Starting phenix.real_space_refine on Tue Jul 29 19:48:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kft_22855/07_2025/7kft_22855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kft_22855/07_2025/7kft_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7kft_22855/07_2025/7kft_22855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kft_22855/07_2025/7kft_22855.map" model { file = "/net/cci-nas-00/data/ceres_data/7kft_22855/07_2025/7kft_22855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kft_22855/07_2025/7kft_22855.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.23, per 1000 atoms: 0.62 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: 2.28 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.23 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: 3.45 Time building geometry restraints manager: 2.78 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: 2.590 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: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.170 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.310 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (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 TRP 0.028 0.002 TRP C 162 HIS 0.009 0.001 HIS A 53 PHE 0.020 0.002 PHE D 819 TYR 0.021 0.002 TYR D 815 ARG 0.028 0.001 ARG E 834 Details of bonding type rmsd hydrogen bonds : bond 0.13900 ( 544) hydrogen bonds : angle 5.94801 ( 1551) covalent geometry : bond 0.00547 (11937) covalent geometry : angle 0.83125 (16121) *********************** 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 : 1.202 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: 0.2506 time to fit residues: 50.5040 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 : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.7980 chunk 106 optimal weight: 0.0070 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 348 ASN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.159973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131765 restraints weight = 14953.755| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.13 r_work: 0.3477 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11937 Z= 0.129 Angle : 0.568 7.334 16121 Z= 0.301 Chirality : 0.043 0.171 1766 Planarity : 0.004 0.064 2069 Dihedral : 4.763 20.012 1554 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.79 % Allowed : 6.02 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1407 helix: 1.11 (0.21), residues: 633 sheet: 0.29 (0.42), residues: 162 loop : -1.61 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 162 HIS 0.007 0.001 HIS C 91 PHE 0.016 0.001 PHE C 70 TYR 0.014 0.001 TYR A 26 ARG 0.005 0.000 ARG E 834 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 544) hydrogen bonds : angle 4.70936 ( 1551) covalent geometry : bond 0.00291 (11937) covalent geometry : angle 0.56788 (16121) *********************** 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 136 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 1.316 Fit side-chains REVERT: D 686 GLN cc_start: 0.8602 (mt0) cc_final: 0.8212 (mp10) REVERT: C 80 GLN cc_start: 0.8046 (pp30) cc_final: 0.7723 (pp30) REVERT: C 355 ARG cc_start: 0.6404 (tpt-90) cc_final: 0.5973 (ttp-110) REVERT: C 368 ARG cc_start: 0.8066 (tmt170) cc_final: 0.7593 (ttm-80) REVERT: C 560 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7787 (tm-30) REVERT: E 779 LYS cc_start: 0.7734 (tmtt) cc_final: 0.7266 (tppt) REVERT: E 946 SER cc_start: 0.7367 (m) cc_final: 0.7097 (p) outliers start: 10 outliers final: 8 residues processed: 131 average time/residue: 0.2594 time to fit residues: 48.2898 Evaluate side-chains 126 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 302 LEU 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 120 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 8 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.159889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131229 restraints weight = 15206.798| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.16 r_work: 0.3462 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11937 Z= 0.128 Angle : 0.539 7.045 16121 Z= 0.284 Chirality : 0.043 0.151 1766 Planarity : 0.004 0.066 2069 Dihedral : 4.538 19.858 1554 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.50 % Allowed : 7.52 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1407 helix: 1.39 (0.21), residues: 634 sheet: 0.52 (0.42), residues: 154 