Starting phenix.real_space_refine on Fri Sep 19 02:53:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0j_50111/09_2025/9f0j_50111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0j_50111/09_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_50111/09_2025/9f0j_50111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0j_50111/09_2025/9f0j_50111.map" model { file = "/net/cci-nas-00/data/ceres_data/9f0j_50111/09_2025/9f0j_50111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0j_50111/09_2025/9f0j_50111.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 60 5.49 5 S 66 5.16 5 C 7116 2.51 5 N 2004 2.21 5 O 2316 1.98 5 H 11172 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22736 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10403 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 20, 'TRANS': 619} Chain breaks: 8 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "X" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 480 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna3p_pur': 7, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Chain: "Z" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 484 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8731 SG CYS A 907 75.791 52.917 82.386 1.00 95.92 S ATOM 8777 SG CYS A 910 79.554 52.913 82.135 1.00111.21 S ATOM 9426 SG CYS A 962 77.813 53.273 85.616 1.00115.12 S ATOM 9458 SG CYS A 964 77.860 56.070 83.087 1.00118.72 S Restraints were copied for chains: B, C, D Time building chain proxies: 14.10, per 1000 atoms: 0.62 Number of scatterers: 22736 At special positions: 0 Unit cell: (99.12, 102.424, 116.466, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 66 16.00 P 60 15.00 O 2316 8.00 N 2004 7.00 C 7116 6.00 H 11172 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 639.6 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 335 through 355 removed outlier: 3.650A pdb=" N VAL A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.603A pdb=" N TYR A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 415 through 427 Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 453 through 476 removed outlier: 3.968A pdb=" N ARG A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 526 through 533 Processing helix chain 'A' and resid 550 through 567 Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.524A pdb=" N GLU A 580 " --> pdb=" O THR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 618 removed outlier: 3.634A pdb=" N THR A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 643 removed outlier: 3.834A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 692 removed outlier: 4.439A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 712 removed outlier: 3.513A pdb=" N GLU A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.614A pdb=" N THR A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 790 through 794 Processing helix chain 'A' and resid 843 through 863 Processing helix chain 'A' and resid 865 through 895 removed outlier: 4.032A pdb=" N GLN A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.580A pdb=" N LYS A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 937 " --> pdb=" O PRO A 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 932 through 937' Processing helix chain 'A' and resid 1002 through 1006 Processing helix chain 'B' and resid 310 through 318 Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 335 through 355 removed outlier: 3.649A pdb=" N VAL B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.602A pdb=" N TYR B 381 " --> pdb=" O GLU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 415 through 427 Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 453 through 476 removed outlier: 3.969A pdb=" N ARG B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 526 through 533 Processing helix chain 'B' and resid 550 through 567 Processing helix chain 'B' and resid 576 through 594 removed outlier: 3.523A pdb=" N GLU B 580 " --> pdb=" O THR B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 618 removed outlier: 3.634A pdb=" N THR B 617 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 643 removed outlier: 3.835A pdb=" N ALA B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 692 removed outlier: 4.438A pdb=" N ASN B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS B 685 " --> pdb=" O PHE B 681 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N MET B 686 " --> pdb=" O ASP B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 712 removed outlier: 3.514A pdb=" N GLU B 710 " --> pdb=" O ASN B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 741 removed outlier: 3.614A pdb=" N THR B 731 " --> pdb=" O THR B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 748 Processing helix chain 'B' and resid 767 through 781 Processing helix chain 'B' and