Starting phenix.real_space_refine on Wed Mar 4 06:47:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kft_22855/03_2026/7kft_22855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kft_22855/03_2026/7kft_22855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kft_22855/03_2026/7kft_22855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kft_22855/03_2026/7kft_22855.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kft_22855/03_2026/7kft_22855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kft_22855/03_2026/7kft_22855.map" } resolution = 3.4 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= 1.000 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 7433 2.51 5 N 2135 2.21 5 O 2087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11680 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "A" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 756 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "D" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2727 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "C" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4601 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 25, 'TRANS': 542} Chain breaks: 5 Chain: "E" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2800 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 8, 'TRANS': 332} Time building chain proxies: 2.33, per 1000 atoms: 0.20 Number of scatterers: 11680 At special positions: 0 Unit cell: (87.838, 142.44, 122.261, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 2087 8.00 N 2135 7.00 C 7433 6.00 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: 0.87 Conformation dependent library (CDL) restraints added in 527.3 milliseconds 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 48.6% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 14 through 24 removed outlier: 3.699A pdb=" N GLU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 57 removed outlier: 3.662A pdb=" N LYS B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 72 through 79 removed outlier: 3.510A pdb=" N ILE B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.831A pdb=" N LYS A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 60 removed outlier: 3.952A pdb=" N LYS A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 709 Processing helix chain 'D' and resid 728 through 733 Processing helix chain 'D' and resid 739 through 746 Processing helix chain 'D' and resid 748 through 773 removed outlier: 3.709A pdb=" N VAL D 760 " --> pdb=" O ALA D 756 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU D 771 " --> pdb=" O GLN D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 794 removed outlier: 5.026A pdb=" N GLN D 783 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR D 784 " --> pdb=" O GLN D 780 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 794 " --> pdb=" O LYS D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 817 removed outlier: 3.525A pdb=" N LEU D 804 " --> pdb=" O LYS D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 822 Processing helix chain 'D' and resid 839 through 863 removed outlier: 3.741A pdb=" N VAL D 843 " --> pdb=" O ASP D 839 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 863 " --> pdb=" O ILE D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 887 Processing helix chain 'D' and resid 891 through 904 removed outlier: 3.816A pdb=" N GLU D 895 " --> pdb=" O ARG D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 910 No H-bonds generated for 'chain 'D' and resid 908 through 910' Processing helix chain 'D' and resid 927 through 944 Processing helix chain 'D' and resid 950 through 969 Processing helix chain 'C' and resid 28 through 41 Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 80 through 91 removed outlier: 4.263A pdb=" N HIS C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 150 removed outlier: 4.004A pdb=" N TRP C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.718A pdb=" N TYR C 184 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 211 removed outlier: 3.883A pdb=" N PHE C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.510A pdb=" N LEU C 227 " --> pdb=" O HIS C 223 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.949A pdb=" N LEU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET C 286 " --> pdb=" O ILE C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.542A pdb=" N CYS C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 352 through 370 removed outlier: 3.782A