Starting phenix.real_space_refine on Wed Jun 11 02:34:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yp7_33995/06_2025/7yp7_33995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yp7_33995/06_2025/7yp7_33995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yp7_33995/06_2025/7yp7_33995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yp7_33995/06_2025/7yp7_33995.map" model { file = "/net/cci-nas-00/data/ceres_data/7yp7_33995/06_2025/7yp7_33995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yp7_33995/06_2025/7yp7_33995.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5515 atoms to isotropic. 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 48 5.16 5 C 5038 2.51 5 N 1371 2.21 5 O 1452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7909 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1859 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2017 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 242} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 5.24, per 1000 atoms: 0.66 Number of scatterers: 7909 At special positions: 0 Unit cell: (92.88, 99.36, 131.76, 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 48 16.00 O 1452 8.00 N 1371 7.00 C 5038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 686 " - pdb=" SG CYS R 770 " distance=2.03 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: 2.06 Conformation dependent library (CDL) restraints added in 985.7 milliseconds 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 10 sheets defined 32.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.680A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.647A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.742A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.581A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.591A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.565A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 removed outlier: 3.908A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.616A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 622 through 644 removed outlier: 4.193A pdb=" N ILE R 633 " --> pdb=" O GLY R 629 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE R 634 " --> pdb=" O LEU R 630 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER R 636 " --> pdb=" O SER R 632 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR R 641 " --> pdb=" O VAL R 637 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR R 642 " --> pdb=" O THR R 638 " (cutoff:3.500A) Processing helix chain 'R' and resid 651 through 674 removed outlier: 3.629A pdb=" N LEU R 657 " --> pdb=" O PRO R 653 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE R 658 " --> pdb=" O SER R 654 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU R 672 " --> pdb=" O ASN R 668 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU R 673 " --> pdb=" O LEU R 669 " (cutoff:3.500A) Processing helix chain 'R' and resid 683 through 716 removed outlier: 3.660A pdb=" N VAL R 689 " --> pdb=" O PHE R 685 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL R 691 " --> pdb=" O ILE R 687 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS R 694 " --> pdb=" O ALA R 690 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE R 696 " --> pdb=" O PHE R 692 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER R 700 " --> pdb=" O PHE R 696 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET R 704 " --> pdb=" O SER R 700 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU R 706 " --> pdb=" O THR R 702 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE R 709 " --> pdb=" O GLY R 705 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR R 712 " --> pdb=" O ALA R 708 " (cutoff:3.500A) Processing helix chain 'R' and resid 726 through 735 removed outlier: 3.737A pdb=" N VAL R 733 " --> pdb=" O LYS R 729 " (cutoff:3.500A) Processing helix chain 'R' and resid 737 through 748 removed outlier: 4.542A pdb=" N SER R 743 " --> pdb=" O ALA R 739 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE R 744 " --> pdb=" O VAL R 740 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL R 745 " --> pdb=" O VAL R 741 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE R 748 " --> pdb=" O ILE R 744 " (cutoff:3.500A) Processing helix chain 'R' and resid 775 through 782 removed outlier: 3.513A pdb=" N TYR R 779 " --> pdb=" O ASN R 775 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE R 780 " --> pdb=" O VAL R 776 " (cutoff:3.500A) Processing helix chain 'R' and resid 782 through 791 removed outlier: 3.895A pdb=" N ILE R 789 " --> pdb=" O TYR R 785 " (cutoff:3.500A) Processing helix chain 'R' and resid 794 through 808 removed outlier: 3.763A pdb=" N VAL R 800 " --> pdb=" O MET R 796 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU R 801 " --> pdb=" O PHE R 797 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE R 807 " --> pdb=" O GLN R 803 " (cutoff:3.500A) Processing helix chain 'R' and resid 823 through 834 removed outlier: 3.533A pdb=" N GLY R 829 " --> pdb=" O ARG R 825 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR R 831 " --> pdb=" O ILE R 827 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE R 832 " --> pdb=" O ALA R 828 " (cutoff:3.500A) Processing helix chain 'R' and resid 835 through 838 removed outlier: 3.935A pdb=" N TRP R 838 " --> pdb=" O GLY R 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 835 through 838' Processing helix chain 'R' and resid 839 through 845 removed outlier: 3.901A pdb=" N PHE R 843 " --> pdb=" O GLY R 839 " (cutoff:3.500A) Processing helix chain 'R' and resid 851 through 860 removed outlier: 3.565A pdb=" N ASN R 860 " --> pdb=" O PHE R 856 " (cutoff:3.500A) Processing helix chain 'R' and resid 862 through 872 Processing helix chain 'R' and resid 875 through 883 removed outlier: 4.348A pdb=" N GLN R 881 " --> pdb=" O ASN R 877 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP R 882 " --> pdb=" O VAL R 878 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG R 883 " --> pdb=" O ARG R 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 3.655A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.568A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.788A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP B 83 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.923A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.622A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.159A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.557A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.100A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.535A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.568A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 780 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: 2.15 Time building geometry restraints manager: 2.45 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: 2550 1.34 - 1.46: 1861 1.46 - 1.58: 3598 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 8074 Sorted by residual: bond pdb=" N VAL R 848 " pdb=" CA VAL R 848 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.10e+01 bond pdb=" N LYS A 280 " pdb=" CA LYS A 280 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.19e+00 bond pdb=" N ILE A 276 " pdb=" CA ILE A 276 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 7.96e+00 bond pdb=" N VAL N 110 " pdb=" CA VAL N 110 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.20e-02 6.94e+03 7.95e+00 bond pdb=" N VAL R 850 " pdb=" CA VAL R 850 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.67e+00 ... (remaining 8069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 10632 2.42 - 4.83: 274 4.83 - 7.25: 25 7.25 - 9.67: 8 9.67 - 12.09: 2 Bond angle restraints: 10941 Sorted by residual: angle pdb=" N ARG R 650 " pdb=" CA ARG R 650 " pdb=" C ARG R 650 " ideal model delta sigma weight residual 112.45 124.54 -12.09 1.39e+00 5.18e-01 7.56e+01 angle pdb=" N TRP R 838 " pdb=" CA TRP R 838 " pdb=" C TRP R 838 " ideal model delta sigma weight residual 113.16 105.61 7.55 1.24e+00 6.50e-01 3.71e+01 angle pdb=" C GLY R 846 " pdb=" N PRO R 847 " pdb=" CA PRO R 847 " ideal model delta sigma weight residual 119.84 126.67 -6.83 1.25e+00 6.40e-01 2.98e+01 angle pdb=" C ILE B 171 " pdb=" N GLU B 172 " pdb=" CA GLU B 172 " ideal model delta sigma weight residual 121.54 131.56 -10.02 1.91e+00 2.74e-01 2.75e+01 angle pdb=" N ILE A 372 " pdb=" CA ILE A 