resid 790 through 794 Processing helix chain 'B' and resid 843 through 863 Processing helix chain 'B' and resid 865 through 895 removed outlier: 4.032A pdb=" N GLN B 895 " --> pdb=" O SER B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 937 removed outlier: 3.581A pdb=" N LYS B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 937 " --> pdb=" O PRO B 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 932 through 937' Processing helix chain 'B' and resid 1002 through 1006 Processing sheet with id=1, first strand: chain 'A' and resid 328 through 329 removed outlier: 6.271A pdb=" N ILE A 441 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU A 488 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE A 443 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 364 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE A 389 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR A 414 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 751 through 754 removed outlier: 6.789A pdb=" N HIS A 752 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY A 721 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA A 788 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A 723 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL A 804 " --> pdb=" O VAL A 831 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL A 833 " --> pdb=" O VAL A 804 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG A 806 " --> pdb=" O VAL A 833 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 913 through 916 removed outlier: 6.573A pdb=" N LEU A 905 " --> pdb=" O VAL A 914 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER A 916 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 903 " --> pdb=" O SER A 916 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 920 through 923 Processing sheet with id=5, first strand: chain 'A' and resid 940 through 942 removed outlier: 6.522A pdb=" N ILE A 960 " --> pdb=" O TRP A 968 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 328 through 329 removed outlier: 6.270A pdb=" N ILE B 441 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU B 488 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE B 443 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 364 " --> pdb=" O SER B 413 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE B 389 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR B 414 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 751 through 754 removed outlier: 6.788A pdb=" N HIS B 752 " --> pdb=" O ILE B 787 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY B 721 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA B 788 " --> pdb=" O GLY B 721 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE B 723 " --> pdb=" O ALA B 788 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL B 804 " --> pdb=" O VAL B 831 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL B 833 " --> pdb=" O VAL B 804 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG B 806 " --> pdb=" O VAL B 833 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 913 through 916 removed outlier: 6.573A pdb=" N LEU B 905 " --> pdb=" O VAL B 914 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER B 916 " --> pdb=" O ILE B 903 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 903 " --> pdb=" O SER B 916 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 920 through 923 Processing sheet with id=10, first strand: chain 'B' and resid 940 through 942 removed outlier: 6.521A pdb=" N ILE B 960 " --> pdb=" O TRP B 968 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 5.57 Time building geometry restraints manager: 3.15 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'X' selection = chain 'C' } ncs_group { reference = chain 'Z' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 41.820 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.710 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.24), residues: 1244 helix: 1.96 (0.20), residues: 632 sheet: -2.37 (0.36), residues: 180 loop : -1.05 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.012 0.001 TYR B 312 PHE 0.009 0.001 PHE A 551 TRP 0.006 0.001 TRP B 737 HIS 0.002 0.001 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00391 (11868) covalent geometry : angle 0.52528 (16232) hydrogen bonds : bond 0.13969 ( 626) hydrogen bonds : angle 5.50141 ( 1722) metal coordination : bond 0.00301 ( 8) metal coordination : angle 2.63998 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.7570 (t80) cc_final: 0.7337 (t80) REVERT: A 628 GLU cc_start: 0.8037 (tt0) cc_final: 0.7667 (tm-30) REVERT: A 898 ASP cc_start: 0.7669 (m-30) cc_final: 0.7244 (m-30) REVERT: A 1002 LYS cc_start: 0.7807 (mttt) cc_final: 0.7317 (mtmt) REVERT: B 489 THR cc_start: 0.7337 (t) cc_final: 0.6516 (t) REVERT: B 