pdb=" N THR C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 420 Proline residue: C 412 - end of helix Processing helix chain 'C' and resid 430 through 445 Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.647A pdb=" N ASP C 456 " --> pdb=" O ASP C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 474 removed outlier: 3.799A pdb=" N LEU C 466 " --> pdb=" O TYR C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 488 removed outlier: 4.218A pdb=" N GLN C 482 " --> pdb=" O PRO C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 518 removed outlier: 4.371A pdb=" N LEU C 515 " --> pdb=" O PRO C 511 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN C 518 " --> pdb=" O PRO C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 523 removed outlier: 3.546A pdb=" N ASP C 523 " --> pdb=" O ILE C 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 523' Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'C' and resid 549 through 572 removed outlier: 3.896A pdb=" N GLN C 553 " --> pdb=" O GLN C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 587 Processing helix chain 'C' and resid 620 through 628 removed outlier: 4.118A pdb=" N ALA C 624 " --> pdb=" O PRO C 620 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN C 625 " --> pdb=" O PRO C 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 709 Processing helix chain 'E' and resid 736 through 746 Processing helix chain 'E' and resid 748 through 771 Processing helix chain 'E' and resid 772 through 773 No H-bonds generated for 'chain 'E' and resid 772 through 773' Processing helix chain 'E' and resid 774 through 780 removed outlier: 3.538A pdb=" N HIS E 777 " --> pdb=" O ARG E 774 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS E 779 " --> pdb=" O ALA E 776 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 796 removed outlier: 3.635A pdb=" N LEU E 785 " --> pdb=" O LEU E 781 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR E 796 " --> pdb=" O GLN E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 801 through 817 removed outlier: 4.509A pdb=" N ASN E 805 " --> pdb=" O ARG E 801 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY E 806 " --> pdb=" O SER E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 824 through 828 removed outlier: 3.738A pdb=" N HIS E 828 " --> pdb=" O GLU E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 839 through 864 removed outlier: 3.699A pdb=" N VAL E 843 " --> pdb=" O ASP E 839 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU E 844 " --> pdb=" O PRO E 840 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 845 " --> pdb=" O PHE E 841 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR E 850 " --> pdb=" O SER E 846 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE E 851 " --> pdb=" O LEU E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 882 through 887 Processing helix chain 'E' and resid 896 through 904 Processing helix chain 'E' and resid 927 through 944 Processing helix chain 'E' and resid 951 through 968 removed outlier: 4.033A pdb=" N GLN E 957 " --> pdb=" O GLN E 953 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 39 removed outlier: 4.255A pdb=" N HIS B 3 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.503A pdb=" N HIS B 80 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 34 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 31 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLU A 36 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG A 29 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 652 through 656 removed outlier: 5.724A pdb=" N THR D 652 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 689 " --> pdb=" O THR D 652 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N HIS D 714 " --> pdb=" O HIS D 688 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL D 690 " --> pdb=" O HIS D 714 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA D 716 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU D 692 " --> pdb=" O ALA D 716 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY D 724 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR E 727 " --> pdb=" O ALA D 725 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 724 " --> pdb=" O ILE E 715 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E 713 " --> pdb=" O VAL E 726 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR E 652 " --> pdb=" O HIS E 688 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL E 690 " --> pdb=" O