Starting phenix.real_space_refine on Thu May 22 07:13:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0j_50111/05_2025/9f0j_50111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0j_50111/05_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_50111/05_2025/9f0j_50111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0j_50111/05_2025/9f0j_50111.map" model { file = "/net/cci-nas-00/data/ceres_data/9f0j_50111/05_2025/9f0j_50111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0j_50111/05_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-5687/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: 30.80, per 1000 atoms: 1.35 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: 6.36 Conformation dependent library (CDL) restraints added in 2.0 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: 11.54 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: 8.74 Time building geometry restraints manager: 7.35 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: 0.07 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: 1.800 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: 0.350 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 85.900 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.340 ------------------------------------------------------------------------------- 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 : 1.727 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: 0.5003 time to fit residues: 142.2582 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 : 1.944 ------------------------------------------------------------------------------- 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: 0.3218 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 1.637 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: 0.8611 (tpt) cc_final: 0.8373 (tpp) REVERT: A 628 GLU cc_start: 0.7973 (tt0) cc_final: 0.7646 (tm-30) REVERT: A 898 ASP cc_start: 0.7807 (m-30) cc_final: 0.7366 (m-30) REVERT: A 1002 LYS cc_start: 0.7983 (mttt) cc_final: 0.7510 (mtmt) REVERT: B 515 ASP cc_start: 0.7827 (t0) cc_final: 0.7513 (t0) REVERT: B 739 MET cc_start: 0.8764 (tpp) cc_final: 0.8438 (tmm) REVERT: B 830 TYR cc_start: 0.7975 (t80) cc_final: 0.7660 (t80) outliers start: 10 outliers final: 6 residues processed: 150 average time/residue: 0.4361 time to fit residues: 98.6295 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 : 1.971 ------------------------------------------------------------------------------- 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: 0.7980 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: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 643 ASN B 711 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.117312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087107 restraints weight = 61863.935| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.74 r_work: 0.3137 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11876 Z= 0.181 Angle : 0.546 6.889 16244 Z= 0.286 Chirality : 0.040 0.154 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.655 73.966 2286 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.22 % Allowed : 7.95 % 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 (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: 0.75 (0.24), residues: 1244 helix: 2.12 (0.20), residues: 646 sheet: -1.98 (0.36), residues: 180 loop : -0.90 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 968 HIS 0.007 0.001 HIS A 447 PHE 0.017 0.001 PHE B 551 TYR 0.015 0.002 TYR B 624 ARG 0.004 0.001 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 626) hydrogen bonds : angle 4.29236 ( 1722) metal coordination : bond 0.00497 ( 8) metal coordination : angle 3.46139 ( 12) covalent geometry : bond 0.00396 (11868) covalent geometry : angle 0.53803 (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 126 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 GLU cc_start: 0.8039 (tt0) cc_final: 0.7825 (tm-30) REVERT: A 701 LEU cc_start: 0.6910 (tp) cc_final: 0.6630 (tp) REVERT: A 1002 LYS cc_start: 0.8252 (mttt) cc_final: 0.7738 (mtmt) REVERT: B 515 ASP cc_start: 0.8053 (t0) cc_final: 0.7594 (t0) REVERT: B 620 MET cc_start: 0.8127 (pmm) cc_final: 0.7782 (ptp) REVERT: B 739 MET cc_start: 0.8810 (tpp) cc_final: 0.8377 (tmm) REVERT: B 830 TYR cc_start: 0.8089 (t80) cc_final: 0.7598 (t80) outliers start: 14 outliers final: 9 residues processed: 123 average time/residue: 0.4444 time to fit residues: 81.9233 Evaluate side-chains 105 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN B 643 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.118383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088470 restraints weight = 62456.244| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.71 r_work: 0.3166 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11876 Z= 0.112 Angle : 0.479 5.646 16244 Z= 0.247 Chirality : 0.038 0.142 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.613 