Starting phenix.real_space_refine on Sat Jul 4 17:56:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0j_50111/07_2026/9f0j_50111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0j_50111/07_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_50111/07_2026/9f0j_50111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0j_50111/07_2026/9f0j_50111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f0j_50111/07_2026/9f0j_50111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0j_50111/07_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-dev-6108/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: 13.74, per 1000 atoms: 0.60 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: 2.14 Conformation dependent library (CDL) restraints added in 547.0 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: 3.89 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: 5.62 Time building geometry restraints manager: 2.89 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: 38351 0.98 - 1.96: 3009 1.96 - 2.94: 318 2.94 - 3.92: 104 3.92 - 4.90: 18 Bond angle restraints: 41800 Sorted by residual: angle pdb=" O4 U D 12 " pdb=" C4 U D 12 " pdb=" C5 U D 12 " ideal model delta sigma weight residual 125.90 124.37 1.53 6.00e-01 2.78e+00 6.54e+00 angle pdb=" O4 U Z 12 " pdb=" C4 U Z 12 " pdb=" C5 U Z 12 " ideal model delta sigma weight residual 125.90 124.38 1.52 6.00e-01 2.78e+00 6.45e+00 angle pdb=" C1' G Z 13 " pdb=" N9 G Z 13 " pdb=" C4 G Z 13 " ideal model delta sigma weight residual 126.50 123.37 3.13 1.30e+00 5.92e-01 5.81e+00 angle pdb=" C VAL B 749 " pdb=" CA VAL B 749 " pdb=" CB VAL B 749 " ideal model delta sigma weight residual 111.23 108.66 2.57 1.08e+00 8.57e-01 5.67e+00 angle pdb=" C1' G D 13 " pdb=" N9 G D 13 " pdb=" C4 G D 13 " ideal model delta sigma weight residual 126.50 123.41 3.09 1.30e+00 5.92e-01 5.65e+00 ... (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: 1206 0.028 - 0.056: 448 0.056 - 0.084: 124 0.084 - 0.112: 72 0.112 - 0.140: 36 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: 0.03 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: 1.510 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: 0.190 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 40.170 Find NCS groups from input model: 0.170 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.700 ------------------------------------------------------------------------------- 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= 0.215 Angle : 0.530 4.896 16244 Z= 0.333 Chirality : 0.038 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 0.00392 / 0.22 (11868) covalent geometry : angle 0.52525 / 0.33 (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 : 0.556 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: 0.7244 (m-30) REVERT: A 1002 LYS cc_start: 0.7807 (mttt) cc_final: 0.7317 (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: 0.7628 (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: 0.2185 time to fit residues: 63.1193 Evaluate side-chains 119 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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: 10.0000 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: 10.0000 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 643 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.122969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.095396 restraints weight = 62724.037| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.80 r_work: 0.3247 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11876 Z= 0.224 Angle : 0.575 8.304 16244 Z= 0.313 Chirality : 0.042 0.199 1886 Planarity : 0.004 0.034 1830 Dihedral : 14.742 73.759 2286 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.96 % Allowed : 5.77 % Favored : 93.27 % 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: 0.25 (0.24), residues: 1244 helix: 1.80 (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 0.004 0.000 ARG B 806 TYR 0.015 0.002 TYR B1018 PHE 0.023 0.002 PHE B 639 TRP 0.009 0.002 TRP A 737 HIS 0.006 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (11868) covalent geometry : angle 0.56358 / 0.31 (16232) hydrogen bonds : bond 0.05068 / 3.37 ( 626) hydrogen bonds : angle 4.90292 / 3.34 ( 1722) metal coordination : bond 0.00524 / 0.26 ( 8) metal coordination : angle 4.16396 / 1.99 ( 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 146 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.673 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: A 314 MET cc_start: 0.8633 (tpt) cc_final: 0.8391 (tpp) REVERT: A 628 