THR E 652 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU E 654 " --> pdb=" O VAL E 690 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 692 " --> pdb=" O LEU E 654 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU E 656 " --> pdb=" O LEU E 692 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 677 through 683 removed outlier: 5.397A pdb=" N ILE D 678 " --> pdb=" O LYS D 674 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS D 674 " --> pdb=" O ILE D 678 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 912 through 916 Processing sheet with id=AA6, first strand: chain 'C' and resid 50 through 53 Processing sheet with id=AA7, first strand: chain 'C' and resid 235 through 244 removed outlier: 5.682A pdb=" N ILE C 236 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER C 268 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N HIS C 238 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLY C 263 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 161 " --> pdb=" O LYS C 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 394 removed outlier: 3.509A pdb=" N HIS C 492 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 580 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 533 through 538 removed outlier: 4.112A pdb=" N ILE C 544 " --> pdb=" O TYR C 450 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 677 through 683 removed outlier: 6.419A pdb=" N VAL E 672 " --> pdb=" O THR E 679 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS E 681 " --> pdb=" O LEU E 670 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU E 670 " --> pdb=" O LYS E 681 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 912 through 916 544 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3866 1.34 - 1.46: 1824 1.46 - 1.57: 6203 1.57 - 1.69: 1 1.69 - 1.81: 43 Bond restraints: 11937 Sorted by residual: bond pdb=" CB VAL E 713 " pdb=" CG1 VAL E 713 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.23e+00 bond pdb=" CB LYS C 346 " pdb=" CG LYS C 346 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.32e+00 bond pdb=" CB VAL E 690 " pdb=" CG1 VAL E 690 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.28e+00 bond pdb=" N LYS C 307 " pdb=" CA LYS C 307 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.97e+00 bond pdb=" CB ASP C 540 " pdb=" CG ASP C 540 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.81e+00 ... (remaining 11932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 15461 1.79 - 3.57: 539 3.57 - 5.36: 85 5.36 - 7.15: 29 7.15 - 8.94: 7 Bond angle restraints: 16121 Sorted by residual: angle pdb=" C ASP D 666 " pdb=" N ASN D 667 " pdb=" CA ASN D 667 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" C GLU E 979 " pdb=" N LEU E 980 " pdb=" CA LEU E 980 " ideal model delta sigma weight residual 120.82 126.55 -5.73 1.47e+00 4.63e-01 1.52e+01 angle pdb=" N LEU E 919 " pdb=" CA LEU E 919 " pdb=" C LEU E 919 " ideal model delta sigma weight residual 114.75 109.95 4.80 1.26e+00 6.30e-01 1.45e+01 angle pdb=" CA GLN C 232 " pdb=" CB GLN C 232 " pdb=" CG GLN C 232 " ideal model delta sigma weight residual 114.10 121.56 -7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" C ALA D 877 " pdb=" N ALA D 878 " pdb=" CA ALA D 878 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 ... (remaining 16116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6425 17.86 - 35.73: 648 35.73 - 53.59: 104 53.59 - 71.45: 22 71.45 - 89.32: 4 Dihedral angle restraints: 7203 sinusoidal: 3012 harmonic: 4191 Sorted by residual: dihedral pdb=" CA ARG E 891 " pdb=" C ARG E 891 " pdb=" N HIS E 892 " pdb=" CA HIS E 892 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG D 835 " pdb=" C ARG D 835 " pdb=" N PRO D 836 " pdb=" CA PRO D 836 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASP E 917 " pdb=" C ASP E 917 " pdb=" N HIS E 918 " pdb=" CA HIS E 918 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 7200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1458 0.065 - 0.130: 280 0.130 - 0.194: 26 0.194 - 0.259: 1 0.259 - 0.324: 1 Chirality restraints: 1766 Sorted by residual: chirality pdb=" CB ILE A 66 " pdb=" CA ILE A 66 " pdb=" CG1 ILE A 66 " pdb=" CG2 ILE A 66 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CG LEU C 36 " pdb=" CB LEU C 36 " pdb=" CD1 LEU C 36 " pdb=" CD2 LEU C 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU C 241 " pdb=" CB LEU C 241 " pdb=" CD1 LEU C 241 " pdb=" CD2 LEU C 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 