Starting phenix.real_space_refine on Fri Aug 7 15:36:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0j_50111/08_2026/9f0j_50111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0j_50111/08_2026/9f0j_50111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9f0j_50111/08_2026/9f0j_50111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0j_50111/08_2026/9f0j_50111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f0j_50111/08_2026/9f0j_50111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0j_50111/08_2026/9f0j_50111.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 60 5.49 5 S 66 5.16 5 C 7116 2.51 5 N 2004 2.21 5 O 2316 1.98 5 H 11172 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22736 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10403 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 20, 'TRANS': 619} Chain breaks: 8 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "X" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 480 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna3p_pur': 7, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Chain: "Z" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 484 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8731 SG CYS A 907 75.791 52.917 82.386 1.00 95.92 S ATOM 8777 SG CYS A 910 79.554 52.913 82.135 1.00111.21 S ATOM 9426 SG CYS A 962 77.813 53.273 85.616 1.00115.12 S ATOM 9458 SG CYS A 964 77.860 56.070 83.087 1.00118.72 S Restraints were copied for chains: B, C, D Time building chain proxies: 14.20, per 1000 atoms: 0.62 Number of scatterers: 22736 At special positions: 0 Unit cell: (99.12, 102.424, 116.466, 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 60 15.00 O 2316 8.00 N 2004 7.00 C 7116 6.00 H 11172 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 448.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " 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 ZN A1101 " - pdb=" SG CYS A 962 " pdb=" ZN B1101 " 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 " pdb="ZN ZN B1101 " - pdb=" SG CYS B 962 " Number of angles added : 12 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2452 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 55.2% alpha, 10.8% beta 30 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 335 through 355 removed outlier: 3.650A pdb=" N VAL A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.603A pdb=" N TYR A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 415 through 427 Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 453 through 476 removed outlier: 3.968A pdb=" N ARG A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 526 through 533 Processing helix chain 'A' and resid 550 through 567 Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.524A pdb=" N GLU A 580 " --> pdb=" O THR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 618 removed outlier: 3.634A pdb=" N THR A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 643 removed outlier: 3.834A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 692 removed outlier: 4.439A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 712 removed outlier: 3.513A pdb=" N GLU A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.614A pdb=" N THR A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 790 through 794 Processing helix chain 'A' and resid 843 through 863 Processing helix chain 'A' and resid 865 through 895 removed outlier: 4.032A pdb=" N GLN A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.580A pdb=" N LYS A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 937 " --> pdb=" O PRO A 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 932 through 937' Processing helix chain 'A' and resid 1002 through 1006 Processing helix chain 'B' and resid 310 through 318 Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 335 through 355 removed outlier: 3.649A pdb=" N VAL B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.602A pdb=" N TYR B 381 " --> pdb=" O GLU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 415 through 427 Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 453 through 476 removed outlier: 3.969A pdb=" N ARG B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 526 through 533 Processing helix chain 'B' and resid 550 through 567 Processing helix chain 'B' and resid 576 through 594 removed outlier: 3.523A pdb=" N GLU B 580 " --> pdb=" O THR B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 618 removed outlier: 3.634A pdb=" N THR B 617 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 643 removed outlier: 3.835A pdb=" N ALA B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 692 removed outlier: 4.438A pdb=" N ASN