73.958 2286 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.79 % Allowed : 9.09 % Favored : 90.12 % 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: 1.14 (0.25), residues: 1244 helix: 2.55 (0.20), residues: 642 sheet: -1.92 (0.36), residues: 180 loop : -0.85 (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 B 927 PHE 0.013 0.001 PHE B 551 TYR 0.009 0.001 TYR A 939 ARG 0.001 0.000 ARG B1009 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 626) hydrogen bonds : angle 4.01089 ( 1722) metal coordination : bond 0.00350 ( 8) metal coordination : angle 2.64950 ( 12) covalent geometry : bond 0.00241 (11868) covalent geometry : angle 0.47365 (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 109 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 LYS cc_start: 0.7871 (mtmt) cc_final: 0.7560 (tttt) REVERT: A 1002 LYS cc_start: 0.8166 (mttt) cc_final: 0.7669 (mtmt) REVERT: B 475 GLN cc_start: 0.8049 (mp10) cc_final: 0.7791 (tt0) REVERT: B 515 ASP cc_start: 0.8105 (t0) cc_final: 0.7651 (t0) REVERT: B 620 MET cc_start: 0.8137 (pmm) cc_final: 0.7742 (ptp) REVERT: B 739 MET cc_start: 0.8866 (tpp) cc_final: 0.8423 (tmm) REVERT: B 830 TYR cc_start: 0.8079 (t80) cc_final: 0.7485 (t80) REVERT: B 961 ILE cc_start: 0.9123 (pt) cc_final: 0.8718 (mm) outliers start: 9 outliers final: 7 residues processed: 108 average time/residue: 0.4541 time to fit residues: 75.0222 Evaluate side-chains 99 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 1.926 ------------------------------------------------------------------------------- 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: 7.9990 chunk 33 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 49 optimal weight: 0.0980 chunk 114 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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 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 = 0.3719 r_free = 0.3719 target = 0.113236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.084885 restraints weight = 62795.025| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.11 r_work: 0.3042 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11876 Z= 0.241 Angle : 0.588 8.658 16244 Z= 0.309 Chirality : 0.041 0.152 1886 Planarity : 0.003 0.033 1830 Dihedral : 14.665 74.025 2286 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.14 % Allowed : 10.23 % Favored : 88.64 % 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: 0.73 (0.24), residues: 1244 helix: 2.10 (0.20), residues: 648 sheet: -1.94 (0.36), residues: 180 loop : -0.95 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 737 HIS 0.006 0.001 HIS A 447 PHE 0.013 0.002 PHE A 438 TYR 0.014 0.002 TYR A1018 ARG 0.004 0.001 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 626) hydrogen bonds : angle 4.29250 ( 1722) metal coordination : bond 0.00699 ( 8) metal coordination : angle 4.77270 ( 12) covalent geometry : bond 0.00530 (11868) covalent geometry : angle 0.57361 (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 109 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 LYS cc_start: 0.8353 (mttt) cc_final: 0.7847 (mtmt) REVERT: B 515 ASP cc_start: 0.8342 (t0) cc_final: 0.7923 (t0) REVERT: B 620 MET cc_start: 0.8334 (pmm) cc_final: 0.7982 (ptp) REVERT: B 739 MET cc_start: 0.8850 (tpp) cc_final: 0.8436 (tmm) REVERT: B 912 MET cc_start: 0.7903 (ptt) cc_final: 0.7623 (ptt) outliers start: 13 outliers final: 10 residues processed: 105 average time/residue: 0.4374 time to fit residues: 69.5641 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 : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 540 PHE 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 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: 4.9990 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: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 706 ASN B 532 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.110283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.080796 restraints weight = 62873.330| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.56 r_work: 0.3028 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.5457 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= 0.230 Angle : 0.563 7.916 16244 Z= 0.296 Chirality : 0.041 0.148 1886 Planarity : 0.003 0.027 1830 Dihedral : 14.680 73.915 2286 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.05 % Allowed : 11.10 % Favored : 87.85 % 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: 0.56 (0.24), residues: 1244 helix: 2.03 (0.20), residues: 648 sheet: -2.27 (0.33), residues: 184 loop : -1.00 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 737 HIS 0.005 0.001 HIS A 447 PHE 0.013 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 0.03888 ( 626) hydrogen bonds : angle 4.26476 ( 1722) metal coordination : bond 0.00716 ( 8) metal coordination : angle 4.36481 ( 12) covalent geometry : bond 0.00496 (11868) covalent geometry : angle 0.55057 (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 