1763 not shown) Planarity restraints: 2069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 41 " -0.044 5.00e-02 4.00e+02 6.79e-02 7.39e+00 pdb=" N PRO A 42 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 42 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 42 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 477 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO C 478 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 478 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 478 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 346 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C LYS C 346 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS C 346 " 0.015 2.00e-02 2.50e+03 pdb=" N THR C 347 " 0.013 2.00e-02 2.50e+03 ... (remaining 2066 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2085 2.77 - 3.30: 10599 3.30 - 3.83: 17653 3.83 - 4.37: 20562 4.37 - 4.90: 37055 Nonbonded interactions: 87954 Sorted by model distance: nonbonded pdb=" OD1 ASP C 415 " pdb=" OH TYR C 425 " model vdw 2.237 3.040 nonbonded pdb=" NE2 HIS E 714 " pdb=" OD2 ASP E 857 " model vdw 2.246 3.120 nonbonded pdb=" O GLN E 906 " pdb=" NH2 ARG E 933 " model vdw 2.277 3.120 nonbonded pdb=" OH TYR D 815 " pdb=" OE1 GLU D 895 " model vdw 2.283 3.040 nonbonded pdb=" NE ARG B 44 " pdb=" OE2 GLU E 685 " model vdw 2.293 3.120 ... (remaining 87949 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 90) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 650 through 981) } 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: 4.420 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.005 0.075 11937 Z= 0.236 Angle : 0.831 8.936 16121 Z= 0.471 Chirality : 0.050 0.324 1766 Planarity : 0.005 0.068 2069 Dihedral : 14.402 89.317 4483 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.21), residues: 1407 helix: 0.28 (0.20), residues: 631 sheet: -0.06 (0.41), residues: 162 loop : -1.82 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG E 834 TYR 0.021 0.002 TYR D 815 PHE 0.020 0.002 PHE D 819 TRP 0.028 0.002 TRP C 162 HIS 0.009 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00547 (11937) covalent geometry : angle 0.83125 (16121) hydrogen bonds : bond 0.13900 ( 544) hydrogen bonds : angle 5.94801 ( 1551) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.380 Fit side-chains REVERT: A 48 LEU cc_start: 0.7020 (tt) cc_final: 0.6482 (mp) REVERT: C 355 ARG cc_start: 0.5808 (tpt-90) cc_final: 0.5605 (ttp80) REVERT: C 368 ARG cc_start: 0.8100 (tmt170) cc_final: 0.7575 (ttm170) REVERT: E 779 LYS cc_start: 0.7532 (tmtt) cc_final: 0.7174 (tppt) REVERT: E 834 ARG cc_start: 0.8072 (ttm110) cc_final: 0.7760 (ttm110) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1175 time to fit residues: 23.6535 Evaluate side-chains 119 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN D 653 HIS ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN D 842 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.158971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130425 restraints weight = 15111.414| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.14 r_work: 0.3455 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11937 Z= 0.145 Angle : 0.584 7.317 16121 Z= 0.310 Chirality : 0.044 0.178 1766 Planarity : 0.005 0.064 2069 Dihedral : 4.841 20.332 1554 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.87 % Allowed : 5.62 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.22), residues: 1407 helix: 1.04 (0.21), residues: 632 sheet: 0.56 (0.43), residues: 152 loop : -1.68 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 834 TYR 0.014 0.001 TYR A 26 PHE 0.017 0.001 PHE C 70 TRP 0.024 0.002 TRP C 162 HIS 0.007 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00336 (11937) covalent geometry : angle 0.58353 (16121) hydrogen bonds : bond 0.04960 ( 544) hydrogen bonds : angle 4.77884 ( 1551) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.488 Fit side-chains REVERT: D 686 GLN cc_start: 0.8624 (mt0) cc_final: 0.8229 (mp10) REVERT: C 80 GLN cc_start: 0.8031 (pp30) cc_final: 0.7699 (pp30) REVERT: C 355 ARG cc_start: 0.6409 (tpt-90) cc_final: 0.5946 (ttp-110) REVERT: C 368 ARG cc_start: 0.8107 (tmt170) cc_final: 0.7546 (ttm-80) REVERT: C 560 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7803 (tm-30) REVERT: E 779 LYS cc_start: 0.7730 (tmtt) cc_final: 0.7269 (tppt) outliers start: 11 outliers final: 10 residues processed: 132 average time/residue: 0.1245 time to fit