372 " pdb=" C ILE A 372 " ideal model delta sigma weight residual 113.22 107.01 6.21 1.23e+00 6.61e-01 2.55e+01 ... (remaining 10936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4243 17.63 - 35.26: 416 35.26 - 52.88: 76 52.88 - 70.51: 16 70.51 - 88.14: 12 Dihedral angle restraints: 4763 sinusoidal: 1839 harmonic: 2924 Sorted by residual: dihedral pdb=" CA GLN R 822 " pdb=" C GLN R 822 " pdb=" N ASP R 823 " pdb=" CA ASP R 823 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA CYS B 204 " pdb=" C CYS B 204 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CB CYS R 686 " pdb=" SG CYS R 686 " pdb=" SG CYS R 770 " pdb=" CB CYS R 770 " ideal model delta sinusoidal sigma weight residual -86.00 -128.11 42.11 1 1.00e+01 1.00e-02 2.48e+01 ... (remaining 4760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1145 0.108 - 0.217: 81 0.217 - 0.325: 2 0.325 - 0.433: 0 0.433 - 0.541: 1 Chirality restraints: 1229 Sorted by residual: chirality pdb=" CA ARG R 650 " pdb=" N ARG R 650 " pdb=" C ARG R 650 " pdb=" CB ARG R 650 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" CA TYR R 652 " pdb=" N TYR R 652 " pdb=" C TYR R 652 " pdb=" CB TYR R 652 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PRO R 847 " pdb=" N PRO R 847 " pdb=" C PRO R 847 " pdb=" CB PRO R 847 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1226 not shown) Planarity restraints: 1397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.060 5.00e-02 4.00e+02 9.17e-02 1.35e+01 pdb=" N PRO B 236 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 837 " 0.013 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C THR R 837 " -0.048 2.00e-02 2.50e+03 pdb=" O THR R 837 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP R 838 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 737 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO R 738 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 738 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 738 " 0.036 5.00e-02 4.00e+02 ... (remaining 1394 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 29 2.44 - 3.05: 4409 3.05 - 3.67: 11444 3.67 - 4.28: 16896 4.28 - 4.90: 28510 Nonbonded interactions: 61288 Sorted by model distance: nonbonded pdb=" NE2 GLN A 213 " pdb=" OD1 ASN A 218 " model vdw 1.823 3.120 nonbonded pdb=" CG GLN A 213 " pdb=" OD1 ASN A 218 " model vdw 2.084 3.440 nonbonded pdb=" CD GLN A 213 " pdb=" OD1 ASN A 218 " model vdw 2.224 3.270 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP A 274 " pdb=" CG2 ILE A 348 " model vdw 2.316 3.460 ... (remaining 61283 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.270 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 : 0.007 0.064 8076 Z= 0.342 Angle : 0.951 12.086 10945 Z= 0.584 Chirality : 0.059 0.541 1229 Planarity : 0.006 0.092 1397 Dihedral : 15.192 88.139 2867 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.68 % Favored : 91.71 % Rotamer: Outliers : 1.44 % Allowed : 6.83 % Favored : 91.73 % 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: -4.81 (0.21), residues: 989 helix: -4.72 (0.10), residues: 316 sheet: -1.51 (0.32), residues: 223 loop : -2.79 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP R 771 HIS 0.011 0.002 HIS A 357 PHE 0.026 0.002 PHE R 730 TYR 0.025 0.002 TYR B 59 ARG 0.006 0.001 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.31657 ( 272) hydrogen bonds : angle 10.24790 ( 780) SS BOND : bond 0.00159 ( 2) SS BOND : angle 1.30206 ( 4) covalent geometry : bond 0.00680 ( 8074) covalent geometry : angle 0.95048 (10941) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 87 LYS cc_start: 0.8694 (mttt) cc_final: 0.8468 (mttm) REVERT: R 646 GLU cc_start: 0.7479 (tm-30) cc_final: 0.6526 (tm-30) REVERT: R 650 ARG cc_start: 0.7730 (mtt180) cc_final: 0.6791 (mtt180) REVERT: R 670 ILE cc_start: 0.9255 (tt) cc_final: 0.9025 (tt) REVERT: R 687 ILE cc_start: 0.9254 (pt) cc_final: 0.9021 (mm) REVERT: R 704 MET cc_start: 0.8667 (mtt) cc_final: 0.8452 (mtt) REVERT: R 849 ASN cc_start: 0.6338 (OUTLIER) cc_final: 0.6042 (t0) REVERT: R 856 PHE cc_start: 0.8768 (t80) cc_final: 0.8269 (t80) REVERT: R 881 GLN cc_start: 0.8538 (mm110) cc_final: 0.8224 (mm-40) outliers start: 12 outliers final: 7 