B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS B 685 " --> pdb=" O PHE B 681 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N MET B 686 " --> pdb=" O ASP B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 712 removed outlier: 3.514A pdb=" N GLU B 710 " --> pdb=" O ASN B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 741 removed outlier: 3.614A pdb=" N THR B 731 " --> pdb=" O THR B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 748 Processing helix chain 'B' and resid 767 through 781 Processing helix chain 'B' and resid 790 through 794 Processing helix chain 'B' and resid 843 through 863 Processing helix chain 'B' and resid 865 through 895 removed outlier: 4.032A pdb=" N GLN B 895 " --> pdb=" O SER B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 937 removed outlier: 3.581A pdb=" N LYS B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 937 " --> pdb=" O PRO B 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 932 through 937' Processing helix chain 'B' and resid 1002 through 1006 Processing sheet with id=1, first strand: chain 'A' and resid 328 through 329 removed outlier: 6.271A pdb=" N ILE A 441 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU A 488 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE A 443 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 364 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE A 389 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR A 414 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 751 through 754 removed outlier: 6.789A pdb=" N HIS A 752 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY A 721 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA A 788 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A 723 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL A 804 " --> pdb=" O VAL A 831 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL A 833 " --> pdb=" O VAL A 804 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG A 806 " --> pdb=" O VAL A 833 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 913 through 916 removed outlier: 6.573A pdb=" N LEU A 905 " --> pdb=" O VAL A 914 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER A 916 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 903 " --> pdb=" O SER A 916 " (cutoff:3.500A) 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: 6.522A pdb=" N ILE A 960 " --> pdb=" O TRP A 968 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 328 through 329 removed outlier: 6.270A pdb=" N ILE B 441 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU B 488 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE B 443 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 364 " --> pdb=" O SER B 413 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE B 389 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR B 414 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 751 through 754 removed outlier: 6.788A pdb=" N HIS B 752 " --> pdb=" O ILE B 787 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY B 721 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA B 788 " --> pdb=" O GLY B 721 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE B 723 " --> pdb=" O ALA B 788 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL B 804 " --> pdb=" O VAL B 831 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL B 833 " --> pdb=" O VAL B 804 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG B 806 " --> pdb=" O VAL B 833 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 913 through 916 removed outlier: 6.573A pdb=" N LEU B 905 " --> pdb=" O VAL B 914 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER B 916 " --> pdb=" O ILE B 903 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 903 " --> pdb=" O SER B 916 " (cutoff:3.500A) 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: 6.521A pdb=" N ILE B 960 " --> pdb=" O TRP B 968 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 2.86 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: 11154 1.03 - 1.23: 36 1.23 - 1.42: 4929 1.42 - 1.62: 6815 1.62 - 1.81: 106 Bond restraints: 23040 Sorted by residual: bond pdb=" NZ LYS A 498 " pdb=" HZ3 LYS A 498 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" NZ LYS B 498 " pdb=" HZ3 LYS B 498 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" NZ LYS A 498 " pdb=" HZ1 LYS A 498 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" NZ LYS A 498 " pdb=" HZ2 LYS A 498 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" NZ LYS B 498 " pdb=" HZ1 LYS B 498 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 23035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 38172 0.98 - 1.96: 3033 1.96 - 2.94: 469 2.94 - 3.92: 108 3.92 - 