residues: 23.1275 Evaluate side-chains 131 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 919 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 137 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 136 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.160476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131605 restraints weight = 15107.079| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.18 r_work: 0.3472 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11937 Z= 0.115 Angle : 0.524 6.945 16121 Z= 0.276 Chirality : 0.042 0.151 1766 Planarity : 0.004 0.065 2069 Dihedral : 4.472 19.780 1554 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.19 % Allowed : 8.00 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1407 helix: 1.52 (0.21), residues: 629 sheet: 0.53 (0.42), residues: 154 loop : -1.52 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 834 TYR 0.011 0.001 TYR C 398 PHE 0.015 0.001 PHE C 70 TRP 0.020 0.001 TRP C 162 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00260 (11937) covalent geometry : angle 0.52363 (16121) hydrogen bonds : bond 0.04146 ( 544) hydrogen bonds : angle 4.40086 ( 1551) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.463 Fit side-chains REVERT: D 686 GLN cc_start: 0.8597 (mt0) cc_final: 0.8215 (mp10) REVERT: C 80 GLN cc_start: 0.8112 (pp30) cc_final: 0.7645 (pp30) REVERT: C 116 SER cc_start: 0.7787 (t) cc_final: 0.7198 (m) REVERT: C 355 ARG cc_start: 0.6444 (tpt-90) cc_final: 0.5914 (ttp80) REVERT: C 368 ARG cc_start: 0.8059 (tmt170) cc_final: 0.7595 (ttm-80) REVERT: C 560 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7782 (tm-30) REVERT: E 779 LYS cc_start: 0.7701 (tmtt) cc_final: 0.7269 (tppt) REVERT: E 944 LYS cc_start: 0.8008 (mttp) cc_final: 0.7720 (mtpt) outliers start: 15 outliers final: 11 residues processed: 141 average time/residue: 0.1143 time to fit residues: 22.9630 Evaluate side-chains 123 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 0.0670 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 56 optimal weight: 0.0370 chunk 128 optimal weight: 1.9990 chunk 140 optimal weight: 0.0170 chunk 91 optimal weight: 1.9990 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 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 = 0.3968 r_free = 0.3968 target = 0.162052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134180 restraints weight = 15008.127| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.14 r_work: 0.3509 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11937 Z= 0.098 Angle : 0.497 6.357 16121 Z= 0.261 Chirality : 0.041 0.152 1766 Planarity : 0.004 0.062 2069 Dihedral : 4.241 19.614 1554 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.35 % Allowed : 9.74 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.23), residues: 1407 helix: 1.80 (0.21), residues: 630 sheet: 0.35 (0.41), residues: 164 loop : -1.38 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 834 TYR 0.009 0.001 TYR C 398 PHE 0.020 0.001 PHE C 35 TRP 0.019 0.001 TRP C 162 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00211 (11937) covalent geometry : angle 0.49665 (16121) hydrogen bonds : bond 0.03658 ( 544) hydrogen bonds : angle 4.18168 ( 1551) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.462 Fit side-chains REVERT: D 686 GLN cc_start: 0.8602 (mt0) cc_final: 0.8234 (mp10) REVERT: C 80 GLN cc_start: 0.8090 (pp30) cc_final: 0.7537 (pp30) REVERT: C 116 SER cc_start: 0.7682 (t) cc_final: 0.7152 (m) REVERT: C 355 ARG cc_start: 0.6485 (tpt-90) cc_final: 0.6021 (ttp-110) REVERT: C 368 ARG cc_start: 0.8052 (tmt170) cc_final: 0.7596 (ttm-80) REVERT: C 560 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7746 (tm-30) REVERT: E 779 LYS cc_start: 0.7732 (tmtt) cc_final: 0.7296 (tppt) REVERT: E 834 ARG cc_start: 0.8235 (ttm110) cc_final: 0.8023 (ttm110) REVERT: E 944 LYS cc_start: 0.7948 (mttp) cc_final: 0.7700 (mtpt) outliers start: 17 outliers final: 14 residues processed: 146 average time/residue: 0.1194 time to fit residues: 24.8848 Evaluate side-chains 136 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 919 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 132 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 2 optimal weight: 0.0570 chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 110 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 973 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.158672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130197 