination : bond 0.00913 ( 8) metal coordination : angle 1.37450 ( 12) covalent geometry : bond 0.00423 (12270) covalent geometry : angle 0.58158 (16804) *********************** 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 165 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.789 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 559 MET cc_start: 0.8215 (tpt) cc_final: 0.7724 (tpt) REVERT: A 690 LEU cc_start: 0.8568 (tp) cc_final: 0.8341 (mt) REVERT: A 926 MET cc_start: 0.8468 (ptp) cc_final: 0.8175 (ptp) REVERT: B 465 GLN cc_start: 0.8658 (tp40) cc_final: 0.7916 (tp40) REVERT: B 499 LYS cc_start: 0.9199 (mptt) cc_final: 0.8813 (mptt) REVERT: B 520 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8201 (mmmm) REVERT: B 755 ILE cc_start: 0.7943 (pt) cc_final: 0.7722 (pt) REVERT: B 766 MET cc_start: 0.8101 (ttt) cc_final: 0.7873 (ttt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.4473 time to fit residues: 111.6281 Evaluate side-chains 142 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 111 optimal weight: 0.0000 chunk 66 optimal weight: 0.0670 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.5926 ------------------------------------------------------------------------------- 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 847 ASN ** A 919 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.090327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.067860 restraints weight = 115898.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.071489 restraints weight = 49111.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.073810 restraints weight = 29824.099| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5919 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= 0.121 Angle : 0.531 8.350 16816 Z= 0.284 Chirality : 0.039 0.174 1954 Planarity : 0.003 0.034 1924 Dihedral : 14.627 89.485 2374 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1330 helix: 1.56 (0.19), residues: 700 sheet: -2.21 (0.33), residues: 196 loop : -2.74 (0.25), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 737 HIS 0.008 0.001 HIS B 974 PHE 0.015 0.001 PHE A 680 TYR 0.012 0.001 TYR A 624 ARG 0.005 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 656) hydrogen bonds : angle 4.26026 ( 1818) metal coordination : bond 0.00882 ( 8) metal coordination : angle 3.31472 ( 12) covalent geometry : bond 0.00255 (12270) covalent geometry : angle 0.52353 (16804) *********************** 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 169 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.810 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 462 TYR cc_start: 0.8929 (t80) cc_final: 0.8676 (t80) REVERT: A 559 MET cc_start: 0.8233 (tpt) cc_final: 0.7743 (tpt) REVERT: A 690 LEU cc_start: 0.8557 (tp) cc_final: 0.8345 (mt) REVERT: A 926 MET cc_start: 0.8391 (ptp) cc_final: 0.8080 (ptp) REVERT: B 499 LYS cc_start: 0.9103 (mptt) cc_final: 0.8829 (mptt) REVERT: B 520 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8191 (mmmm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.4584 time to fit residues: 116.2902 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 : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 76 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.090297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068116 restraints weight = 115948.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.071709 restraints weight = 49286.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.073894 restraints weight = 29784.578| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12278 Z= 0.129 Angle : 0.520 6.164 16816 Z= 0.280 Chirality : 0.038 0.165 1954 Planarity : 0.003 0.035 1924 Dihedral : 14.536 87.429 2374 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.23), residues: 1330 helix: 1.64 (0.19), residues: 702 sheet: -2.17 (0.33), residues: 196 loop : -2.71 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 737 HIS 0.007 0.001 HIS B 974 PHE 0.016 0.001 PHE A 680 TYR 0.011 0.001 TYR A 624 ARG 0.004 0.000 ARG A 890 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 656) hydrogen bonds : angle 4.23803 ( 1818) metal coordination : bond 0.00518 ( 8) metal coordination : angle 2.14064 ( 12) covalent geometry : bond 0.00268 (12270) covalent geometry : angle 0.51732 (16804) ********************** 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 165 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.811 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 462 TYR cc_start: 0.8898 (t80) cc_final: 0.8634 (t80) REVERT: A 559 MET cc_start: 0.8184 (tpt) cc_final: 0.7705 (tpt) REVERT: A 690 LEU cc_start: 0.8555 (tp) cc_final: 0.8326 (mt) REVERT: A 926 MET cc_start: 0.8337 (ptp) cc_final: 0.8055 (ptp) REVERT: B 499 LYS cc_start: 0.9082 (mptt) cc_final: 0.8823 (mptt) REVERT: B 520 LYS cc_start: 0.8542 (mmmt) cc_final: 0.8198 (mmmm) REVERT: B 582 TRP cc_start: 0.8202 (t-100) cc_final: 0.7763 (t60) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.4561 time to fit residues: 113.8666 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 : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 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 = 0.3741 r_free = 0.3741 target = 0.091056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068393 restraints weight = 116910.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.072090 restraints weight = 49181.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.074451 restraints weight = 29693.491| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12278 Z= 0.117 Angle : 0.517 6.330 16816 Z= 0.277 Chirality : 0.038 0.220 1954 Planarity : 0.003 0.034 1924 Dihedral : 14.474 85.656 2374 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.09 % Allowed : 0.34 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1330 helix: 1.68 (0.19), residues: 702 sheet: -2.06 (0.34), residues: 196 loop : -2.64 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 582 HIS 0.006 0.001 HIS B 974 PHE 0.015 0.001 PHE A 680 TYR 0.011 0.001 TYR A 624 ARG 0.003 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 656) hydrogen bonds : angle 4.17982 ( 1818) metal coordination : bond 0.00435 ( 8) metal coordination : angle 2.08418 ( 12) covalent geometry : bond 0.00247 (12270) covalent geometry : angle 0.51423 (16804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6890.34 seconds wall clock time: 120 minutes 10.34 seconds (7210.34 seconds total)