loop : -1.59 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 162 HIS 0.005 0.001 HIS C 91 PHE 0.015 0.001 PHE C 70 TYR 0.012 0.001 TYR C 398 ARG 0.007 0.000 ARG E 834 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 544) hydrogen bonds : angle 4.46801 ( 1551) covalent geometry : bond 0.00297 (11937) covalent geometry : angle 0.53941 (16121) *********************** 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 146 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.274 Fit side-chains REVERT: D 686 GLN cc_start: 0.8608 (mt0) cc_final: 0.8223 (mp10) REVERT: C 80 GLN cc_start: 0.8128 (pp30) cc_final: 0.7664 (pp30) REVERT: C 355 ARG cc_start: 0.6377 (tpt-90) cc_final: 0.5863 (ttp80) REVERT: C 368 ARG cc_start: 0.8073 (tmt170) cc_final: 0.7596 (ttm-80) REVERT: C 560 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7785 (tm-30) REVERT: E 779 LYS cc_start: 0.7701 (tmtt) cc_final: 0.7257 (tppt) REVERT: E 946 SER cc_start: 0.7324 (m) cc_final: 0.7121 (p) outliers start: 19 outliers final: 14 residues processed: 141 average time/residue: 0.2454 time to fit residues: 50.3035 Evaluate side-chains 131 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 267 LEU 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 690 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 919 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.159926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132363 restraints weight = 14920.568| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.13 r_work: 0.3470 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1381 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= 0.118 Angle : 0.514 6.502 16121 Z= 0.270 Chirality : 0.042 0.157 1766 Planarity : 0.004 0.062 2069 Dihedral : 4.372 19.615 1554 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.58 % Allowed : 9.74 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1407 helix: 1.68 (0.21), residues: 629 sheet: 0.50 (0.42), residues: 154 loop : -1.50 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 162 HIS 0.004 0.001 HIS C 91 PHE 0.021 0.001 PHE C 35 TYR 0.011 0.001 TYR C 398 ARG 0.010 0.000 ARG E 834 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 544) hydrogen bonds : angle 4.29097 ( 1551) covalent geometry : bond 0.00272 (11937) covalent geometry : angle 0.51367 (16121) *********************** 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: 20 poor density : 130 time to evaluate : 1.254 Fit side-chains REVERT: D 686 GLN cc_start: 0.8588 (mt0) cc_final: 0.8235 (mp10) REVERT: D 938 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7941 (tp) REVERT: C 80 GLN cc_start: 0.8100 (pp30) cc_final: 0.7534 (pp30) REVERT: C 116 SER cc_start: 0.7796 (t) cc_final: 0.7268 (m) REVERT: C 355 ARG cc_start: 0.6452 (tpt-90) cc_final: 0.5996 (ttp-110) REVERT: C 368 ARG cc_start: 0.8066 (tmt170) cc_final: 0.7594 (ttm-80) REVERT: C 560 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7793 (tm-30) REVERT: E 779 LYS cc_start: 0.7773 (tmtt) cc_final: 0.7345 (tppt) REVERT: E 834 ARG cc_start: 0.8281 (ttm110) cc_final: 0.8028 (ttm110) REVERT: E 944 LYS cc_start: 0.8014 (mttp) cc_final: 0.7751 (mtpt) outliers start: 20 outliers final: 15 residues processed: 144 average time/residue: 0.2422 time to fit residues: 50.7444 Evaluate side-chains 131 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain D residue 938 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 125 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.157734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129219 restraints weight = 15098.412| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.14 r_work: 0.3444 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11937 Z= 0.167 Angle : 0.556 6.624 16121 Z= 0.292 Chirality : 0.044 0.160 1766 Planarity : 0.004 0.060 2069 Dihedral : 4.475 20.261 1554 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.50 % Allowed : 11.56 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.23), residues: 1407 helix: 1.49 (0.21), residues: 635 sheet: 0.46 (0.42), residues: 153 loop : -1.57 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 162 HIS 0.004 0.001 HIS E 696 PHE 0.021 0.002 PHE C 35 TYR 0.022 0.002 TYR C 210 ARG 0.006 0.000 ARG E 834 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 544) hydrogen bonds : angle 4.35302 ( 1551) covalent geometry : bond 0.00404 (11937) covalent geometry : angle 0.55579 (16121) *********************** 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 134 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.291 Fit side-chains REVERT: D 686 GLN cc_start: 0.8595 (mt0) cc_final: 0.8337 (mp10) REVERT: D 938 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7986 (tp) REVERT: C 80 GLN cc_start: 0.8120 (pp30) cc_final: 0.7461 (pp30) REVERT: C 116 SER cc_start: 0.7655 (t) cc_final: 0.7040 (m) REVERT: C 355 ARG cc_start: 0.6474 (tpt-90) cc_final: 0.6012 (ttp-110) REVERT: C 368 ARG cc_start: 0.8111 (tmt170) cc_final: 0.7575 (ttm-80) REVERT: E 779 LYS cc_start: 0.7781 (tmtt) cc_final: 0.7423 (tppt) outliers start: 19 outliers final: 15 residues processed: 128 average time/residue: 0.2450 time to fit residues: 46.0072 Evaluate side-chains 126 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain D residue 938 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.158623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130130 restraints weight = 15124.535| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.15 r_work: 0.3457 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1514 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= 0.137 Angle : 0.529 6.783 16121 Z= 0.279 Chirality : 0.043 0.159 1766 Planarity : 0.004 0.060 2069 Dihedral : 4.390 19.671 1554 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.58 % Allowed : 12.11 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.23), residues: 1407 helix: 1.61 (0.21), residues: 635 sheet: 0.35 (0.42), residues: 154 loop : -1.53 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 162 HIS 0.004 0.001 HIS D 653 PHE 0.022 0.001 PHE C 35 TYR 0.016 0.001 TYR C 210 ARG 0.011 0.000 ARG E 834 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 544) hydrogen bonds : angle 4.24803 ( 1551) covalent geometry : bond 0.00325 (11937) covalent geometry : angle 0.52914 (16121) *********************** 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 142 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.236 Fit side-chains REVERT: D 686 GLN cc_start: 0.8584 (mt0) cc_final: 0.8329 (mp10) REVERT: D 938 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7961 (tp) REVERT: C 80 GLN cc_start: 0.8121 (pp30) cc_final: 0.7521 (pp30) REVERT: C 116 SER cc_start: 0.7617 (t) cc_final: 0.6984 (m) REVERT: C 355 ARG cc_start: 0.6374 (tpt-90) cc_final: 0.5924 (ttp-110) REVERT: C 368 ARG cc_start: 0.8095 (tmt170) cc_final: 0.7575 (ttm-80) REVERT: C 560 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7889 (tm-30) REVERT: E 779 LYS cc_start: 0.7808 (tmtt) cc_final: 0.7450 (tppt) outliers start: 20 outliers final: 16 residues processed: 137 average time/residue: 0.2489 time to fit residues: 48.7843 Evaluate side-chains 134 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain D residue 938 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 0.0170 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 111 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.160867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133045 restraints weight = 15209.432| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.16 r_work: 0.3481 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11937 Z= 0.101 Angle : 0.487 6.015 16121 Z= 0.257 Chirality : 0.041 0.157 1766 Planarity : 0.004 0.059 2069 Dihedral : 4.141 19.370 1554 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.27 % Allowed : 13.06 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.23), residues: 1407 helix: 1.94 (0.21), residues: 630 sheet: 0.24 (0.41), residues: 160 loop : -1.34 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 162 HIS 0.004 0.001 HIS E 952 PHE 0.023 0.001 PHE C 35 TYR 0.015 0.001 TYR C 210 ARG 0.012 0.000 ARG E 834 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 544) hydrogen bonds : angle 4.06208 ( 1551) covalent geometry : bond 0.00226 (11937) covalent geometry : angle 0.48673 (16121) *********************** 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 146 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.325 Fit side-chains REVERT: D 686 GLN cc_start: 0.8622 (mt0) cc_final: 0.8356 (mp10) REVERT: C 80 GLN cc_start: 0.8107 (pp30) cc_final: 0.7597 (pp30) REVERT: C 116 SER cc_start: 0.7397 (t) cc_final: 0.6736 (m) REVERT: C 355 ARG cc_start: 0.6441 (tpt-90) cc_final: 0.5979 (ttp-110) REVERT: C 368 ARG cc_start: 0.8066 (tmt170) cc_final: 0.7476 (ttm170) REVERT: C 442 TYR cc_start: 