GLU cc_start: 0.7972 (tt0) cc_final: 0.7618 (tm-30) REVERT: A 898 ASP cc_start: 0.7847 (m-30) cc_final: 0.7381 (m-30) REVERT: A 1002 LYS cc_start: 0.7917 (mttt) cc_final: 0.7533 (mtpt) REVERT: B 515 ASP cc_start: 0.7684 (t0) cc_final: 0.7422 (t0) REVERT: B 566 CYS cc_start: 0.8104 (m) cc_final: 0.7611 (t) REVERT: B 739 MET cc_start: 0.8758 (tpp) cc_final: 0.8443 (tmm) outliers start: 11 outliers final: 6 residues processed: 143 average time/residue: 0.1763 time to fit residues: 39.0875 Evaluate side-chains 115 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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: 0.9990 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN B 643 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.122682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.095734 restraints weight = 62082.480| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.85 r_work: 0.3245 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11876 Z= 0.136 Angle : 0.493 6.721 16244 Z= 0.267 Chirality : 0.039 0.196 1886 Planarity : 0.003 0.032 1830 Dihedral : 14.781 73.799 2286 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.79 % Allowed : 7.60 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1244 helix: 1.94 (0.20), residues: 640 sheet: -2.03 (0.35), residues: 184 loop : -1.17 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 596 TYR 0.008 0.001 TYR B 939 PHE 0.018 0.001 PHE B 551 TRP 0.009 0.001 TRP A 737 HIS 0.007 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (11868) covalent geometry : angle 0.48427 / 0.27 (16232) hydrogen bonds : bond 0.04448 / 2.94 ( 626) hydrogen bonds : angle 4.66855 / 3.19 ( 1722) metal coordination : bond 0.00370 / 0.16 ( 8) metal coordination : angle 3.42810 / 1.65 ( 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: 9 poor density : 112 time to evaluate : 0.427 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 628 GLU cc_start: 0.7945 (tt0) cc_final: 0.7648 (tm-30) REVERT: A 898 ASP cc_start: 0.7745 (m-30) cc_final: 0.7308 (m-30) REVERT: A 932 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.7844 (p) REVERT: A 1002 LYS cc_start: 0.7960 (mttt) cc_final: 0.7498 (mtmt) REVERT: B 515 ASP cc_start: 0.7775 (t0) cc_final: 0.7364 (t0) REVERT: B 566 CYS cc_start: 0.8089 (m) cc_final: 0.7695 (t) REVERT: B 739 MET cc_start: 0.8721 (tpp) cc_final: 0.8419 (tmm) REVERT: B 912 MET cc_start: 0.7906 (ptm) cc_final: 0.7415 (ptm) outliers start: 9 outliers final: 4 residues processed: 118 average time/residue: 0.1872 time to fit residues: 34.4687 Evaluate side-chains 102 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 932 THR Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 121 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 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: 10.0000 chunk 81 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 ASN A 500 GLN B 711 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.119156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.090172 restraints weight = 63094.590| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.07 r_work: 0.3149 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11876 Z= 0.231 Angle : 0.560 9.970 16244 Z= 0.304 Chirality : 0.041 0.153 1886 Planarity : 0.004 0.026 1830 Dihedral : 14.619 73.862 2286 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.31 % Allowed : 7.87 % Favored : 90.82 % 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: 0.37 (0.24), residues: 1244 helix: 1.82 (0.20), residues: 646 sheet: -2.01 (0.36), residues: 184 loop : -1.16 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 619 TYR 0.013 0.001 TYR A 312 PHE 0.020 0.001 PHE B 639 TRP 0.011 0.002 TRP A 737 HIS 0.007 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (11868) covalent geometry : angle 0.55186 / 0.30 (16232) hydrogen bonds : bond 0.04442 / 2.94 ( 626) hydrogen bonds : angle 4.66256 / 3.18 ( 1722) metal coordination : bond 0.00544 / 0.26 ( 8) metal coordination : angle 3.61195 / 1.70 ( 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 123 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 GLU cc_start: 0.7989 (tt0) cc_final: 0.7687 (tm-30) REVERT: A 932 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.7970 (p) REVERT: A 959 GLU cc_start: 0.7189 (tt0) cc_final: 0.6782 (tt0) REVERT: A 1002 LYS cc_start: 0.8176 (mttt) cc_final: 0.7708 (mtmt) REVERT: B 314 MET cc_start: 0.8186 (tpt) cc_final: 0.7800 (tpt) REVERT: B 515 ASP cc_start: 0.7951 (t0) cc_final: 0.7497 (t0) REVERT: B 739 MET cc_start: 0.8759 (tpp) cc_final: 0.8467 (tmm) REVERT: B 912 MET cc_start: 0.7975 (ptm) cc_final: 0.7467 (ptm) outliers start: 15 outliers final: 10 residues processed: 119 average time/residue: 0.1883 time to fit residues: 34.4274 Evaluate side-chains 109 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 932 THR 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 898 ASP 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: 2.