Starting phenix.real_space_refine on Thu Jun 19 13:41:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0j_50111/06_2025/9f0j_50111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0j_50111/06_2025/9f0j_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9f0j_50111/06_2025/9f0j_50111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0j_50111/06_2025/9f0j_50111.map" model { file = "/net/cci-nas-00/data/ceres_data/9f0j_50111/06_2025/9f0j_50111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0j_50111/06_2025/9f0j_50111.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" 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: "D" 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} 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: X, Z, B Time building chain proxies: 32.15, per 1000 atoms: 1.41 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: 6.27 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 9.79 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: 8.72 Time building geometry restraints manager: 7.49 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=" 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=" C VAL A 749 " pdb=" CA VAL A 749 " pdb=" CB VAL A 749 " ideal model delta sigma weight residual 111.23 108.68 2.55 1.08e+00 8.57e-01 5.59e+00 angle pdb=" N LYS B 498 " pdb=" CA LYS B 498 " pdb=" C LYS B 498 " ideal model delta sigma weight residual 114.12 110.87 3.25 1.39e+00 5.18e-01 5.46e+00 angle pdb=" N LYS A 498 " pdb=" CA LYS A 498 " pdb=" C LYS A 498 " ideal model delta sigma weight residual 114.12 110.92 3.20 1.39e+00 5.18e-01 5.30e+00 angle pdb=" O ALA B 497 " pdb=" C ALA B 497 " pdb=" N LYS B 498 " ideal model delta sigma weight residual 123.29 120.71 2.58 1.18e+00 7.18e-01 4.78e+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: 0.06 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'X' } ncs_group { reference = chain 'D' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.470 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: 0.420 Extract box with map and model: 0.970 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 87.010 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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= 0.187 Angle : 0.530 4.896 16244 Z= 0.294 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (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 TRP 0.006 0.001 TRP B 737 HIS 0.002 0.001 HIS A 927 PHE 0.009 0.001 PHE A 551 TYR 0.012 0.001 TYR B 312 ARG 0.002 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.13969 ( 626) hydrogen bonds : angle 5.50141 ( 1722) metal coordination : bond 0.00301 ( 8) metal coordination : angle 2.63998 ( 12) covalent geometry : bond 0.00391 (11868) covalent geometry : angle 0.52528 (16232) *********************** 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 : 1.822 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: 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: 0.5148 time to fit residues: 147.6973 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 : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.0370 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN B 476 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 = 0.3862 r_free = 0.3862 target = 0.122822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.094416 restraints weight = 62124.078| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.00 r_work: 0.3217 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2256 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= 0.145 Angle : 0.523 6.874 16244 Z= 0.275 Chirality : 0.039 0.150 1886 Planarity : 0.003 0.030 1830 Dihedral : 14.700 73.865 2286 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.87 % Allowed : 6.03 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.24), residues: 1244 helix: 2.17 (0.20), residues: 640 sheet: -2.08 (0.35), residues: 182 loop : -1.08 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1003 HIS 0.007 0.001 HIS B 578 PHE 0.019 0.001 PHE B 551 TYR 0.014 0.001 TYR B 807 ARG 0.003 0.000 ARG B 596 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 626) hydrogen bonds : angle 4.40772 ( 1722) metal coordination : bond 0.00430 ( 8) metal coordination : angle 3.48274 ( 12) covalent geometry : bond 0.00316 (11868) covalent geometry : angle 0.51477 (16232) *********************** 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 151 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.693 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 MET cc_start: 0.8597 (tpt) cc_final: 0.8367 (tpp) REVERT: A 628 GLU cc_start: 0.7985 (tt0) cc_final: 0.7651 (tm-30) REVERT: A 898 ASP cc_start: 0.7810 (m-30) cc_final: 0.7371 (m-30) REVERT: A 1002 LYS cc_start: 0.7994 (mttt) cc_final: 0.7525 (mtmt) REVERT: B 515 ASP cc_start: 0.7824 (t0) cc_final: 0.7510 (t0) REVERT: B 739 MET cc_start: 0.8767 (tpp) cc_final: 0.8436 (tmm) REVERT: B 830 TYR cc_start: 0.7975 (t80) cc_final: 0.7657 (t80) outliers start: 10 outliers final: 6 residues processed: 150 average time/residue: 0.4363 time to fit residues: 98.6405 Evaluate side-chains 117 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 1019 CYS Chi-restraints excluded: chain B residue 540 PHE 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 24 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 928 HIS A 994 ASN B 532 GLN B 643 ASN B 711 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.116347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086038 restraints weight = 61867.371| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.73 r_work: 0.3116 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3825 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= 0.200 Angle : 0.577 7.711 16244 Z= 0.303 Chirality : 0.041 0.164 1886 Planarity : 0.003 0.026 1830 Dihedral : 14.684 73.982 2286 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.22 % Allowed : 8.13 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1244 helix: 2.02 (0.20), residues: 646 sheet: -2.01 (0.35), residues: 180 loop : -0.93 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 737 HIS 0.008 0.001 HIS B 927 PHE 0.017 0.002 PHE B 551 TYR 0.018 0.002 TYR B 624 ARG 0.004 0.001 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 626) hydrogen bonds : angle 4.34830 ( 1722) metal coordination : bond 0.00579 ( 8) metal coordination : angle 3.70286 ( 12) covalent geometry : bond 0.00443 (11868) covalent geometry : angle 0.56876 (16232) *********************** 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 123 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 THR cc_start: 0.9368 (m) cc_final: 0.8973 (p) REVERT: A 571 MET cc_start: 0.7690 (tpt) cc_final: 0.7487 (tpt) REVERT: A 701 LEU cc_start: 0.6918 (tp) cc_final: 0.6642 (tp) REVERT: A 959 GLU cc_start: 0.7518 (tt0) cc_final: 0.7168 (tt0) REVERT: A 1002 LYS cc_start: 0.8272 (mttt) cc_final: 0.7763 (mtmt) REVERT: B 515 ASP cc_start: 0.8143 (t0) cc_final: 0.7634 (t0) REVERT: B 566 CYS cc_start: 0.7964 (m) cc_final: 0.7750 (t) REVERT: B 620 MET cc_start: 0.8146 (pmm) cc_final: 0.7815 (ptp) REVERT: B 739 MET cc_start: 0.8817 (tpp) cc_final: 0.8383 (tmm) REVERT: B 830 TYR cc_start: 0.8104 (t80) cc_final: 0.7580 (t80) outliers start: 14 outliers final: 10 residues processed: 120 average time/residue: 0.4544 time to fit residues: 81.6707 Evaluate side-chains 104 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 709 LEU 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 540 PHE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 121 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN A 683 ASN 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 = 0.3782 r_free = 0.3782 target = 0.117389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087201 restraints weight = 62350.264| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.74 r_work: 0.3143 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11876 Z= 0.124 Angle : 0.488 5.889 16244 Z= 0.253 Chirality : 0.038 0.143 1886 Planarity : 0.003 0.023 1830 Dihedral : 14.616 73.959 2286 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.79 % Allowed : 9.70 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1244 helix: 2.44 (0.20), residues: 642 sheet: -1.90 (0.36), residues: 180 loop : -0.93 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.003 0.001 HIS A 447 PHE 0.013 0.001 PHE B 551 TYR 0.009 0.001 TYR B 939 ARG 0.002 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 626) hydrogen bonds : angle 4.06830 ( 1722) metal coordination : bond 0.00391 ( 8) metal coordination : angle 2.87940 ( 12) covalent geometry : bond 0.00268 (11868) covalent geometry : angle 0.48206 (16232) *********************** 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 107 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 701 LEU cc_start: 0.6868 (tp) cc_final: 0.6596 (tp) REVERT: A 1002 LYS cc_start: 0.8212 (mttt) cc_final: 0.7704 (mtmt) REVERT: B 475 GLN cc_start: 0.8042 (mp10) cc_final: 0.7802 (tt0) REVERT: B 515 ASP cc_start: 0.8179 (t0) cc_final: 0.7710 (t0) REVERT: B 620 MET cc_start: 0.8133 (pmm) cc_final: 0.7811 (ptp) REVERT: B 739 MET cc_start: 0.8866 (tpp) cc_final: 0.8401 (tmm) REVERT: B 830 TYR cc_start: 0.8134 (t80) cc_final: 0.7503 (t80) REVERT: B 961 ILE cc_start: 0.9120 (pt) cc_final: 0.8724 (mm) outliers start: 9 outliers final: 7 residues processed: 106 average time/residue: 0.6546 time to fit residues: 107.5680 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 : 2.171 ------------------------------------------------------------------------------- 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 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 982 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 45 optimal weight: 0.2980 chunk 106 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN A 469 ASN A 475 GLN B 643 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.113895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.084891 restraints weight = 62536.021| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.01 r_work: 0.3053 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11876 Z= 0.189 Angle : 0.545 7.629 16244 Z= 0.285 Chirality : 0.039 0.147 1886 Planarity : 0.003 0.026 1830 Dihedral : 14.633 74.014 2286 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.05 % Allowed : 10.93 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.24), residues: 1244 helix: 2.30 (0.20), residues: 646 sheet: -1.87 (0.36), residues: 180 loop : -0.94 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 737 HIS 0.005 0.001 HIS A 447 PHE 0.015 0.001 PHE A 639 TYR 0.013 0.002 TYR A1018 ARG 0.004 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 626) hydrogen bonds : angle 4.15491 ( 1722) metal coordination : bond 0.00590 ( 8) metal coordination : angle 4.22606 ( 12) covalent geometry : bond 0.00414 (11868) covalent geometry : angle 0.53286 (16232) *********************** 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 110 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 LEU cc_start: 0.6997 (tp) cc_final: 0.6715 (tp) REVERT: A 847 ASN cc_start: 0.7576 (OUTLIER) cc_final: 0.7166 (m110) REVERT: A 1002 LYS cc_start: 0.8337 (mttt) cc_final: 0.7840 (mtmt) REVERT: B 515 ASP cc_start: 0.8336 (t0) cc_final: 0.7880 (t0) REVERT: B 620 MET cc_start: 0.8266 (pmm) cc_final: 0.7955 (ptp) REVERT: B 739 MET cc_start: 0.8864 (tpp) cc_final: 0.8436 (tmm) REVERT: B 912 MET cc_start: 0.7868 (ptt) cc_final: 0.7572 (ptt) outliers start: 12 outliers final: 7 residues processed: 106 average time/residue: 0.7020 time to fit residues: 113.8267 Evaluate side-chains 95 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 2.834 ------------------------------------------------------------------------------- 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 846 VAL Chi-restraints excluded: chain A residue 847 ASN 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 961 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN A 706 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.110197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.081885 restraints weight = 62867.204| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.85 r_work: 0.3007 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11876 Z= 0.229 Angle : 0.569 8.468 16244 Z= 0.298 Chirality : 0.041 0.150 1886 Planarity : 0.003 0.027 1830 Dihedral : 14.675 73.956 2286 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.05 % Allowed : 11.45 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1244 helix: 2.11 (0.20), residues: 646 sheet: -2.15 (0.34), residues: 180 loop : -0.99 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 737 HIS 0.005 0.001 HIS A 447 PHE 0.012 0.002 PHE A1010 TYR 0.017 0.002 TYR B1000 ARG 0.004 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 626) hydrogen bonds : angle 4.22404 ( 1722) metal coordination : bond 0.00690 ( 8) metal coordination : angle 4.24619 ( 12) covalent geometry : bond 0.00497 (11868) covalent geometry : angle 0.55733 (16232) *********************** 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 105 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7877 (tttt) REVERT: A 701 LEU cc_start: 0.7091 (tp) cc_final: 0.6833 (tp) REVERT: A 1002 LYS cc_start: 0.8389 (mttt) cc_final: 0.7870 (mtmt) REVERT: B 515 ASP cc_start: 0.8422 (t0) cc_final: 0.7978 (t0) REVERT: B 620 MET cc_start: 0.8361 (pmm) cc_final: 0.7865 (ptp) REVERT: B 739 MET cc_start: 0.8845 (tpp) cc_final: 0.8447 (tmm) REVERT: B 912 MET cc_start: 0.7832 (ptt) cc_final: 0.7500 (ptt) outliers start: 12 outliers final: 11 residues processed: 102 average