0.7050 (t80) cc_final: 0.6821 (t80) REVERT: C 560 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7859 (tm-30) REVERT: E 779 LYS cc_start: 0.7795 (tmtt) cc_final: 0.7406 (tppt) REVERT: E 944 LYS cc_start: 0.7962 (mttp) cc_final: 0.7680 (mtpt) REVERT: E 977 TRP cc_start: 0.8306 (t60) cc_final: 0.8059 (t60) outliers start: 16 outliers final: 12 residues processed: 143 average time/residue: 0.2807 time to fit residues: 56.8178 Evaluate side-chains 134 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.955 ------------------------------------------------------------------------------- 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 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 623 LEU 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 137 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.159663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131188 restraints weight = 15108.384| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.14 r_work: 0.3469 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1752 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= 0.124 Angle : 0.515 7.458 16121 Z= 0.270 Chirality : 0.042 0.165 1766 Planarity : 0.004 0.057 2069 Dihedral : 4.171 19.583 1554 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.35 % Allowed : 13.30 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1407 helix: 1.92 (0.21), residues: 628 sheet: 0.25 (0.41), residues: 160 loop : -1.33 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 162 HIS 0.003 0.001 HIS D 653 PHE 0.024 0.001 PHE C 35 TYR 0.013 0.001 TYR C 210 ARG 0.013 0.000 ARG E 834 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 544) hydrogen bonds : angle 4.09629 ( 1551) covalent geometry : bond 0.00292 (11937) covalent geometry : angle 0.51508 (16121) *********************** 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 143 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.346 Fit side-chains REVERT: D 686 GLN cc_start: 0.8608 (mt0) cc_final: 0.8317 (mp10) REVERT: C 80 GLN cc_start: 0.8087 (pp30) cc_final: 0.7575 (pp30) REVERT: C 116 SER cc_start: 0.7545 (t) cc_final: 0.6938 (m) REVERT: C 355 ARG cc_start: 0.6461 (tpt-90) cc_final: 0.5998 (ttp-110) REVERT: C 368 ARG cc_start: 0.8079 (tmt170) cc_final: 0.7618 (ttm-80) REVERT: C 442 TYR cc_start: 0.7225 (t80) cc_final: 0.7004 (t80) REVERT: C 560 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7856 (tm-30) REVERT: E 779 LYS cc_start: 0.7810 (tmtt) cc_final: 0.7418 (tppt) REVERT: E 834 ARG cc_start: 0.8210 (ttm110) cc_final: 0.7944 (ttm110) REVERT: E 944 LYS cc_start: 0.8040 (mttp) cc_final: 0.7737 (mtpt) REVERT: E 977 TRP cc_start: 0.8367 (t60) cc_final: 0.8139 (t60) outliers start: 17 outliers final: 16 residues processed: 138 average time/residue: 0.2737 time to fit residues: 53.5285 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 : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 74 ASP 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 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 C residue 559 VAL Chi-restraints excluded: chain C residue 623 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 127 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.131017 restraints weight = 15134.422| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.16 r_work: 0.3466 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1756 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= 0.133 Angle : 0.523 7.121 16121 Z= 0.274 Chirality : 0.043 0.165 1766 Planarity : 0.004 0.057 2069 Dihedral : 4.211 19.626 1554 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.58 % Allowed : 13.54 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1407 helix: 1.81 (0.21), residues: 634 sheet: 0.24 (0.41), residues: 160 loop : -1.39 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 162 HIS 0.003 0.001 HIS A 53 PHE 0.026 0.001 PHE C 35 TYR 0.018 0.001 TYR C 210 ARG 0.012 0.000 ARG E 834 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 544) hydrogen bonds : angle 4.12486 ( 1551) covalent geometry : bond 0.00315 (11937) covalent geometry : angle 0.52304 (16121) *********************** 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 145 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.705 Fit side-chains REVERT: D 686 GLN cc_start: 0.8607 (mt0) cc_final: 0.8303 (mp10) REVERT: C 80 GLN cc_start: 0.8085 (pp30) cc_final: 0.7622 (pp30) REVERT: C 116 SER