4.90: 18 Bond angle restraints: 41800 Sorted by residual: angle pdb=" O5' U Z 12 " pdb=" C5' U Z 12 " pdb=" C4' U Z 12 " ideal model delta sigma weight residual 109.40 112.50 -3.10 8.00e-01 1.56e+00 1.50e+01 angle pdb=" O5' C Z 1 " pdb=" C5' C Z 1 " pdb=" C4' C Z 1 " ideal model delta sigma weight residual 109.40 112.47 -3.07 8.00e-01 1.56e+00 1.48e+01 angle pdb=" O5' U D 12 " pdb=" C5' U D 12 " pdb=" C4' U D 12 " ideal model delta sigma weight residual 109.40 112.47 -3.07 8.00e-01 1.56e+00 1.47e+01 angle pdb=" O5' C D 1 " pdb=" C5' C D 1 " pdb=" C4' C D 1 " ideal model delta sigma weight residual 109.40 112.46 -3.06 8.00e-01 1.56e+00 1.47e+01 angle pdb=" O5' U X 11 " pdb=" C5' U X 11 " pdb=" C4' U X 11 " ideal model delta sigma weight residual 109.40 112.22 -2.82 8.00e-01 1.56e+00 1.24e+01 ... (remaining 41795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 9792 17.83 - 35.66: 717 35.66 - 53.49: 137 53.49 - 71.32: 104 71.32 - 89.15: 32 Dihedral angle restraints: 10782 sinusoidal: 6482 harmonic: 4300 Sorted by residual: dihedral pdb=" CA ARG A 375 " pdb=" C ARG A 375 " pdb=" N LYS A 376 " pdb=" CA LYS A 376 " ideal model delta harmonic sigma weight residual 180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA ARG B 375 " pdb=" C ARG B 375 " pdb=" N LYS B 376 " pdb=" CA LYS B 376 " ideal model delta harmonic sigma weight residual -180.00 -163.57 -16.43 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU A 674 " pdb=" CG GLU A 674 " pdb=" CD GLU A 674 " pdb=" OE1 GLU A 674 " ideal model delta sinusoidal sigma weight residual 0.00 87.69 -87.69 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 10779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1165 0.028 - 0.056: 427 0.056 - 0.084: 126 0.084 - 0.112: 115 0.112 - 0.140: 53 Chirality restraints: 1886 Sorted by residual: chirality pdb=" CA VAL B 749 " pdb=" N VAL B 749 " pdb=" C VAL B 749 " pdb=" CB VAL B 749 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA VAL A 749 " pdb=" N VAL A 749 " pdb=" C VAL A 749 " pdb=" CB VAL A 749 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE B 480 " pdb=" N ILE B 480 " pdb=" C ILE B 480 " pdb=" CB ILE B 480 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1883 not shown) Planarity restraints: 3100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 497 " -0.017 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" N LYS B 498 " 0.055 2.00e-02 2.50e+03 pdb=" CA LYS B 498 " -0.013 2.00e-02 2.50e+03 pdb=" H LYS B 498 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 497 " 0.017 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" N LYS A 498 " -0.055 2.00e-02 2.50e+03 pdb=" CA LYS A 498 " 0.013 2.00e-02 2.50e+03 pdb=" H LYS A 498 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 930 " -0.015 2.00e-02 2.50e+03 2.29e-02 7.87e+00 pdb=" CG ASN A 930 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 930 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 930 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN A 930 " 0.035 2.00e-02 2.50e+03 pdb="HD22 ASN A 930 " -0.029 2.00e-02 2.50e+03 ... (remaining 3097 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1186 2.19 - 2.79: 45778 2.79 - 3.40: 60535 3.40 - 4.00: 77825 4.00 - 4.60: 121552 Nonbonded interactions: 306876 Sorted by model distance: nonbonded pdb=" O ARG B 728 " pdb=" HG1 THR B 731 " model vdw 1.589 2.450 nonbonded pdb=" O ARG A 728 " pdb=" HG1 THR A 731 " model vdw 1.589 2.450 nonbonded pdb=" OE1 GLU A 867 " pdb=" H GLU A 867 " model vdw 1.598 2.450 nonbonded pdb=" OE1 GLU B 867 " pdb=" H GLU B 867 " model vdw 1.599 2.450 nonbonded pdb=" OE1 GLU B 934 " pdb=" H GLU B 934 " model vdw 1.623 2.450 ... (remaining 306871 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'X' selection = chain 'C' } ncs_group { reference = chain 'Z' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.430 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: 0.110 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 37.790 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:0.