time/residue: 0.4006 time to fit residues: 65.1340 Evaluate side-chains 96 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 982 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.112616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.084101 restraints weight = 62781.695| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.95 r_work: 0.3051 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5601 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= 0.120 Angle : 0.484 5.453 16244 Z= 0.251 Chirality : 0.038 0.143 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.625 73.860 2286 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.87 % Allowed : 11.98 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1244 helix: 2.50 (0.20), residues: 652 sheet: -2.07 (0.34), residues: 180 loop : -1.05 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.005 0.001 HIS B 927 PHE 0.012 0.001 PHE B 551 TYR 0.010 0.001 TYR B1000 ARG 0.002 0.000 ARG B1009 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 626) hydrogen bonds : angle 3.91635 ( 1722) metal coordination : bond 0.00444 ( 8) metal coordination : angle 2.94161 ( 12) covalent geometry : bond 0.00260 (11868) covalent geometry : angle 0.47779 (16232) *********************** 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 106 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1002 LYS cc_start: 0.8369 (mttt) cc_final: 0.7890 (mtmt) REVERT: B 515 ASP cc_start: 0.8382 (t0) cc_final: 0.7827 (t0) REVERT: B 559 MET cc_start: 0.8540 (mtp) cc_final: 0.8319 (mtp) REVERT: B 712 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7330 (t80) REVERT: B 739 MET cc_start: 0.8821 (tpp) cc_final: 0.8429 (tmm) REVERT: B 912 MET cc_start: 0.7725 (ptt) cc_final: 0.7387 (ptt) outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 0.4159 time to fit residues: 67.6160 Evaluate side-chains 92 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 846 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 982 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.082231 restraints weight = 62359.463| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.58 r_work: 0.3054 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.5779 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= 0.151 Angle : 0.499 5.726 16244 Z= 0.260 Chirality : 0.038 0.142 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.606 73.946 2286 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.31 % Allowed : 11.89 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1244 helix: 2.56 (0.20), residues: 646 sheet: -2.00 (0.34), residues: 180 loop : -1.07 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 737 HIS 0.009 0.001 HIS A 927 PHE 0.011 0.001 PHE B 551 TYR 0.011 0.001 TYR B 624 ARG 0.002 0.000 ARG B 942 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 626) hydrogen bonds : angle 3.91488 ( 1722) metal coordination : bond 0.00496 ( 8) metal coordination : angle 3.23027 ( 12) covalent geometry : bond 0.00329 (11868) covalent geometry : angle 0.49130 (16232) *********************** 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: 15 poor density : 86 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 LYS cc_start: 0.8481 (mttt) cc_final: 0.7971 (mtmt) REVERT: B 515 ASP cc_start: 0.8558 (t0) cc_final: 0.8131 (t0) REVERT: B 559 MET cc_start: 0.8646 (mtp) cc_final: 0.8416 (mtp) REVERT: B 712 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.7354 (t80) REVERT: B 739 MET cc_start: 0.8921 (tpp) cc_final: 0.8480 (tmm) outliers start: 15 outliers final: 12 residues processed: 98 average time/residue: 0.3902 time to fit residues: 61.4795 Evaluate side-chains 98 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 982 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 0.0570 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.113469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084500 restraints weight = 62227.984| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.55 r_work: 0.3097 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11876 Z= 0.099 Angle : 0.461 5.062 16244 Z= 0.239 Chirality : 0.037 0.143 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.589 73.876 2286 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.87 % Allowed : 12.59 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1244 helix: 2.77 (0.20), residues: 648 sheet: -1.97 (0.34), residues: 184 loop : -0.93 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.004 0.000 HIS B 927 PHE 0.012 0.001 PHE B 551 TYR 0.009 0.001 TYR B 624 ARG 0.003 