107 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 LYS cc_start: 0.8153 (mtmt) cc_final: 0.7862 (tttt) REVERT: A 847 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7310 (m-40) REVERT: A 1002 LYS cc_start: 0.8471 (mttt) cc_final: 0.7960 (mtmt) REVERT: B 515 ASP cc_start: 0.8580 (t0) cc_final: 0.8148 (t0) REVERT: B 584 ILE cc_start: 0.8861 (mm) cc_final: 0.8654 (mt) REVERT: B 620 MET cc_start: 0.8495 (pmm) cc_final: 0.7950 (ptp) REVERT: B 739 MET cc_start: 0.8935 (tpp) cc_final: 0.8475 (tmm) REVERT: B 912 MET cc_start: 0.7897 (ptt) cc_final: 0.7560 (ptt) outliers start: 12 outliers final: 11 residues processed: 103 average time/residue: 0.4572 time to fit residues: 72.8956 Evaluate side-chains 97 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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 847 ASN 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: 0.9990 chunk 71 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.113224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.083852 restraints weight = 62693.711| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.61 r_work: 0.3081 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11876 Z= 0.107 Angle : 0.478 7.943 16244 Z= 0.246 Chirality : 0.038 0.143 1886 Planarity : 0.003 0.022 1830 Dihedral : 14.624 73.858 2286 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.61 % Allowed : 12.06 % Favored : 87.33 % 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: 1.03 (0.24), residues: 1244 helix: 2.49 (0.20), residues: 654 sheet: -2.17 (0.33), residues: 184 loop : -0.92 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 737 HIS 0.004 0.001 HIS B 927 PHE 0.013 0.001 PHE B 551 TYR 0.009 0.001 TYR A 312 ARG 0.002 0.000 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 626) hydrogen bonds : angle 3.87642 ( 1722) metal coordination : bond 0.00394 ( 8) metal coordination : angle 2.71537 ( 12) covalent geometry : bond 0.00234 (11868) covalent geometry : angle 0.47263 (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 101 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 1.706 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 597 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7947 (tttt) REVERT: A 1002 LYS cc_start: 0.8417 (mttt) cc_final: 0.7947 (mtmt) REVERT: B 515 ASP cc_start: 0.8600 (t0) cc_final: 0.8078 (t0) REVERT: B 584 ILE cc_start: 0.8852 (mm) cc_final: 0.8643 (mt) REVERT: B 620 MET cc_start: 0.8395 (pmm) cc_final: 0.7863 (ptp) REVERT: B 739 MET cc_start: 0.8912 (tpp) cc_final: 0.8439 (tmm) REVERT: B 912 MET cc_start: 0.7821 (ptt) cc_final: 0.7456 (ptt) outliers start: 7 outliers final: 6 residues processed: 98 average time/residue: 0.4025 time to fit residues: 62.2654 Evaluate side-chains 94 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.112531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.083158 restraints weight = 62618.432| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.60 r_work: 0.3072 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.5635 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= 0.131 Angle : 0.486 5.720 16244 Z= 0.252 Chirality : 0.038 0.142 1886 Planarity : 0.003 0.023 1830 Dihedral : 14.590 73.945 2286 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.61 % Allowed : 12.15 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.24), residues: 1244 helix: 2.59 (0.20), residues: 654 sheet: -2.03 (0.34), residues: 180 loop : -1.02 (0.30), residues: 410 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 0.010 0.001 TYR B 624 ARG 0.002 0.000 ARG B 461 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 626) hydrogen bonds : angle 3.86525 ( 1722) metal coordination : bond 0.00455 ( 8) metal coordination : angle 3.02991 ( 12) covalent geometry : bond 0.00287 (11868) covalent geometry : angle 0.47913 (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 99 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 LYS cc_start: 0.8462 (mttt) cc_final: 0.7972 (mtmt) REVERT: B 515 ASP cc_start: 0.8580 (t0) cc_final: 0.8154 (t0) REVERT: B 620 MET cc_start: 0.8355 (pmm) cc_final: 0.7857 (ptp) REVERT: B 739 MET cc_start: 0.8892 (tpp) cc_final: 0.8483 (tmm) outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.4040 time to fit residues: 60.6706 Evaluate side-chains 92 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 972 MET Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 982 LEU 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: 0.9990 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** ** B 475 GLN ** 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 = 0.3705 r_free = 0.3705 target = 0.112252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.083149 restraints weight = 62333.447| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.57 r_work: 0.3069 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11876 Z= 0.132 Angle : 0.490 8.179 16244 Z= 0.253 Chirality : 