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.004 0.035 11876 Z= 0.225 Angle : 0.578 4.896 16244 Z= 0.390 Chirality : 0.043 0.140 1886 Planarity : 0.004 0.039 1830 Dihedral : 15.045 89.150 4966 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.24), residues: 1244 helix: 1.96 (0.20), residues: 632 sheet: -2.37 (0.36), residues: 180 loop : -1.05 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.012 0.001 TYR B 312 PHE 0.009 0.001 PHE A 551 TRP 0.006 0.001 TRP B 737 HIS 0.002 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.23 (11868) covalent geometry : angle 0.57421 / 0.39 (16232) hydrogen bonds : bond 0.13969 / 9.15 ( 626) hydrogen bonds : angle 5.50141 / 3.77 ( 1722) metal coordination : bond 0.00301 / 0.13 ( 8) metal coordination : angle 2.63998 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.435 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: A 374 PHE cc_start: 0.7570 (t80) cc_final: 0.7337 (t80) REVERT: A 628 GLU cc_start: 0.8037 (tt0) cc_final: 0.7667 (tm-30) REVERT: A 898 ASP cc_start: 0.7669 (m-30) cc_final: 0.7243 (m-30) REVERT: A 1002 LYS cc_start: 0.7807 (mttt) cc_final: 0.7323 (mtmt) REVERT: B 489 THR cc_start: 0.7337 (t) cc_final: 0.6516 (t) REVERT: B 610 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7629 (mt-10) REVERT: B 739 MET cc_start: 0.8743 (tpp) cc_final: 0.8366 (tmm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1971 time to fit residues: 56.9191 Evaluate side-chains 120 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN A 615 ASN A 729 GLN B 476 ASN B 532 GLN B 578 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.123208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.096252 restraints weight = 62734.428| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.72 r_work: 0.3256 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11876 Z= 0.225 Angle : 0.581 8.426 16244 Z= 0.320 Chirality : 0.041 0.191 1886 Planarity : 0.004 0.034 1830 Dihedral : 14.738 73.798 2286 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.96 % Allowed : 5.68 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1244 helix: 1.78 (0.20), residues: 640 sheet: -2.19 (0.35), residues: 184 loop : -1.24 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.014 0.001 TYR A 312 PHE 0.020 0.001 PHE B 551 TRP 0.009 0.002 TRP A 737 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 (11868) covalent geometry : angle 0.56998 / 0.32 (16232) hydrogen bonds : bond 0.04865 / 3.24 ( 626) hydrogen bonds : angle 4.94701 / 3.37 ( 1722) metal coordination : bond 0.00593 / 0.30 ( 8) metal coordination : angle 4.22168 / 2.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.566 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: A 314 MET cc_start: 0.8622 (tpt) cc_final: 0.8394 (tpp) REVERT: A 628 GLU cc_start: 0.7960 (tt0) cc_final: 0.7611 (tm-30) REVERT: A 898 ASP cc_start: 0.7830 (m-30) cc_final: 0.7367 (m-30) REVERT: A 1002 LYS cc_start: 0.7873 (mttt) cc_final: 0.7447 (mtmt) REVERT: B 515 ASP cc_start: 0.7697 (t0) cc_final: 0.7437 (t0) REVERT: B 566 CYS cc_start: 0.8111 (m) cc_final: 0.7625 (t) REVERT: B 739 MET cc_start: 0.8765 (tpp) cc_final: 0.8449 (tmm) REVERT: B 912 MET cc_start: 0.7877 (ptm) cc_final: 0.7481 (ptm) outliers start: 11 outliers final: 6 residues processed: 145 average time/residue: 0.1688 time to fit residues: 38.3376 Evaluate side-chains 112 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1019 CYS Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 834 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 62 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN A 615 ASN A 957 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.121843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.094767 restraints weight = 62085.074| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.86 r_work: 0.3225 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11876 Z= 0.159 Angle : 0.510 6.889 16244 Z= 0.280 Chirality : 0.039 0.215 1886 Planarity : 0.003 0.034 1830 Dihedral : 14.742 73.871 2286 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.87 % Allowed : 7.69 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1244 helix: 1.89 (0.20), residues: 640 sheet: -2.01 (0.36), residues: 184 loop : -1.21 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 619 TYR 0.009 0.001 TYR A 807 PHE 0.018 0.001 PHE B 551 TRP 0.010 0.001 TRP A 737 HIS 0.007 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (11868) covalent geometry : angle 0.50094 / 0.28 (16232) hydrogen bonds : bond 0.04538 / 3.00 ( 626) hydrogen bonds : angle 4.68443 / 3.20 ( 1722) metal coordination : bond 0.00409 / 0.18 ( 8) metal coordination : angle 3.47091 / 1.