residues processed: 191 average time/residue: 0.2799 time to fit residues: 66.9467 Evaluate side-chains 157 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain R residue 809 LYS Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 847 PRO Chi-restraints excluded: chain R residue 849 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 0.0040 chunk 88 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 218 ASN A 227 GLN B 88 ASN B 183 HIS B 230 ASN B 239 ASN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.090962 restraints weight = 14145.016| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.40 r_work: 0.3116 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8076 Z= 0.126 Angle : 0.572 6.193 10945 Z= 0.318 Chirality : 0.043 0.197 1229 Planarity : 0.005 0.070 1397 Dihedral : 6.066 48.653 1118 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.85 % Favored : 94.84 % Rotamer: Outliers : 1.92 % Allowed : 11.51 % Favored : 86.57 % 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: -3.26 (0.24), residues: 989 helix: -2.58 (0.23), residues: 325 sheet: -1.19 (0.34), residues: 222 loop : -2.24 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.008 0.001 PHE B 241 TYR 0.015 0.001 TYR R 785 ARG 0.005 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.05098 ( 272) hydrogen bonds : angle 5.35982 ( 780) SS BOND : bond 0.00339 ( 2) SS BOND : angle 1.07639 ( 4) covalent geometry : bond 0.00275 ( 8074) covalent geometry : angle 0.57160 (10941) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.8219 (ptm160) cc_final: 0.7970 (ptm160) REVERT: B 84 SER cc_start: 0.9344 (p) cc_final: 0.9109 (p) REVERT: G 32 LYS cc_start: 0.8836 (tppt) cc_final: 0.8590 (tppt) REVERT: G 53 PRO cc_start: 0.7425 (Cg_exo) cc_final: 0.7109 (Cg_endo) REVERT: N 50 ASP cc_start: 0.8641 (p0) cc_final: 0.8395 (p0) REVERT: R 646 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7198 (tm-30) REVERT: R 650 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7007 (mtt180) REVERT: R 670 ILE cc_start: 0.9346 (tt) cc_final: 0.9065 (tt) REVERT: R 785 TYR cc_start: 0.8810 (t80) cc_final: 0.8385 (t80) REVERT: R 849 ASN cc_start: 0.6918 (OUTLIER) cc_final: 0.6465 (t0) REVERT: R 856 PHE cc_start: 0.8817 (t80) cc_final: 0.8568 (t80) REVERT: R 881 GLN cc_start: 0.8456 (mm110) cc_final: 0.8208 (mm-40) outliers start: 16 outliers final: 10 residues processed: 201 average time/residue: 0.2345 time to fit residues: 60.6042 Evaluate side-chains 160 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 681 ASN Chi-restraints excluded: chain R residue 740 VAL Chi-restraints excluded: chain R residue 745 VAL Chi-restraints excluded: chain R residue 809 LYS Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 849 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 77 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: A 377 ASN B 259 GLN B 340 ASN N 5 GLN R 710 HIS R 863 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.089900 restraints weight = 14360.981| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.41 r_work: 0.3097 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8076 Z= 0.122 Angle : 0.541 6.937 10945 Z= 0.296 Chirality : 0.042 0.197 1229 Planarity : 0.004 0.064 1397 Dihedral : 5.467 42.539 1109 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.36 % Favored : 94.34 % Rotamer: Outliers : 2.40 % Allowed : 15.47 % Favored : 82.13 % 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: -2.37 (0.26), residues: 989 helix: -1.39 (0.27), residues: 326 sheet: -0.97 (0.33), residues: 237 loop : -1.96 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.008 0.001 PHE R 730 TYR 0.010 0.001 TYR R 625 ARG 0.007 0.000 ARG R 825 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 272) hydrogen bonds : angle 4.79012 ( 780) SS BOND : bond 0.00351 ( 2) SS BOND : angle 1.21914 ( 4) covalent geometry : bond 0.00272 ( 8074) covalent geometry : angle 0.54046 (10941) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 GLU cc_start: 0.7858 (pm20) cc_final: 0.7629 (tm-30) REVERT: B 84 SER cc_start: 0.9369 (p) cc_final: 0.9165 (p) REVERT: G 15 LEU cc_start: 0.9120 (tp) cc_final: 0.8913 (mt) REVERT: N 50 ASP cc_start: 0.8623 (p0) cc_final: 