0.038 0.141 1886 Planarity : 0.003 0.023 1830 Dihedral : 14.586 73.938 2286 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.96 % Allowed : 12.06 % Favored : 86.98 % 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: 1.16 (0.25), residues: 1244 helix: 2.62 (0.20), residues: 656 sheet: -2.05 (0.34), residues: 184 loop : -0.96 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 737 HIS 0.011 0.001 HIS A 927 PHE 0.016 0.001 PHE A 639 TYR 0.010 0.001 TYR B 624 ARG 0.002 0.000 ARG B 461 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 626) hydrogen bonds : angle 3.81800 ( 1722) metal coordination : bond 0.00432 ( 8) metal coordination : angle 2.83508 ( 12) covalent geometry : bond 0.00289 (11868) covalent geometry : angle 0.48399 (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 99 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 LYS cc_start: 0.8458 (mttt) cc_final: 0.7963 (mtmt) REVERT: B 515 ASP cc_start: 0.8546 (t0) cc_final: 0.7990 (t0) REVERT: B 620 MET cc_start: 0.8371 (pmm) cc_final: 0.7833 (ptp) REVERT: B 712 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7330 (t80) REVERT: B 739 MET cc_start: 0.8888 (tpp) cc_final: 0.8483 (tmm) REVERT: B 961 ILE cc_start: 0.9125 (pt) cc_final: 0.8881 (mm) outliers start: 11 outliers final: 7 residues processed: 95 average time/residue: 0.3861 time to fit residues: 58.8325 Evaluate side-chains 96 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.628 ------------------------------------------------------------------------------- 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 555 LEU 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: 2.9990 chunk 46 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** B 475 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.113031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.084114 restraints weight = 62239.350| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.56 r_work: 0.3089 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11876 Z= 0.111 Angle : 0.472 5.981 16244 Z= 0.244 Chirality : 0.037 0.142 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.565 73.903 2286 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.79 % Allowed : 12.15 % Favored : 87.06 % 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: 1.28 (0.25), residues: 1244 helix: 2.74 (0.20), residues: 656 sheet: -1.95 (0.34), residues: 184 loop : -0.97 (0.31), residues: 404 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 0.010 0.001 TYR B1000 ARG 0.002 0.000 ARG B 461 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 626) hydrogen bonds : angle 3.70985 ( 1722) metal coordination : bond 0.00383 ( 8) metal coordination : angle 2.47548 ( 12) covalent geometry : bond 0.00245 (11868) covalent geometry : angle 0.46723 (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: 9 poor density : 88 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 LYS cc_start: 0.8456 (mttt) cc_final: 0.7963 (mtmt) REVERT: B 371 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7848 (mt-10) REVERT: B 515 ASP cc_start: 0.8552 (t0) cc_final: 0.7989 (t0) REVERT: B 620 MET cc_start: 0.8271 (pmm) cc_final: 0.7807 (ptp) REVERT: B 712 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7335 (t80) REVERT: B 739 MET cc_start: 0.8900 (tpp) cc_final: 0.8452 (tmm) REVERT: B 961 ILE cc_start: 0.9132 (pt) cc_final: 0.8903 (mm) outliers start: 9 outliers final: 5 residues processed: 93 average time/residue: 0.3825 time to fit residues: 56.9736 Evaluate side-chains 90 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 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: 8.9990 chunk 60 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** ** B 930 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 = 0.3697 r_free = 0.3697 target = 0.111753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.082723 restraints weight = 62532.982| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.56 r_work: 0.3060 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11876 Z= 0.147 Angle : 0.503 8.484 16244 Z= 0.261 Chirality : 0.038 0.142 1886 Planarity : 0.003 0.037 1830 Dihedral : 14.570 73.948 2286 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.61 % Allowed : 13.02 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.30 (0.25), residues: 1244 helix: 2.75 (0.20), residues: 646 sheet: -1.76 (0.36), residues: 168 loop : -1.02 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 737 HIS 0.012 0.001 HIS A 927 PHE 0.018 0.001 PHE A 639 TYR 0.011 0.001 TYR B 624 ARG 0.002 0.000 ARG B1009 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 626) hydrogen bonds : angle 3.78657 ( 1722) metal coordination : bond 0.00475 ( 8) metal coordination : angle 3.01732 ( 12) covalent geometry : bond 0.00321 (11868) covalent geometry : angle 0.49640 (16232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11210.59 seconds wall clock time: 192 minutes 36.43 seconds (11556.43 seconds total)