610 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7628 (mt-10) REVERT: B 739 MET cc_start: 0.8743 (tpp) cc_final: 0.8366 (tmm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2378 time to fit residues: 68.0666 Evaluate side-chains 119 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 A 928 HIS B 476 ASN B 643 ASN B 711 GLN B 928 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.117687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.088264 restraints weight = 62848.827| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.15 r_work: 0.3110 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11876 Z= 0.235 Angle : 0.612 9.524 16244 Z= 0.325 Chirality : 0.042 0.168 1886 Planarity : 0.004 0.033 1830 Dihedral : 14.733 73.933 2286 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.22 % Allowed : 6.38 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.24), residues: 1244 helix: 1.67 (0.20), residues: 648 sheet: -2.12 (0.35), residues: 182 loop : -1.14 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 596 TYR 0.021 0.002 TYR B 807 PHE 0.021 0.002 PHE B 551 TRP 0.009 0.002 TRP A 737 HIS 0.008 0.002 HIS B 578 Details of bonding type rmsd covalent geometry : bond 0.00516 (11868) covalent geometry : angle 0.59932 (16232) hydrogen bonds : bond 0.04410 ( 626) hydrogen bonds : angle 4.57195 ( 1722) metal coordination : bond 0.00724 ( 8) metal coordination : angle 4.67613 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 MET cc_start: 0.8521 (pmm) cc_final: 0.8266 (pmm) REVERT: A 628 GLU cc_start: 0.8082 (tt0) cc_final: 0.7760 (tm-30) REVERT: A 1002 LYS cc_start: 0.8255 (mttt) cc_final: 0.7747 (mtmt) REVERT: B 515 ASP cc_start: 0.8116 (t0) cc_final: 0.7845 (t0) REVERT: B 605 LEU cc_start: 0.8951 (mt) cc_final: 0.8511 (mt) REVERT: B 830 TYR cc_start: 0.8182 (t80) cc_final: 0.7623 (t80) REVERT: B 912 MET cc_start: 0.7917 (ptm) cc_final: 0.7453 (ptm) outliers start: 14 outliers final: 9 residues processed: 143 average time/residue: 0.2182 time to fit residues: 47.1596 Evaluate side-chains 106 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1019 CYS Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 982 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 62 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN A 475 GLN B 532 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 = 0.3801 r_free = 0.3801 target = 0.118661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088460 restraints weight = 61978.963| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.78 r_work: 0.3161 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11876 Z= 0.123 Angle : 0.493 6.044 16244 Z= 0.256 Chirality : 0.038 0.142 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.651 73.864 2286 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.96 % Allowed : 9.00 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.24), residues: 1244 helix: 2.31 (0.20), residues: 640 sheet: -2.11 (0.35), residues: 182 loop : -1.00 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.009 0.001 TYR B 939 PHE 0.016 0.001 PHE B 639 TRP 0.008 0.001 TRP A 737 HIS 0.004 0.001 HIS B 927 Details of bonding type rmsd covalent geometry : bond 0.00265 (11868) covalent geometry : angle 0.48731 (16232) hydrogen bonds : bond 0.03576 ( 626) hydrogen bonds : angle 4.18772 ( 1722) metal coordination : bond 0.00386 ( 8) metal coordination : angle 2.71248 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 MET cc_start: 0.8524 (pmm) cc_final: 0.8243 (pmm) REVERT: A 628 GLU cc_start: 0.7980 (tt0) cc_final: 0.7760 (tm-30) REVERT: A 1002 LYS cc_start: 0.8179 (mttt) cc_final: 0.7671 (mtmt) REVERT: B 515 ASP cc_start: 0.8040 (t0) cc_final: 0.7627 (t0) REVERT: B 566 CYS cc_start: 0.7960 (m) cc_final: 0.7677 (t) REVERT: B 568 LYS cc_start: 0.6733 (mmtt) cc_final: 0.6162 (mmtm) REVERT: B 639 PHE cc_start: 0.8170 (t80) cc_final: 0.7946 (t80) REVERT: B 739 MET cc_start: 0.8838 (tpp) cc_final: 0.8391 (tmm) REVERT: B 830 TYR cc_start: 0.8187 (t80) cc_final: 0.7612 (t80) outliers start: 11 outliers final: 4 residues processed: 111 average time/residue: 0.2149 time to fit residues: 36.4433 Evaluate side-chains 97 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 540 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 121 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 532 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.118135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088038 restraints weight = 62558.939| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.73 r_work: 0.3154 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4033 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= 0.116 Angle : 0.471 6.196 16244 Z= 0.244 Chirality : 0.038 0.145 1886 Planarity : 0.003 0.022 1830 Dihedral : 14.607 73.977 