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.614 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: A 314 MET cc_start: 0.8624 (tpt) cc_final: 0.8365 (tpp) REVERT: A 628 GLU cc_start: 0.7915 (tt0) cc_final: 0.7648 (tm-30) REVERT: A 898 ASP cc_start: 0.7727 (m-30) cc_final: 0.7284 (m-30) REVERT: A 972 MET cc_start: 0.7478 (mtm) cc_final: 0.7269 (mtm) REVERT: A 1002 LYS cc_start: 0.8086 (mttt) cc_final: 0.7620 (mtmt) REVERT: B 515 ASP cc_start: 0.7794 (t0) cc_final: 0.7377 (t0) REVERT: B 566 CYS cc_start: 0.8099 (m) cc_final: 0.7702 (t) REVERT: B 739 MET cc_start: 0.8731 (tpp) cc_final: 0.8435 (tmm) REVERT: B 830 TYR cc_start: 0.7880 (t80) cc_final: 0.7679 (t80) REVERT: B 912 MET cc_start: 0.7914 (ptm) cc_final: 0.7406 (ptm) outliers start: 10 outliers final: 5 residues processed: 118 average time/residue: 0.1699 time to fit residues: 31.8521 Evaluate side-chains 101 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 898 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 121 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 ASN A 994 ASN B 643 ASN B 711 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.118484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089412 restraints weight = 62633.147| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.04 r_work: 0.3134 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11876 Z= 0.220 Angle : 0.556 6.408 16244 Z= 0.304 Chirality : 0.041 0.152 1886 Planarity : 0.004 0.025 1830 Dihedral : 14.613 73.962 2286 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.14 % Allowed : 8.39 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.24), residues: 1244 helix: 1.81 (0.20), residues: 646 sheet: -2.03 (0.36), residues: 184 loop : -1.20 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 619 TYR 0.013 0.001 TYR B 624 PHE 0.016 0.001 PHE B 639 TRP 0.017 0.002 TRP A 968 HIS 0.006 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (11868) covalent geometry : angle 0.54839 / 0.30 (16232) hydrogen bonds : bond 0.04342 / 2.87 ( 626) hydrogen bonds : angle 4.61183 / 3.14 ( 1722) metal coordination : bond 0.00579 / 0.27 ( 8) metal coordination : angle 3.44158 / 1.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 GLU cc_start: 0.7986 (tt0) cc_final: 0.7702 (tm-30) REVERT: A 1002 LYS cc_start: 0.8205 (mttt) cc_final: 0.7735 (mtmt) REVERT: B 314 MET cc_start: 0.8183 (tpt) cc_final: 0.7794 (tpt) REVERT: B 515 ASP cc_start: 0.7990 (t0) cc_final: 0.7543 (t0) REVERT: B 739 MET cc_start: 0.8737 (tpp) cc_final: 0.8380 (tmm) REVERT: B 830 TYR cc_start: 0.8023 (t80) cc_final: 0.7700 (t80) outliers start: 13 outliers final: 9 residues processed: 118 average time/residue: 0.1814 time to fit residues: 32.4505 Evaluate side-chains 104 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1019 CYS Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 961 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 ASN A 475 GLN B 643 ASN B 928 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.120043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.090059 restraints weight = 61640.346| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.74 r_work: 0.3192 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11876 Z= 0.108 Angle : 0.481 5.052 16244 Z= 0.261 Chirality : 0.038 0.142 1886 Planarity : 0.003 0.027 1830 Dihedral : 14.738 73.974 2286 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.44 % Allowed : 9.70 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.24), residues: 1244 helix: 2.15 (0.20), residues: 640 sheet: -1.97 (0.36), residues: 182 loop : -1.11 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 720 TYR 0.009 0.001 TYR A 807 PHE 0.016 0.001 PHE B 639 TRP 0.009 0.001 TRP A 737 HIS 0.006 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (11868) covalent geometry : angle 0.47571 / 0.26 (16232) hydrogen bonds : bond 0.03844 / 2.53 ( 626) hydrogen bonds : angle 4.38710 / 2.99 ( 1722) metal coordination : bond 0.00374 / 0.16 ( 8) metal coordination : angle 2.72965 / 1.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 GLU cc_start: 0.7912 (tt0) cc_final: 0.7654 (tm-30) REVERT: A 1002 LYS cc_start: 0.8127 (mttt) cc_final: 0.7605 (mtmt) REVERT: B 515 ASP cc_start: 0.7934 (t0) cc_final: 0.7451 (t0) REVERT: B 739 MET cc_start: 0.8747 (tpp) cc_final: 0.8393 (tmm) REVERT: B 830 TYR cc_start: 0.7985 (t80) cc_final: 0.7634 (t80) REVERT: B 912 MET cc_start: 0.7912 (ptt) cc_final: 0.7398 (ptm) outliers start: 5 outliers final: 5 residues processed: 102 average time/residue: 0.1787 time to fit residues: 28.2789 Evaluate side-chains 100 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 898 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 62 optimal weight: 0.1980 chunk 97 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 GLN A 475 GLN B 643 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.116877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087940 restraints weight = 62907.301| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.11 r_work: 0.3107 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11876 Z= 0.228 Angle : 0.555 7.485 16244 Z= 0.301 Chirality : 0.040 0.149 1886 Planarity : 0.003 0.026 1830 Dihedral : 14.551 73.918 2286 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.96 % Allowed : 9.62 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.24), residues: 1244 helix: 2.02 (0.20), residues: 646 sheet: -2.02 (0.35), residues: 182 loop : -1.14 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 843 TYR 0.029 0.002 TYR A1018 PHE 0.019 0.002 PHE B 639 TRP 0.011 0.002 TRP A 737 HIS 0.006 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (11868) covalent geometry : angle 0.54771 / 0.30 (16232) hydrogen bonds : bond 0.04228 / 2.79 ( 626) hydrogen bonds : angle 4.43612 / 3.03 ( 1722) metal coordination : bond 0.00509 / 0.24 ( 8) metal coordination : angle 3.40319 / 1.