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN B 928 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.120789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.092162 restraints weight = 61668.200| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.10 r_work: 0.3192 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11876 Z= 0.106 Angle : 0.479 5.265 16244 Z= 0.257 Chirality : 0.038 0.144 1886 Planarity : 0.003 0.027 1830 Dihedral : 14.776 73.892 2286 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.52 % Allowed : 9.18 % Favored : 90.30 % 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: 0.67 (0.24), residues: 1244 helix: 2.13 (0.20), residues: 640 sheet: -1.91 (0.36), residues: 182 loop : -1.07 (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 0.005 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (11868) covalent geometry : angle 0.47229 / 0.26 (16232) hydrogen bonds : bond 0.03838 / 2.54 ( 626) hydrogen bonds : angle 4.42254 / 3.02 ( 1722) metal coordination : bond 0.00370 / 0.16 ( 8) metal coordination : angle 2.89871 / 1.36 ( 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 106 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.693 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: 0.8549 (tpp) cc_final: 0.8173 (tpp) REVERT: A 628 GLU cc_start: 0.8021 (tt0) cc_final: 0.7704 (tm-30) REVERT: A 932 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8029 (p) REVERT: A 1002 LYS cc_start: 0.8104 (mttt) cc_final: 0.7608 (mtmt) REVERT: B 515 ASP cc_start: 0.7900 (t0) cc_final: 0.7449 (t0) REVERT: B 739 MET cc_start: 0.8730 (tpp) cc_final: 0.8363 (tmm) REVERT: B 912 MET cc_start: 0.7938 (ptm) cc_final: 0.7461 (ptm) outliers start: 6 outliers final: 3 residues processed: 104 average time/residue: 0.2173 time to fit residues: 34.7282 Evaluate side-chains 99 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 932 THR 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: 0.7980 chunk 67 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 GLN A 469 ASN B 643 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.118797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088564 restraints weight = 62547.594| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.76 r_work: 0.3164 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11876 Z= 0.171 Angle : 0.500 6.084 16244 Z= 0.270 Chirality : 0.039 0.144 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.609 73.883 2286 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.14 % Allowed : 8.65 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1244 helix: 2.14 (0.20), residues: 646 sheet: -1.96 (0.36), residues: 184 loop : -1.00 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.009 0.001 TYR B 939 PHE 0.017 0.001 PHE B 639 TRP 0.010 0.001 TRP A 737 HIS 0.012 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (11868) covalent geometry : angle 0.49302 / 0.27 (16232) hydrogen bonds : bond 0.03916 / 2.59 ( 626) hydrogen bonds : angle 4.38095 / 2.99 ( 1722) metal coordination : bond 0.00441 / 0.20 ( 8) metal coordination : angle 3.12265 / 1.46 ( 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 113 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 GLU cc_start: 0.7949 (tt0) cc_final: 0.7687 (tm-30) REVERT: A 932 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8137 (p) REVERT: A 1002 LYS cc_start: 0.8126 (mttt) cc_final: 0.7623 (mtmt) REVERT: B 314 MET cc_start: 0.8092 (tpt) cc_final: 0.7745 (tpt) REVERT: B 515 ASP cc_start: 0.7965 (t0) cc_final: 0.7500 (t0) REVERT: B 739 MET cc_start: 0.8753 (tpp) cc_final: 0.8393 (tmm) REVERT: B 912 MET cc_start: 0.7947 (ptm) cc_final: 0.7443 (ptm) outliers start: 13 outliers final: 10 residues processed: 109 average time/residue: 0.2023 time to fit residues: 34.4430 Evaluate side-chains 107 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 932 THR Chi-restraints excluded: chain A residue 972 MET 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 961 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 927 HIS ** 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 = 0.3776 r_free = 0.3776 target = 