0.000 ARG B 843 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 626) hydrogen bonds : angle 3.71533 ( 1722) metal coordination : bond 0.00362 ( 8) metal coordination : angle 2.33568 ( 12) covalent geometry : bond 0.00217 (11868) covalent geometry : angle 0.45691 (16232) *********************** 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 103 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 GLN cc_start: 0.8561 (tt0) cc_final: 0.8277 (tm-30) REVERT: A 1002 LYS cc_start: 0.8425 (mttt) cc_final: 0.7933 (mtmt) REVERT: B 371 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7819 (mt-10) REVERT: B 515 ASP cc_start: 0.8533 (t0) cc_final: 0.7962 (t0) REVERT: B 559 MET cc_start: 0.8630 (mtp) cc_final: 0.8406 (mtp) REVERT: B 712 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7339 (t80) REVERT: B 739 MET cc_start: 0.8906 (tpp) cc_final: 0.8474 (tmm) REVERT: B 961 ILE cc_start: 0.9128 (pt) cc_final: 0.8902 (mm) outliers start: 10 outliers final: 8 residues processed: 100 average time/residue: 0.3874 time to fit residues: 62.5543 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 : 1.809 ------------------------------------------------------------------------------- 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 846 VAL Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 93 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.112453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.083443 restraints weight = 62270.809| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.56 r_work: 0.3074 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11876 Z= 0.126 Angle : 0.480 5.066 16244 Z= 0.250 Chirality : 0.038 0.142 1886 Planarity : 0.003 0.025 1830 Dihedral : 14.566 73.939 2286 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.87 % Allowed : 12.85 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1244 helix: 2.73 (0.20), residues: 656 sheet: -1.86 (0.35), residues: 180 loop : -1.02 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 737 HIS 0.010 0.001 HIS A 927 PHE 0.011 0.001 PHE B 551 TYR 0.010 0.001 TYR B 624 ARG 0.002 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 626) hydrogen bonds : angle 3.75421 ( 1722) metal coordination : bond 0.00421 ( 8) metal coordination : angle 2.68788 ( 12) covalent geometry : bond 0.00274 (11868) covalent geometry : angle 0.47477 (16232) ********************** 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 97 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 LYS cc_start: 0.8468 (mttt) cc_final: 0.7971 (mtmt) REVERT: B 515 ASP cc_start: 0.8538 (t0) cc_final: 0.8111 (t0) REVERT: B 559 MET cc_start: 0.8664 (mtp) cc_final: 0.8450 (mtp) REVERT: B 620 MET cc_start: 0.8284 (pmm) cc_final: 0.8021 (ptp) REVERT: B 712 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7367 (t80) REVERT: B 739 MET cc_start: 0.8873 (tpp) cc_final: 0.8481 (tmm) REVERT: B 961 ILE cc_start: 0.9134 (pt) cc_final: 0.8915 (mm) REVERT: B 972 MET cc_start: 0.8093 (ptp) cc_final: 0.7710 (ptp) outliers start: 10 outliers final: 9 residues processed: 95 average time/residue: 0.3915 time to fit residues: 60.0081 Evaluate side-chains 95 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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 846 VAL Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 0.0980 chunk 60 optimal weight: 0.1980 chunk 116 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.113484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.084655 restraints weight = 62214.079| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.54 r_work: 0.3102 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11876 Z= 0.100 Angle : 0.457 5.053 16244 Z= 0.237 Chirality : 0.037 0.142 1886 Planarity : 0.003 0.042 1830 Dihedral : 14.563 73.902 2286 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.87 % Allowed : 12.94 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1244 helix: 2.91 (0.20), residues: 648 sheet: -1.87 (0.34), residues: 184 loop : -0.92 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.006 0.001 HIS A 927 PHE 0.012 0.001 PHE B 551 TYR 0.009 0.001 TYR B 624 ARG 0.002 0.000 ARG B 461 Details of bonding type rmsd hydrogen bonds : bond 0.02885 ( 626) hydrogen bonds : angle 3.65696 ( 1722) metal coordination : bond 0.00367 ( 8) metal coordination : angle 2.27652 ( 12) covalent geometry : bond 0.00220 (11868) covalent geometry : angle 0.45285 (16232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11906.27 seconds wall clock time: 207 minutes 5.17 seconds (12425.17 seconds total)