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 628 GLU cc_start: 0.7939 (tt0) cc_final: 0.7716 (tm-30) REVERT: A 1002 LYS cc_start: 0.8220 (mttt) cc_final: 0.7728 (mtmt) REVERT: B 515 ASP cc_start: 0.8086 (t0) cc_final: 0.7627 (t0) REVERT: B 739 MET cc_start: 0.8774 (tpp) cc_final: 0.8423 (tmm) REVERT: B 830 TYR cc_start: 0.8066 (t80) cc_final: 0.7647 (t80) REVERT: B 912 MET cc_start: 0.7990 (ptt) cc_final: 0.7510 (ptm) outliers start: 11 outliers final: 11 residues processed: 102 average time/residue: 0.1733 time to fit residues: 28.0653 Evaluate side-chains 101 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 961 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN B 643 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.118133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087892 restraints weight = 61876.155| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.74 r_work: 0.3156 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11876 Z= 0.126 Angle : 0.486 5.777 16244 Z= 0.263 Chirality : 0.038 0.145 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.705 74.007 2286 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.52 % Allowed : 10.31 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1244 helix: 2.27 (0.20), residues: 640 sheet: -1.95 (0.35), residues: 180 loop : -1.07 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.024 0.001 TYR A1018 PHE 0.021 0.001 PHE B 639 TRP 0.009 0.001 TRP A 737 HIS 0.005 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (11868) covalent geometry : angle 0.48007 / 0.26 (16232) hydrogen bonds : bond 0.03758 / 2.47 ( 626) hydrogen bonds : angle 4.23411 / 2.90 ( 1722) metal coordination : bond 0.00429 / 0.19 ( 8) metal coordination : angle 2.93194 / 1.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 GLU cc_start: 0.7968 (tt0) cc_final: 0.7747 (tm-30) REVERT: A 1002 LYS cc_start: 0.8163 (mttt) cc_final: 0.7658 (mtmt) REVERT: B 515 ASP cc_start: 0.8069 (t0) cc_final: 0.7581 (t0) REVERT: B 739 MET cc_start: 0.8770 (tpp) cc_final: 0.8409 (tmm) REVERT: B 830 TYR cc_start: 0.8091 (t80) cc_final: 0.7569 (t80) REVERT: B 912 MET cc_start: 0.7963 (ptt) cc_final: 0.7465 (ptm) outliers start: 6 outliers final: 6 residues processed: 95 average time/residue: 0.1946 time to fit residues: 29.0510 Evaluate side-chains 96 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 898 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 643 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.118332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.088174 restraints weight = 61617.024| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.74 r_work: 0.3157 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11876 Z= 0.115 Angle : 0.477 8.076 16244 Z= 0.256 Chirality : 0.037 0.139 1886 Planarity : 0.003 0.025 1830 Dihedral : 14.638 73.958 2286 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.52 % Allowed : 10.49 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.25), residues: 1244 helix: 2.44 (0.20), residues: 640 sheet: -1.92 (0.35), residues: 180 loop : -0.97 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 375 TYR 0.025 0.001 TYR A1018 PHE 0.026 0.001 PHE B 639 TRP 0.009 0.001 TRP A 737 HIS 0.006 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (11868) covalent geometry : angle 0.47210 / 0.26 (16232) hydrogen bonds : bond 0.03567 / 2.34 ( 626) hydrogen bonds : angle 4.11216 / 2.82 ( 1722) metal coordination : bond 0.00345 / 0.15 ( 8) metal coordination : angle 2.60863 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 GLU cc_start: 0.7990 (tt0) cc_final: 0.7760 (tm-30) REVERT: A 1002 LYS cc_start: 0.8114 (mttt) cc_final: 0.7615 (mtmt) REVERT: B 314 MET cc_start: 0.8062 (tpt) cc_final: 0.7691 (tpt) REVERT: B 515 ASP cc_start: 0.8103 (t0) cc_final: 0.7566 (t0) REVERT: B 739 MET cc_start: 0.8795 (tpp) cc_final: 0.8409 (tmm) REVERT: B 830 TYR cc_start: 0.8099 (t80) cc_final: 0.7551 (t80) REVERT: B 912 MET cc_start: 0.7900 (ptt) cc_final: 0.7398 (ptm) outliers start: 6 outliers final: 6 residues processed: 100 average time/residue: 0.1764 time to fit residues: 27.8471 Evaluate side-chains 98 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 