0.117073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088206 restraints weight = 62301.204| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.06 r_work: 0.3113 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11876 Z= 0.185 Angle : 0.524 6.575 16244 Z= 0.284 Chirality : 0.040 0.149 1886 Planarity : 0.003 0.027 1830 Dihedral : 14.675 74.031 2286 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.96 % Allowed : 9.44 % Favored : 89.60 % 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: 0.67 (0.24), residues: 1244 helix: 2.11 (0.20), residues: 646 sheet: -1.99 (0.36), residues: 180 loop : -1.07 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.045 0.002 TYR A1018 PHE 0.021 0.002 PHE B 639 TRP 0.010 0.002 TRP A 737 HIS 0.005 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (11868) covalent geometry : angle 0.51582 / 0.28 (16232) hydrogen bonds : bond 0.03953 / 2.60 ( 626) hydrogen bonds : angle 4.34460 / 2.97 ( 1722) metal coordination : bond 0.00542 / 0.25 ( 8) metal coordination : angle 3.44116 / 1.63 ( 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 103 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.685 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: 0.7759 (tm-30) REVERT: A 932 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 1002 LYS cc_start: 0.8214 (mttt) cc_final: 0.7673 (mtmt) REVERT: B 515 ASP cc_start: 0.8129 (t0) cc_final: 0.7647 (t0) REVERT: B 605 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8457 (mt) REVERT: B 739 MET cc_start: 0.8778 (tpp) cc_final: 0.8413 (tmm) REVERT: B 912 MET cc_start: 0.8011 (ptm) cc_final: 0.7494 (ptm) outliers start: 11 outliers final: 8 residues processed: 100 average time/residue: 0.2033 time to fit residues: 31.7277 Evaluate side-chains 99 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 932 THR Chi-restraints excluded: chain A residue 981 CYS 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 834 THR Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 961 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN A 928 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.115865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086841 restraints weight = 62074.275| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.01 r_work: 0.3091 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11876 Z= 0.201 Angle : 0.534 8.513 16244 Z= 0.287 Chirality : 0.040 0.149 1886 Planarity : 0.003 0.027 1830 Dihedral : 14.596 73.932 2286 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.05 % Allowed : 9.53 % 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: 0.71 (0.24), residues: 1244 helix: 2.15 (0.20), residues: 646 sheet: -2.01 (0.35), residues: 180 loop : -1.03 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.013 0.001 TYR B1018 PHE 0.022 0.001 PHE B 639 TRP 0.011 0.001 TRP A 737 HIS 0.004 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (11868) covalent geometry : angle 0.52599 / 0.29 (16232) hydrogen bonds : bond 0.03974 / 2.62 ( 626) hydrogen bonds : angle 4.28069 / 2.94 ( 1722) metal coordination : bond 0.00535 / 0.26 ( 8) metal coordination : angle 3.42987 / 1.64 ( 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 100 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8290 (t) REVERT: A 972 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6985 (mtt) REVERT: A 1002 LYS cc_start: 0.8210 (mttt) cc_final: 0.7675 (mtmt) REVERT: B 515 ASP cc_start: 0.8166 (t0) cc_final: 0.7643 (t0) REVERT: B 605 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8504 (mt) REVERT: B 739 MET cc_start: 0.8799 (tpp) cc_final: 0.8410 (tmm) REVERT: B 912 MET cc_start: 0.8011 (ptm) cc_final: 0.7494 (ptm) outliers start: 12 outliers final: 8 residues processed: 96 average time/residue: 0.2068 time to fit residues: 30.9671 Evaluate side-chains 97 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 932 THR Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain A residue 981 CYS 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 834 THR Chi-restraints excluded: chain B residue 961 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.116665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086228 restraints weight = 62335.311| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.75 r_work: 0.3124 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11876 Z= 0.139 Angle : 0.500 6.326 16244 Z= 0.269 Chirality : 0.039 0.146 1886 Planarity : 0.003 0.026 1830 Dihedral : 14.678 73.998 2286 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.79 % Allowed : 9.88 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.24), residues: 