0.8327 (p0) REVERT: N 87 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8569 (mttt) REVERT: R 646 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7539 (tm-30) REVERT: R 650 ARG cc_start: 0.7459 (mtt180) cc_final: 0.7009 (mtt180) REVERT: R 670 ILE cc_start: 0.9384 (tt) cc_final: 0.9142 (tt) REVERT: R 785 TYR cc_start: 0.8739 (t80) cc_final: 0.8341 (t80) REVERT: R 825 ARG cc_start: 0.7747 (ttp-110) cc_final: 0.7397 (ptt90) REVERT: R 849 ASN cc_start: 0.6730 (OUTLIER) cc_final: 0.6315 (t0) REVERT: R 856 PHE cc_start: 0.8808 (t80) cc_final: 0.8582 (t80) REVERT: R 881 GLN cc_start: 0.8378 (mm110) cc_final: 0.8063 (mm-40) outliers start: 20 outliers final: 15 residues processed: 176 average time/residue: 0.2434 time to fit residues: 56.5019 Evaluate side-chains 168 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 681 ASN Chi-restraints excluded: chain R residue 740 VAL Chi-restraints excluded: chain R residue 745 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 791 LEU Chi-restraints excluded: chain R residue 792 LEU Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 849 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** R 863 GLN ** 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 = 0.3523 r_free = 0.3523 target = 0.110780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.090285 restraints weight = 14362.157| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.41 r_work: 0.3103 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8076 Z= 0.116 Angle : 0.522 5.774 10945 Z= 0.285 Chirality : 0.042 0.191 1229 Planarity : 0.004 0.062 1397 Dihedral : 5.013 38.797 1104 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.65 % Favored : 95.05 % Rotamer: Outliers : 3.24 % Allowed : 16.31 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.26), residues: 989 helix: -0.71 (0.29), residues: 326 sheet: -0.74 (0.35), residues: 221 loop : -1.85 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.008 0.001 PHE B 241 TYR 0.014 0.001 TYR R 625 ARG 0.004 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 272) hydrogen bonds : angle 4.53771 ( 780) SS BOND : bond 0.00197 ( 2) SS BOND : angle 1.08495 ( 4) covalent geometry : bond 0.00262 ( 8074) covalent geometry : angle 0.52165 (10941) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.9091 (tmm) cc_final: 0.8872 (ttp) REVERT: B 59 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: G 15 LEU cc_start: 0.9082 (tp) cc_final: 0.8878 (mt) REVERT: N 50 ASP cc_start: 0.8630 (p0) cc_final: 0.8331 (p0) REVERT: R 646 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7499 (tm-30) REVERT: R 650 ARG cc_start: 0.7426 (mtt180) cc_final: 0.6959 (mtt180) REVERT: R 670 ILE cc_start: 0.9371 (tt) cc_final: 0.9110 (tt) REVERT: R 785 TYR cc_start: 0.8697 (t80) cc_final: 0.8288 (t80) outliers start: 27 outliers final: 19 residues processed: 173 average time/residue: 0.2263 time to fit residues: 51.1066 Evaluate side-chains 166 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 681 ASN Chi-restraints excluded: chain R residue 743 SER Chi-restraints excluded: chain R residue 745 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 792 LEU Chi-restraints excluded: chain R residue 809 LYS Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 852 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 863 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 = 0.3521 r_free = 0.3521 target = 0.110578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090138 restraints weight = 14227.708| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.39 r_work: 0.3103 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8076 Z= 0.120 Angle : 0.526 6.930 10945 Z= 0.285 Chirality : 0.042 0.187 1229 Planarity : 0.004 0.061 1397 Dihedral : 4.847 37.328 1102 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.75 % Favored : 94.94 % Rotamer: Outliers : 3.48 % Allowed : 17.03 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.27), residues: 989 helix: -0.38 (0.29), residues: 326 sheet: -0.57 (0.34), residues: 229 loop : -1.83 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.011 0.001 PHE R 856 TYR 0.013 0.001 TYR R 625 ARG 0.009 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 