898 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 118 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 928 HIS B 643 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.116974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086943 restraints weight = 62561.859| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.69 r_work: 0.3135 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11876 Z= 0.152 Angle : 0.503 6.999 16244 Z= 0.272 Chirality : 0.038 0.142 1886 Planarity : 0.003 0.023 1830 Dihedral : 14.603 74.010 2286 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.52 % Allowed : 10.49 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.24), residues: 1244 helix: 2.47 (0.20), residues: 640 sheet: -1.97 (0.35), residues: 180 loop : -0.99 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.020 0.001 TYR A1018 PHE 0.020 0.001 PHE B 639 TRP 0.011 0.001 TRP A 737 HIS 0.006 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (11868) covalent geometry : angle 0.49672 / 0.27 (16232) hydrogen bonds : bond 0.03680 / 2.42 ( 626) hydrogen bonds : angle 4.14428 / 2.84 ( 1722) metal coordination : bond 0.00430 / 0.19 ( 8) metal coordination : angle 2.93843 / 1.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7289 (tttt) REVERT: A 1002 LYS cc_start: 0.8234 (mttt) cc_final: 0.7695 (mtmt) REVERT: B 515 ASP cc_start: 0.8148 (t0) cc_final: 0.7630 (t0) REVERT: B 739 MET cc_start: 0.8783 (tpp) cc_final: 0.8422 (tmm) REVERT: B 830 TYR cc_start: 0.8123 (t80) cc_final: 0.7551 (t80) REVERT: B 912 MET cc_start: 0.7907 (ptt) cc_final: 0.7382 (ptm) outliers start: 6 outliers final: 6 residues processed: 97 average time/residue: 0.1681 time to fit residues: 25.3382 Evaluate side-chains 95 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 898 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.117426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.088166 restraints weight = 62329.305| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.04 r_work: 0.3118 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11876 Z= 0.124 Angle : 0.489 6.889 16244 Z= 0.263 Chirality : 0.038 0.140 1886 Planarity : 0.003 0.026 1830 Dihedral : 14.637 74.014 2286 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.61 % Allowed : 10.66 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.25), residues: 1244 helix: 2.53 (0.20), residues: 640 sheet: -1.92 (0.35), residues: 180 loop : -0.96 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.013 0.001 TYR A1018 PHE 0.028 0.001 PHE B 639 TRP 0.009 0.001 TRP A 737 HIS 0.008 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (11868) covalent geometry : angle 0.48348 / 0.26 (16232) hydrogen bonds : bond 0.03527 / 2.32 ( 626) hydrogen bonds : angle 4.04623 / 2.78 ( 1722) metal coordination : bond 0.00393 / 0.17 ( 8) metal coordination : angle 2.79314 / 1.29 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 LYS cc_start: 0.8193 (mttt) cc_final: 0.7654 (mtmt) REVERT: B 515 ASP cc_start: 0.8177 (t0) cc_final: 0.7651 (t0) REVERT: B 605 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8858 (mt) REVERT: B 739 MET cc_start: 0.8780 (tpp) cc_final: 0.8390 (tmm) REVERT: B 830 TYR cc_start: 0.8143 (t80) cc_final: 0.7534 (t80) REVERT: B 912 MET cc_start: 0.7880 (ptt) cc_final: 0.7346 (ptm) outliers start: 7 outliers final: 6 residues processed: 97 average time/residue: 0.1921 time to fit residues: 28.9935 Evaluate side-chains 95 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 898 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.117526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087314 restraints weight = 62223.401| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.74 r_work: 0.3142 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11876 Z= 0.119 Angle : 0.478 5.540 16244 Z= 0.257 Chirality : 0.037 0.141 1886 Planarity : 0.003 0.023 1830 Dihedral : 14.629 74.005 2286 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.70 % Allowed : 10.75 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1244 helix: 2.58 (0.20), residues: 642 sheet: -1.86 (0.35), residues: 180 loop : -0.87 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.014 0.001 TYR A1018 PHE 0.023 0.001 PHE B 639 TRP 0.009 0.001 TRP A 737 HIS 0.007 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (11868) covalent geometry : angle 0.47294 / 0.26 (16232) hydrogen bonds : bond 0.03446 / 2.27 ( 626) hydrogen bonds : angle 3.99995 / 2.75 ( 1722) metal coordination : bond 0.00382 / 0.17 ( 8) metal coordination : angle 2.67436 / 1.22 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4587.08 seconds wall clock time: 78 minutes 44.46 seconds (4724.46 seconds total)