1244 helix: 2.32 (0.20), residues: 640 sheet: -2.00 (0.35), residues: 180 loop : -1.03 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.015 0.001 TYR A1018 PHE 0.020 0.001 PHE B 639 TRP 0.010 0.001 TRP A 737 HIS 0.003 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (11868) covalent geometry : angle 0.49270 / 0.27 (16232) hydrogen bonds : bond 0.03739 / 2.46 ( 626) hydrogen bonds : angle 4.17640 / 2.87 ( 1722) metal coordination : bond 0.00473 / 0.22 ( 8) metal coordination : angle 3.11193 / 1.46 ( 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 99 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8258 (t) REVERT: A 1002 LYS cc_start: 0.8221 (mttt) cc_final: 0.7685 (mtmt) REVERT: B 515 ASP cc_start: 0.8139 (t0) cc_final: 0.7614 (t0) REVERT: B 567 GLN cc_start: 0.8272 (mp10) cc_final: 0.8066 (mp10) REVERT: B 605 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8518 (mt) REVERT: B 739 MET cc_start: 0.8817 (tpp) cc_final: 0.8413 (tmm) REVERT: B 912 MET cc_start: 0.8011 (ptm) cc_final: 0.7589 (ptm) outliers start: 9 outliers final: 7 residues processed: 97 average time/residue: 0.2069 time to fit residues: 31.2788 Evaluate side-chains 96 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 932 THR Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 981 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 643 ASN B 930 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.117773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087522 restraints weight = 62076.853| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.75 r_work: 0.3149 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11876 Z= 0.105 Angle : 0.480 6.797 16244 Z= 0.254 Chirality : 0.038 0.141 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.696 73.963 2286 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.87 % Allowed : 10.05 % Favored : 89.07 % 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: 1.09 (0.25), residues: 1244 helix: 2.52 (0.20), residues: 640 sheet: -1.93 (0.35), residues: 180 loop : -0.86 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 461 TYR 0.011 0.001 TYR A1018 PHE 0.025 0.001 PHE B 639 TRP 0.009 0.001 TRP A 737 HIS 0.004 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (11868) covalent geometry : angle 0.47445 / 0.25 (16232) hydrogen bonds : bond 0.03432 / 2.26 ( 626) hydrogen bonds : angle 4.03390 / 2.77 ( 1722) metal coordination : bond 0.00364 / 0.15 ( 8) metal coordination : angle 2.61794 / 1.18 ( 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 105 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8267 (t) REVERT: A 959 GLU cc_start: 0.7331 (tt0) cc_final: 0.7002 (tt0) REVERT: A 1002 LYS cc_start: 0.8139 (mttt) cc_final: 0.7612 (mtmt) REVERT: B 515 ASP cc_start: 0.8149 (t0) cc_final: 0.7634 (t0) REVERT: B 605 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8869 (mt) REVERT: B 739 MET cc_start: 0.8798 (tpp) cc_final: 0.8397 (tmm) REVERT: B 912 MET cc_start: 0.7963 (ptm) cc_final: 0.7569 (ptm) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.2052 time to fit residues: 33.0242 Evaluate side-chains 94 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 932 THR Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 981 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 66 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 683 ASN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.117455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087175 restraints weight = 62507.989| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.76 r_work: 0.3137 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11876 Z= 0.120 Angle : 0.480 7.906 16244 Z= 0.257 Chirality : 0.038 0.140 1886 Planarity : 0.003 0.023 1830 Dihedral : 14.634 73.968 2286 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.70 % Allowed : 10.49 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1244 helix: 2.56 (0.20), residues: 642 sheet: -1.92 (0.35), residues: 180 loop : -0.80 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.011 0.001 TYR A1018 PHE 0.023 0.001 PHE B 639 TRP 0.010 0.001 TRP A 737 HIS 0.003 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (11868) covalent geometry : angle 0.47447 / 0.26 (16232) hydrogen bonds : bond 0.03416 / 2.24 ( 626) hydrogen bonds : angle 4.01575 / 2.76 ( 1722) metal coordination : bond 0.00382 / 0.16 ( 8) metal coordination : angle 2.71333 / 1.23 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4857.02 seconds wall clock time: 83 minutes 40.96 seconds (5020.96 seconds total)