restraints weight = 15041.308| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.13 r_work: 0.3462 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11937 Z= 0.135 Angle : 0.527 7.008 16121 Z= 0.275 Chirality : 0.043 0.162 1766 Planarity : 0.004 0.060 2069 Dihedral : 4.270 19.736 1554 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.50 % Allowed : 11.40 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.23), residues: 1407 helix: 1.77 (0.21), residues: 630 sheet: 0.52 (0.42), residues: 154 loop : -1.42 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 834 TYR 0.022 0.001 TYR C 210 PHE 0.021 0.001 PHE C 35 TRP 0.017 0.001 TRP C 162 HIS 0.004 0.001 HIS E 892 Details of bonding type rmsd covalent geometry : bond 0.00320 (11937) covalent geometry : angle 0.52668 (16121) hydrogen bonds : bond 0.04188 ( 544) hydrogen bonds : angle 4.19450 ( 1551) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.479 Fit side-chains REVERT: D 686 GLN cc_start: 0.8595 (mt0) cc_final: 0.8342 (mp10) REVERT: C 30 MET cc_start: 0.7620 (mtm) cc_final: 0.6034 (mmp) REVERT: C 80 GLN cc_start: 0.8094 (pp30) cc_final: 0.7475 (pp30) REVERT: C 116 SER cc_start: 0.7760 (t) cc_final: 0.7214 (m) REVERT: C 355 ARG cc_start: 0.6446 (tpt-90) cc_final: 0.5983 (ttp-110) REVERT: C 368 ARG cc_start: 0.8067 (tmt170) cc_final: 0.7607 (ttm-80) REVERT: E 779 LYS cc_start: 0.7767 (tmtt) cc_final: 0.7380 (tppt) REVERT: E 944 LYS cc_start: 0.8087 (mttp) cc_final: 0.7793 (mtpt) outliers start: 19 outliers final: 16 residues processed: 140 average time/residue: 0.1149 time to fit residues: 23.2115 Evaluate side-chains 137 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 919 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 133 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.158919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130459 restraints weight = 15053.442| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.21 r_work: 0.3455 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11937 Z= 0.126 Angle : 0.518 6.847 16121 Z= 0.271 Chirality : 0.042 0.162 1766 Planarity : 0.004 0.059 2069 Dihedral : 4.233 19.708 1554 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.43 % Allowed : 12.11 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.23), residues: 1407 helix: 1.83 (0.21), residues: 629 sheet: 0.47 (0.42), residues: 154 loop : -1.39 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 834 TYR 0.015 0.001 TYR C 210 PHE 0.022 0.001 PHE C 35 TRP 0.017 0.001 TRP C 162 HIS 0.004 0.001 HIS D 653 Details of bonding type rmsd covalent geometry : bond 0.00296 (11937) covalent geometry : angle 0.51759 (16121) hydrogen bonds : bond 0.04012 ( 544) hydrogen bonds : angle 4.13579 ( 1551) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.401 Fit side-chains REVERT: D 686 GLN cc_start: 0.8597 (mt0) cc_final: 0.8341 (mp10) REVERT: C 30 MET cc_start: 0.7616 (mtm) cc_final: 0.6031 (mmp) REVERT: C 80 GLN cc_start: 0.8156 (pp30) cc_final: 0.7589 (pp30) REVERT: C 116 SER cc_start: 0.7667 (t) cc_final: 0.7142 (m) REVERT: C 355 ARG cc_start: 0.6413 (tpt-90) cc_final: 0.5950 (ttp-110) REVERT: C 368 ARG cc_start: 0.8084 (tmt170) cc_final: 0.7510 (ttm170) REVERT: C 560 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7914 (tm-30) REVERT: E 779 LYS cc_start: 0.7845 (tmtt) cc_final: 0.7443 (tppt) outliers start: 18 outliers final: 14 residues processed: 138 average time/residue: 0.1101 time to fit residues: 22.0250 Evaluate side-chains 135 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 122 optimal weight: 0.0270 chunk 32 optimal weight: 0.0770 chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 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 = 0.3957 r_free = 0.3957 target = 0.161072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131558 restraints weight = 15048.419| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.22 r_work: 0.3505 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11937 Z= 0.094 Angle : 0.479 6.629 16121 Z= 0.251 Chirality : 0.041 0.166 1766 Planarity : 0.004 0.058 2069 Dihedral : 3.996 19.410 1554 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.19 % Allowed : 12.35 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1407 helix: 2.10 (0.22), residues: 630 sheet: 0.52 (0.42), residues: 154 loop : -1.31 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 834 TYR 0.015 0.001 TYR C 210 PHE 0.023 0.001 PHE C 35 TRP 0.018 0.001 TRP C 162 HIS 0.003 0.001 HIS