cc_start: 0.7554 (t) cc_final: 0.6943 (m) REVERT: C 355 ARG cc_start: 0.6377 (tpt-90) cc_final: 0.5963 (ttp-110) REVERT: C 368 ARG cc_start: 0.8082 (tmt170) cc_final: 0.7617 (ttm-80) REVERT: C 442 TYR cc_start: 0.7196 (t80) cc_final: 0.6976 (t80) REVERT: C 560 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7850 (tm-30) REVERT: E 779 LYS cc_start: 0.7824 (tmtt) cc_final: 0.7433 (tppt) REVERT: E 977 TRP cc_start: 0.8372 (t60) cc_final: 0.8148 (t60) outliers start: 20 outliers final: 15 residues processed: 140 average time/residue: 0.3269 time to fit residues: 66.0269 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 : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 74 ASP 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 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 C residue 559 VAL Chi-restraints excluded: chain C residue 623 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 52 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 70 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.157852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129384 restraints weight = 15064.090| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.14 r_work: 0.3449 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11937 Z= 0.154 Angle : 0.562 10.787 16121 Z= 0.290 Chirality : 0.044 0.206 1766 Planarity : 0.004 0.063 2069 Dihedral : 4.315 19.588 1554 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.27 % Allowed : 13.94 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1407 helix: 1.69 (0.21), residues: 633 sheet: 0.18 (0.41), residues: 160 loop : -1.40 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 162 HIS 0.004 0.001 HIS E 696 PHE 0.026 0.002 PHE C 35 TYR 0.015 0.002 TYR C 210 ARG 0.014 0.000 ARG E 834 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 544) hydrogen bonds : angle 4.19852 ( 1551) covalent geometry : bond 0.00373 (11937) covalent geometry : angle 0.56174 (16121) ********************** 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 134 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 2.389 Fit side-chains REVERT: D 686 GLN cc_start: 0.8612 (mt0) cc_final: 0.8307 (mp10) REVERT: C 80 GLN cc_start: 0.8149 (pp30) cc_final: 0.7668 (pp30) REVERT: C 116 SER cc_start: 0.7579 (t) cc_final: 0.6967 (m) REVERT: C 355 ARG cc_start: 0.6391 (tpt-90) cc_final: 0.5974 (ttp-110) REVERT: C 368 ARG cc_start: 0.8086 (tmt170) cc_final: 0.7624 (ttm-80) REVERT: C 442 TYR cc_start: 0.7196 (t80) cc_final: 0.6976 (t80) REVERT: C 560 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7882 (tm-30) REVERT: E 779 LYS cc_start: 0.7857 (tmtt) cc_final: 0.7460 (tppt) REVERT: E 834 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7963 (ttm110) REVERT: E 977 TRP cc_start: 0.8389 (t60) cc_final: 0.8174 (t60) outliers start: 16 outliers final: 15 residues processed: 128 average time/residue: 0.2874 time to fit residues: 54.5116 Evaluate side-chains 132 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 74 ASP 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 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 C residue 559 VAL Chi-restraints excluded: chain C residue 623 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 95 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 140 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.158885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.131031 restraints weight = 14945.824| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.18 r_work: 0.3466 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1817 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 : 0.526 10.068 16121 Z= 0.273 Chirality : 0.043 0.190 1766 Planarity : 0.004 0.060 2069 Dihedral : 4.197 19.498 1554 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.19 % Allowed : 14.17 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1407 helix: 1.86 (0.21), residues: 634 sheet: 0.18 (0.41), residues: 160 loop : -1.36 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 162 HIS 0.003 0.001 HIS D 653 PHE 0.026 0.001 PHE C 35 TYR 0.016 0.001 TYR C 210 ARG 0.013 0.000 ARG E 834 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 544) hydrogen bonds : angle 4.09208 ( 1551) covalent geometry : bond 0.00282 (11937) covalent geometry : angle 0.52636 (16121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6186.57 seconds wall clock time: 108 minutes 59.66 seconds (6539.66 seconds total)