2286 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.96 % Allowed : 9.18 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.25), residues: 1244 helix: 2.57 (0.20), residues: 642 sheet: -1.91 (0.35), residues: 180 loop : -0.89 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.013 0.001 TYR A1018 PHE 0.020 0.001 PHE B 639 TRP 0.009 0.001 TRP A 737 HIS 0.005 0.001 HIS B 927 Details of bonding type rmsd covalent geometry : bond 0.00252 (11868) covalent geometry : angle 0.46482 (16232) hydrogen bonds : bond 0.03236 ( 626) hydrogen bonds : angle 3.98664 ( 1722) metal coordination : bond 0.00378 ( 8) metal coordination : angle 2.84005 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 LYS cc_start: 0.7832 (mtmt) cc_final: 0.7523 (tttt) REVERT: A 620 MET cc_start: 0.8484 (pmm) cc_final: 0.8207 (pmm) REVERT: A 932 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8220 (p) REVERT: A 1002 LYS cc_start: 0.8152 (mttt) cc_final: 0.7670 (mtmt) REVERT: B 515 ASP cc_start: 0.8114 (t0) cc_final: 0.7618 (t0) REVERT: B 566 CYS cc_start: 0.8011 (m) cc_final: 0.7722 (t) REVERT: B 739 MET cc_start: 0.8841 (tpp) cc_final: 0.8409 (tmm) REVERT: B 830 TYR cc_start: 0.8194 (t80) cc_final: 0.7515 (t80) REVERT: B 961 ILE cc_start: 0.9141 (pt) cc_final: 0.8737 (mm) outliers start: 11 outliers final: 6 residues processed: 107 average time/residue: 0.2089 time to fit residues: 34.3103 Evaluate side-chains 96 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 834 THR 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 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN B 683 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.086342 restraints weight = 62042.074| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.73 r_work: 0.3123 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11876 Z= 0.133 Angle : 0.481 6.003 16244 Z= 0.250 Chirality : 0.038 0.141 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.576 74.005 2286 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.87 % Allowed : 10.75 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.25), residues: 1244 helix: 2.61 (0.20), residues: 644 sheet: -1.85 (0.36), residues: 180 loop : -0.92 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.010 0.001 TYR B 624 PHE 0.020 0.001 PHE B 639 TRP 0.009 0.001 TRP A 737 HIS 0.005 0.001 HIS B 927 Details of bonding type rmsd covalent geometry : bond 0.00283 (11868) covalent geometry : angle 0.47461 (16232) hydrogen bonds : bond 0.03260 ( 626) hydrogen bonds : angle 3.91690 ( 1722) metal coordination : bond 0.00402 ( 8) metal coordination : angle 2.90770 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 MET cc_start: 0.8473 (pmm) cc_final: 0.8133 (pmm) REVERT: A 978 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: A 1002 LYS cc_start: 0.8241 (mttt) cc_final: 0.7737 (mtmt) REVERT: B 515 ASP cc_start: 0.8131 (t0) cc_final: 0.7596 (t0) REVERT: B 739 MET cc_start: 0.8835 (tpp) cc_final: 0.8411 (tmm) REVERT: B 961 ILE cc_start: 0.9135 (pt) cc_final: 0.8785 (mm) outliers start: 10 outliers final: 7 residues processed: 102 average time/residue: 0.1934 time to fit residues: 30.8764 Evaluate side-chains 99 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 121 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 62 optimal weight: 0.1980 chunk 97 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN B 643 ASN B 930 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.116040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087648 restraints weight = 62876.354| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.20 r_work: 0.3093 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11876 Z= 0.127 Angle : 0.469 6.025 16244 Z= 0.244 Chirality : 0.037 0.141 1886 Planarity : 0.003 0.025 1830 Dihedral : 14.554 73.944 2286 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.22 % Allowed : 10.66 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.25), residues: 1244 helix: 2.70 (0.20), residues: 646 sheet: -1.77 (0.36), residues: 180 loop : -0.92 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.011 0.001 TYR A1018 PHE 0.022 0.001 PHE B 639 TRP 0.009 0.001 TRP A 737 HIS 0.009 0.001 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00276 (11868) covalent geometry : angle 0.46238 (16232) hydrogen bonds : bond 0.03110 ( 626) hydrogen bonds : angle 3.85887 ( 1722) metal coordination : bond 0.00402 ( 8) metal coordination : angle 2.93351 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7628 (tttt) REVERT: A 620 MET cc_start: 0.8474 (pmm) cc_final: 0.8084 (pmm) REVERT: A 978 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8334 (m-30) REVERT: A 1002 LYS cc_start: 0.8244 (mttt) cc_final: 0.7758 (mtmt) REVERT: B 515 ASP cc_start: 0.8256 (t0) cc_final: 0.7724 (t0) REVERT: B 739 MET cc_start: 