E 952 Details of bonding type rmsd covalent geometry : bond 0.00205 (11937) covalent geometry : angle 0.47887 (16121) hydrogen bonds : bond 0.03357 ( 544) hydrogen bonds : angle 3.96540 ( 1551) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.443 Fit side-chains REVERT: D 686 GLN cc_start: 0.8607 (mt0) cc_final: 0.8334 (mp10) REVERT: C 30 MET cc_start: 0.7539 (mtm) cc_final: 0.5992 (mmp) REVERT: C 80 GLN cc_start: 0.8111 (pp30) cc_final: 0.7618 (pp30) REVERT: C 116 SER cc_start: 0.7659 (t) cc_final: 0.7119 (m) REVERT: C 355 ARG cc_start: 0.6414 (tpt-90) cc_final: 0.5980 (ttp-110) REVERT: C 368 ARG cc_start: 0.8057 (tmt170) cc_final: 0.7596 (mtt-85) REVERT: C 560 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7851 (tm-30) REVERT: E 779 LYS cc_start: 0.7774 (tmtt) cc_final: 0.7389 (tppt) REVERT: E 944 LYS cc_start: 0.7937 (mttp) cc_final: 0.7644 (mtpt) REVERT: E 977 TRP cc_start: 0.8251 (t60) cc_final: 0.7958 (t60) outliers start: 15 outliers final: 11 residues processed: 135 average time/residue: 0.1110 time to fit residues: 21.2982 Evaluate side-chains 130 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 88 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 84 optimal weight: 0.0270 chunk 129 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 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 = 0.3951 r_free = 0.3951 target = 0.160438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132175 restraints weight = 15053.629| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.16 r_work: 0.3476 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11937 Z= 0.120 Angle : 0.512 7.018 16121 Z= 0.266 Chirality : 0.042 0.167 1766 Planarity : 0.004 0.058 2069 Dihedral : 4.058 19.679 1554 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.43 % Allowed : 12.83 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.23), residues: 1407 helix: 2.08 (0.21), residues: 631 sheet: 0.49 (0.42), residues: 154 loop : -1.33 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 834 TYR 0.013 0.001 TYR C 210 PHE 0.024 0.001 PHE C 35 TRP 0.015 0.001 TRP C 162 HIS 0.003 0.001 HIS E 892 Details of bonding type rmsd covalent geometry : bond 0.00282 (11937) covalent geometry : angle 0.51229 (16121) hydrogen bonds : bond 0.03788 ( 544) hydrogen bonds : angle 4.02727 ( 1551) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.480 Fit side-chains REVERT: D 686 GLN cc_start: 0.8605 (mt0) cc_final: 0.8315 (mp10) REVERT: C 30 MET cc_start: 0.7571 (mtm) cc_final: 0.6002 (mmp) REVERT: C 80 GLN cc_start: 0.8084 (pp30) cc_final: 0.7587 (pp30) REVERT: C 116 SER cc_start: 0.7603 (t) cc_final: 0.7052 (m) REVERT: C 117 LEU cc_start: 0.7870 (mt) cc_final: 0.7629 (mp) REVERT: C 355 ARG cc_start: 0.6455 (tpt-90) cc_final: 0.6010 (ttp-110) REVERT: C 368 ARG cc_start: 0.8066 (tmt170) cc_final: 0.7613 (mtt-85) REVERT: C 560 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7847 (tm-30) REVERT: E 779 LYS cc_start: 0.7799 (tmtt) cc_final: 0.7404 (tppt) REVERT: E 834 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7901 (ttm110) REVERT: E 944 LYS cc_start: 0.8007 (mttp) cc_final: 0.7707 (mtpt) REVERT: E 977 TRP cc_start: 0.8319 (t60) cc_final: 0.8029 (t60) outliers start: 18 outliers final: 15 residues processed: 133 average time/residue: 0.1231 time to fit residues: 23.1448 Evaluate side-chains 133 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 59 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 132 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 61 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.160326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.132284 restraints weight = 14978.016| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.18 r_work: 0.3485 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11937 Z= 0.111 Angle : 0.504 7.673 16121 Z= 0.261 Chirality : 0.042 0.159 1766 Planarity : 0.004 0.056 2069 Dihedral : 4.032 19.522 1554 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.19 % Allowed : 12.83 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.23), residues: 1407 helix: 2.11 (0.21), residues: 630 sheet: 0.33 (0.41), residues: 160 loop : -1.24 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 834 TYR 0.012 0.001 TYR C 210 PHE 0.024 0.001 PHE C 35 TRP 0.016 0.001 TRP C 162 HIS 0.003 0.001 HIS E 892 Details of bonding type rmsd covalent geometry : bond 0.00257 (11937) covalent geometry : angle 0.50397 (16121) hydrogen bonds : bond 0.03699 ( 544) hydrogen