272) hydrogen bonds : angle 4.44528 ( 780) SS BOND : bond 0.00174 ( 2) SS BOND : angle 0.89953 ( 4) covalent geometry : bond 0.00274 ( 8074) covalent geometry : angle 0.52560 (10941) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8725 (tp40) cc_final: 0.8037 (tp40) REVERT: A 322 GLU cc_start: 0.7858 (pm20) cc_final: 0.7622 (tm-30) REVERT: A 386 MET cc_start: 0.9071 (tmm) cc_final: 0.8827 (ttp) REVERT: B 59 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: B 228 ASP cc_start: 0.8753 (m-30) cc_final: 0.8468 (m-30) REVERT: G 15 LEU cc_start: 0.9083 (tp) cc_final: 0.8876 (mt) REVERT: N 50 ASP cc_start: 0.8640 (p0) cc_final: 0.8342 (p0) REVERT: R 625 TYR cc_start: 0.7139 (m-80) cc_final: 0.6216 (m-10) REVERT: R 646 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7475 (tm-30) REVERT: R 650 ARG cc_start: 0.7504 (mtt180) cc_final: 0.7023 (mtt180) REVERT: R 670 ILE cc_start: 0.9352 (tt) cc_final: 0.9097 (tt) REVERT: R 785 TYR cc_start: 0.8669 (t80) cc_final: 0.8216 (t80) REVERT: R 853 MET cc_start: 0.7089 (pmm) cc_final: 0.6865 (ttt) outliers start: 29 outliers final: 23 residues processed: 171 average time/residue: 0.2515 time to fit residues: 56.2910 Evaluate side-chains 171 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 681 ASN Chi-restraints excluded: chain R residue 743 SER Chi-restraints excluded: chain R residue 745 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 791 LEU Chi-restraints excluded: chain R residue 792 LEU Chi-restraints excluded: chain R residue 809 LYS Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 831 THR Chi-restraints excluded: chain R residue 852 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 53 GLN N 77 ASN ** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.087455 restraints weight = 14342.836| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.38 r_work: 0.3062 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8076 Z= 0.174 Angle : 0.579 6.943 10945 Z= 0.314 Chirality : 0.044 0.184 1229 Planarity : 0.004 0.063 1397 Dihedral : 5.150 38.491 1102 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.56 % Favored : 94.14 % Rotamer: Outliers : 3.96 % Allowed : 17.63 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.27), residues: 989 helix: -0.18 (0.30), residues: 325 sheet: -0.71 (0.33), residues: 237 loop : -1.77 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS A 220 PHE 0.010 0.001 PHE B 253 TYR 0.012 0.001 TYR B 105 ARG 0.007 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 272) hydrogen bonds : angle 4.64616 ( 780) SS BOND : bond 0.00090 ( 2) SS BOND : angle 1.06155 ( 4) covalent geometry : bond 0.00399 ( 8074) covalent geometry : angle 0.57835 (10941) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 368 ASP cc_start: 0.6928 (p0) cc_final: 0.6414 (p0) REVERT: B 45 MET cc_start: 0.8139 (mtt) cc_final: 0.7827 (mtt) REVERT: B 59 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: G 15 LEU cc_start: 0.9111 (tp) cc_final: 0.8904 (mt) REVERT: N 50 ASP cc_start: 0.8579 (p0) cc_final: 0.8251 (p0) REVERT: R 646 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7423 (tm-30) REVERT: R 650 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7152 (mtt180) REVERT: R 670 ILE cc_start: 0.9374 (tt) cc_final: 0.9146 (tt) REVERT: R 785 TYR cc_start: 0.8678 (t80) cc_final: 0.8224 (t80) outliers start: 33 outliers final: 27 residues processed: 167 average time/residue: 0.2629 time to fit residues: 57.3940 Evaluate side-chains 170 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 633 ILE Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 681 ASN Chi-restraints excluded: chain R residue 743 SER Chi-restraints excluded: chain R residue 745 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 791 LEU Chi-restraints excluded: chain R residue 792 LEU Chi-restraints excluded: chain R residue 809 LYS Chi-restraints excluded: chain R residue 831 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 0.0010 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN ** R 863 GLN ** 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 = 0.3528 r_free = 0.3528 target = 0.111047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.090610 restraints