0.8833 (tpp) cc_final: 0.8420 (tmm) REVERT: B 912 MET cc_start: 0.7810 (ptt) cc_final: 0.7500 (ptt) REVERT: B 961 ILE cc_start: 0.9098 (pt) cc_final: 0.8800 (mm) outliers start: 14 outliers final: 8 residues processed: 108 average time/residue: 0.1905 time to fit residues: 32.7564 Evaluate side-chains 99 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 475 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 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 683 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 = 0.3764 r_free = 0.3764 target = 0.116236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088004 restraints weight = 62394.612| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.12 r_work: 0.3097 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11876 Z= 0.108 Angle : 0.454 5.266 16244 Z= 0.235 Chirality : 0.037 0.142 1886 Planarity : 0.003 0.025 1830 Dihedral : 14.559 73.948 2286 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.70 % Allowed : 11.63 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.25), residues: 1244 helix: 2.80 (0.20), residues: 654 sheet: -1.68 (0.36), residues: 180 loop : -0.89 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.009 0.001 TYR B 624 PHE 0.019 0.001 PHE B 639 TRP 0.008 0.001 TRP A 737 HIS 0.004 0.001 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00233 (11868) covalent geometry : angle 0.44843 (16232) hydrogen bonds : bond 0.02991 ( 626) hydrogen bonds : angle 3.76225 ( 1722) metal coordination : bond 0.00370 ( 8) metal coordination : angle 2.61004 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.598 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: 0.7987 (mtmt) cc_final: 0.7745 (tttt) REVERT: A 620 MET cc_start: 0.8451 (pmm) cc_final: 0.8016 (pmm) REVERT: A 978 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8335 (m-30) REVERT: A 1002 LYS cc_start: 0.8247 (mttt) cc_final: 0.7757 (mtmt) REVERT: B 515 ASP cc_start: 0.8303 (t0) cc_final: 0.7743 (t0) REVERT: B 584 ILE cc_start: 0.8689 (mm) cc_final: 0.8425 (mt) REVERT: B 739 MET cc_start: 0.8796 (tpp) cc_final: 0.8400 (tmm) REVERT: B 912 MET cc_start: 0.7771 (ptt) cc_final: 0.7461 (ptt) REVERT: B 961 ILE cc_start: 0.9091 (pt) cc_final: 0.8832 (mm) outliers start: 8 outliers final: 5 residues processed: 99 average time/residue: 0.1886 time to fit residues: 29.9001 Evaluate side-chains 96 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 476 ASN A 615 ASN B 643 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.111479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.083354 restraints weight = 62063.421| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.82 r_work: 0.3031 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11876 Z= 0.182 Angle : 0.516 6.779 16244 Z= 0.270 Chirality : 0.039 0.149 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.585 73.994 2286 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.79 % Allowed : 11.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.25), residues: 1244 helix: 2.57 (0.20), residues: 654 sheet: -1.69 (0.36), residues: 180 loop : -0.97 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.010 0.001 TYR B 624 PHE 0.016 0.001 PHE B 639 TRP 0.009 0.001 TRP A 737 HIS 0.006 0.001 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00398 (11868) covalent geometry : angle 0.50568 (16232) hydrogen bonds : bond 0.03528 ( 626) hydrogen bonds : angle 3.94796 ( 1722) metal coordination : bond 0.00554 ( 8) metal coordination : angle 3.73515 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.675 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: 0.8104 (mtmt) cc_final: 0.7894 (tttt) REVERT: A 620 MET cc_start: 0.8483 (pmm) cc_final: 0.8031 (pmm) REVERT: A 978 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: A 1002 LYS cc_start: 0.8386 (mttt) cc_final: 0.7875 (mtmt) REVERT: B 515 ASP cc_start: 0.8328 (t0) cc_final: 0.7753 (t0) REVERT: B 739 MET cc_start: 0.8777 (tpp) cc_final: 0.8417 (tmm) REVERT: B 912 MET cc_start: 0.7823 (ptt) cc_final: 0.7515 (ptt) REVERT: B 961 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8871 (mm) outliers start: 9 outliers final: 6 residues processed: 97 average time/residue: 0.1967 time to fit residues: 30.3620 Evaluate side-chains 94 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 978 ASP 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 0.0870 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.113080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.083574 restraints weight = 62897.580| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.64 r_work: 0.3077 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 11876 Z= 0.119 Angle : 0.466 5.183 16244 Z= 0.242 Chirality : 0.037 0.140 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.574 73.897 2286 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.70 % Allowed : 12.