bonds : angle 4.00420 ( 1551) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.393 Fit side-chains REVERT: D 686 GLN cc_start: 0.8594 (mt0) cc_final: 0.8323 (mp10) REVERT: C 30 MET cc_start: 0.7561 (mtm) cc_final: 0.6005 (mmp) REVERT: C 80 GLN cc_start: 0.8076 (pp30) cc_final: 0.7609 (pp30) REVERT: C 116 SER cc_start: 0.7581 (t) cc_final: 0.7032 (m) REVERT: C 117 LEU cc_start: 0.7863 (mt) cc_final: 0.7624 (mp) REVERT: C 355 ARG cc_start: 0.6439 (tpt-90) cc_final: 0.5998 (ttp-110) REVERT: C 368 ARG cc_start: 0.8061 (tmt170) cc_final: 0.7621 (mtt-85) REVERT: C 560 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7860 (tm-30) REVERT: E 779 LYS cc_start: 0.7851 (tmtt) cc_final: 0.7454 (tppt) REVERT: E 944 LYS cc_start: 0.8033 (mttp) cc_final: 0.7703 (mtpt) REVERT: E 977 TRP cc_start: 0.8297 (t60) cc_final: 0.8026 (t60) outliers start: 15 outliers final: 15 residues processed: 131 average time/residue: 0.1221 time to fit residues: 22.5401 Evaluate side-chains 135 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 40 optimal weight: 0.0060 chunk 113 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 chunk 62 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.161771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133795 restraints weight = 15043.563| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.18 r_work: 0.3499 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11937 Z= 0.097 Angle : 0.495 6.960 16121 Z= 0.255 Chirality : 0.041 0.152 1766 Planarity : 0.004 0.056 2069 Dihedral : 3.908 19.427 1554 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.27 % Allowed : 12.83 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.23), residues: 1407 helix: 2.23 (0.22), residues: 630 sheet: 0.35 (0.41), residues: 160 loop : -1.17 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 834 TYR 0.020 0.001 TYR C 442 PHE 0.024 0.001 PHE C 35 TRP 0.017 0.001 TRP C 162 HIS 0.003 0.001 HIS E 952 Details of bonding type rmsd covalent geometry : bond 0.00216 (11937) covalent geometry : angle 0.49506 (16121) hydrogen bonds : bond 0.03411 ( 544) hydrogen bonds : angle 3.92017 ( 1551) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.410 Fit side-chains REVERT: D 686 GLN cc_start: 0.8597 (mt0) cc_final: 0.8330 (mp10) REVERT: C 80 GLN cc_start: 0.8093 (pp30) cc_final: 0.7619 (pp30) REVERT: C 116 SER cc_start: 0.7469 (t) cc_final: 0.6867 (m) REVERT: C 117 LEU cc_start: 0.7841 (mt) cc_final: 0.7624 (mp) REVERT: C 355 ARG cc_start: 0.6412 (tpt-90) cc_final: 0.5989 (ttp-110) REVERT: C 368 ARG cc_start: 0.8095 (tmt170) cc_final: 0.7594 (ttm-80) REVERT: C 373 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7300 (tm-30) REVERT: C 560 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7806 (tm-30) REVERT: E 779 LYS cc_start: 0.7871 (tmtt) cc_final: 0.7495 (tppt) REVERT: E 834 ARG cc_start: 0.8108 (ttm110) cc_final: 0.6615 (tpt170) REVERT: E 944 LYS cc_start: 0.7937 (mttp) cc_final: 0.7618 (mtpt) REVERT: E 977 TRP cc_start: 0.8287 (t60) cc_final: 0.8011 (t60) outliers start: 16 outliers final: 13 residues processed: 141 average time/residue: 0.1104 time to fit residues: 22.1548 Evaluate side-chains 135 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 107 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 65 optimal weight: 0.0570 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN A 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.159973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131874 restraints weight = 15123.394| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.21 r_work: 0.3473 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11937 Z= 0.128 Angle : 0.529 10.354 16121 Z= 0.271 Chirality : 0.043 0.154 1766 Planarity : 0.004 0.063 2069 Dihedral : 4.010 19.623 1554 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.43 % Allowed : 13.14 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1407 helix: 2.12 (0.21), residues: 630 sheet: 0.38 (0.41), residues: 160 loop : -1.18 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 834 TYR 0.017 0.001 TYR C 210 PHE 0.025 0.001 PHE C 35 TRP 0.015 0.001 TRP C 162 HIS 0.004 0.001 HIS D 954 Details of bonding type rmsd covalent geometry : bond 0.00305 (11937) covalent geometry : angle 0.52914 (16121) hydrogen bonds : bond 0.03849 ( 544) hydrogen bonds : angle 4.01180 ( 1551) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2972.51 seconds wall clock time: 51 minutes 50.49 seconds (3110.49 seconds total)