weight = 14302.092| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.40 r_work: 0.3109 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 8076 Z= 0.107 Angle : 0.548 10.788 10945 Z= 0.290 Chirality : 0.042 0.184 1229 Planarity : 0.004 0.061 1397 Dihedral : 4.625 24.422 1098 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.45 % Favored : 95.25 % Rotamer: Outliers : 2.88 % Allowed : 19.66 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.27), residues: 989 helix: 0.08 (0.30), residues: 325 sheet: -0.49 (0.34), residues: 229 loop : -1.72 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 220 PHE 0.011 0.001 PHE R 622 TYR 0.015 0.001 TYR R 625 ARG 0.007 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 272) hydrogen bonds : angle 4.32513 ( 780) SS BOND : bond 0.00069 ( 2) SS BOND : angle 0.77613 ( 4) covalent geometry : bond 0.00241 ( 8074) covalent geometry : angle 0.54747 (10941) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.6870 (p0) cc_final: 0.6338 (p0) REVERT: A 386 MET cc_start: 0.9127 (tmm) cc_final: 0.8894 (ttp) REVERT: B 10 GLU cc_start: 0.7512 (tp30) cc_final: 0.7284 (tp30) REVERT: B 59 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: G 15 LEU cc_start: 0.9108 (tp) cc_final: 0.8874 (mt) REVERT: N 50 ASP cc_start: 0.8616 (p0) cc_final: 0.8307 (p0) REVERT: N 85 SER cc_start: 0.9529 (m) cc_final: 0.8930 (p) REVERT: R 646 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7454 (tm-30) REVERT: R 650 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7106 (mtt180) REVERT: R 670 ILE cc_start: 0.9343 (tt) cc_final: 0.9104 (tt) REVERT: R 785 TYR cc_start: 0.8632 (t80) cc_final: 0.8208 (t80) outliers start: 24 outliers final: 21 residues processed: 166 average time/residue: 0.2584 time to fit residues: 56.3672 Evaluate side-chains 163 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 681 ASN Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 743 SER Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 791 LEU Chi-restraints excluded: chain R residue 809 LYS Chi-restraints excluded: chain R residue 831 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.0030 chunk 92 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.7972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 863 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 = 0.3520 r_free = 0.3520 target = 0.110731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.089871 restraints weight = 14371.382| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.41 r_work: 0.3096 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8076 Z= 0.125 Angle : 0.557 8.816 10945 Z= 0.296 Chirality : 0.043 0.183 1229 Planarity : 0.004 0.061 1397 Dihedral : 4.654 24.522 1098 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.36 % Favored : 94.34 % Rotamer: Outliers : 2.76 % Allowed : 20.74 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.27), residues: 989 helix: 0.16 (0.30), residues: 324 sheet: -0.54 (0.34), residues: 231 loop : -1.70 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.011 0.001 PHE R 622 TYR 0.016 0.001 TYR R 625 ARG 0.004 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 272) hydrogen bonds : angle 4.36799 ( 780) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.75961 ( 4) covalent geometry : bond 0.00287 ( 8074) covalent geometry : angle 0.55698 (10941) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.6923 (p0) cc_final: 0.6414 (p0) REVERT: A 386 MET cc_start: 0.9106 (tmm) cc_final: 0.8860 (ttp) REVERT: B 59 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.7553 (m-80) REVERT: B 228 ASP cc_start: 0.8723 (m-30) cc_final: 0.8367 (m-30) REVERT: G 15 LEU cc_start: 0.9110 (tp) cc_final: 0.8875 (mt) REVERT: N 50 ASP cc_start: 0.8649 (p0) cc_final: 0.8340 (p0) REVERT: N 85 SER cc_start: 0.9537 (m) cc_final: 0.8962 (p) REVERT: R 646 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7449 (tm-30) REVERT: R 650 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7195 (mtt180) REVERT: R 670 ILE cc_start: 0.9354 (tt) cc_final: 0.9097 (tt) REVERT: R 785 TYR cc_start: 0.8650 (t80) cc_final: 0.8211 (t80) outliers start: 23 outliers final: 22 residues processed: 167 average time/residue: 