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.25), residues: 1244 helix: 2.73 (0.20), residues: 654 sheet: -1.60 (0.36), residues: 180 loop : -0.95 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 460 TYR 0.010 0.001 TYR B1000 PHE 0.022 0.001 PHE B 639 TRP 0.009 0.001 TRP A 737 HIS 0.007 0.001 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00257 (11868) covalent geometry : angle 0.46022 (16232) hydrogen bonds : bond 0.03111 ( 626) hydrogen bonds : angle 3.79184 ( 1722) metal coordination : bond 0.00408 ( 8) metal coordination : angle 2.70088 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.641 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 620 MET cc_start: 0.8425 (pmm) cc_final: 0.7924 (pmm) REVERT: A 978 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: A 1002 LYS cc_start: 0.8340 (mttt) cc_final: 0.7846 (mtmt) REVERT: B 515 ASP cc_start: 0.8304 (t0) cc_final: 0.7745 (t0) REVERT: B 739 MET cc_start: 0.8765 (tpp) cc_final: 0.8407 (tmm) REVERT: B 912 MET cc_start: 0.7763 (ptt) cc_final: 0.7443 (ptt) REVERT: B 961 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8844 (mm) outliers start: 8 outliers final: 6 residues processed: 94 average time/residue: 0.1893 time to fit residues: 28.1183 Evaluate side-chains 93 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 978 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 683 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.112324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.084027 restraints weight = 62470.840| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.92 r_work: 0.3049 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.5701 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= 0.133 Angle : 0.474 5.505 16244 Z= 0.246 Chirality : 0.038 0.142 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.561 73.938 2286 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.87 % Allowed : 11.71 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.25), residues: 1244 helix: 2.75 (0.20), residues: 654 sheet: -1.57 (0.36), residues: 180 loop : -0.97 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 843 TYR 0.010 0.001 TYR B 624 PHE 0.022 0.001 PHE B 639 TRP 0.008 0.001 TRP A 737 HIS 0.006 0.001 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00291 (11868) covalent geometry : angle 0.46758 (16232) hydrogen bonds : bond 0.03137 ( 626) hydrogen bonds : angle 3.78186 ( 1722) metal coordination : bond 0.00445 ( 8) metal coordination : angle 2.98634 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue VAL 749 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue TYR 896 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 MET cc_start: 0.8419 (pmm) cc_final: 0.7906 (pmm) REVERT: A 978 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8259 (m-30) REVERT: A 1002 LYS cc_start: 0.8368 (mttt) cc_final: 0.7869 (mtmt) REVERT: B 515 ASP cc_start: 0.8346 (t0) cc_final: 0.7820 (t0) REVERT: B 739 MET cc_start: 0.8788 (tpp) cc_final: 0.8426 (tmm) REVERT: B 912 MET cc_start: 0.7751 (ptt) cc_final: 0.7422 (ptt) REVERT: B 961 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8878 (mm) REVERT: B 972 MET cc_start: 0.7964 (ptp) cc_final: 0.7610 (ptp) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 0.1595 time to fit residues: 23.7802 Evaluate side-chains 91 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 934 GLU Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain A residue 978 ASP 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 961 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.111336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.083101 restraints weight = 62545.169| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.90 r_work: 0.3027 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11876 Z= 0.161 Angle : 0.495 5.779 16244 Z= 0.258 Chirality : 0.038 0.143 1886 Planarity : 0.003 0.024 1830 Dihedral : 14.581 73.954 2286 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.87 % Allowed : 11.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.25), residues: 1244 helix: 2.67 (0.20), residues: 654 sheet: -1.59 (0.36), residues: 180 loop : -1.03 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 942 TYR 0.012 0.001 TYR B1000 PHE 0.022 0.001 PHE B 639 TRP 0.008 0.001 TRP A 737 HIS 0.007 0.001 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00348 (11868) covalent geometry : angle 0.48734 (16232) hydrogen bonds : bond 0.03358 ( 626) hydrogen bonds : angle 3.82292 ( 1722) metal coordination : bond 0.00512 ( 8) metal coordination : angle 3.22613 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5144.70 seconds wall clock time: 88 minutes 15.03 seconds (5295.03 seconds total)