0.2740 time to fit residues: 61.8687 Evaluate side-chains 172 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 681 ASN Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 743 SER Chi-restraints excluded: chain R residue 745 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 791 LEU Chi-restraints excluded: chain R residue 809 LYS Chi-restraints excluded: chain R residue 831 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 0.0370 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN ** R 863 GLN ** 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 = 0.3534 r_free = 0.3534 target = 0.111520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.090977 restraints weight = 14411.818| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.40 r_work: 0.3115 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8076 Z= 0.113 Angle : 0.563 10.074 10945 Z= 0.293 Chirality : 0.042 0.186 1229 Planarity : 0.004 0.061 1397 Dihedral : 4.508 24.659 1098 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.55 % Favored : 95.15 % Rotamer: Outliers : 2.88 % Allowed : 20.86 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.27), residues: 989 helix: 0.35 (0.30), residues: 326 sheet: -0.38 (0.34), residues: 220 loop : -1.72 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.024 0.001 PHE R 622 TYR 0.019 0.001 TYR R 625 ARG 0.005 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 272) hydrogen bonds : angle 4.24599 ( 780) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.66249 ( 4) covalent geometry : bond 0.00260 ( 8074) covalent geometry : angle 0.56296 (10941) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.6920 (p0) cc_final: 0.6402 (p0) REVERT: A 386 MET cc_start: 0.9125 (tmm) cc_final: 0.8882 (ttp) REVERT: B 10 GLU cc_start: 0.7590 (tp30) cc_final: 0.7358 (tp30) REVERT: B 59 TYR cc_start: 0.9176 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: B 228 ASP cc_start: 0.8684 (m-30) cc_final: 0.8361 (m-30) REVERT: G 15 LEU cc_start: 0.9105 (tp) cc_final: 0.8868 (mt) REVERT: N 50 ASP cc_start: 0.8624 (p0) cc_final: 0.8314 (p0) REVERT: N 85 SER cc_start: 0.9534 (m) cc_final: 0.8954 (p) REVERT: R 646 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7795 (tm-30) REVERT: R 650 ARG cc_start: 0.7781 (mtt180) cc_final: 0.7376 (mtt180) REVERT: R 670 ILE cc_start: 0.9336 (tt) cc_final: 0.9089 (tt) REVERT: R 785 TYR cc_start: 0.8664 (t80) cc_final: 0.8209 (t80) outliers start: 24 outliers final: 22 residues processed: 173 average time/residue: 0.2471 time to fit residues: 54.8335 Evaluate side-chains 168 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 681 ASN Chi-restraints excluded: chain R residue 743 SER Chi-restraints excluded: chain R residue 745 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 791 LEU Chi-restraints excluded: chain R residue 792 LEU Chi-restraints excluded: chain R residue 809 LYS Chi-restraints excluded: chain R residue 831 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 34 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN ** R 863 GLN ** 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 = 0.3525 r_free = 0.3525 target = 0.111012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.090219 restraints weight = 14252.643| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.38 r_work: 0.3103 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8076 Z= 0.131 Angle : 0.589 10.001 10945 Z= 0.309 Chirality : 0.043 0.180 1229 Planarity : 0.004 0.061 1397 Dihedral : 4.613 24.538 1098 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.95 % Favored : 94.74 % Rotamer: Outliers : 2.76 % Allowed : 21.34 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.27), residues: 989 helix: 0.34 (0.30), residues: 326 sheet: -0.36 (0.34), residues: 219 loop : -1.76 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.009 0.001 PHE B 241 TYR 0.018 0.001 TYR R 625 ARG 0.004 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 272) hydrogen bonds : angle 4.29250 ( 780) SS BOND : bond 0.00027 ( 2) SS BOND : angle 0.70660 ( 4) covalent geometry : bond 0.00304 ( 8074) covalent geometry : angle 0.58893 (10941) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.6958 (p0) cc_final: 0.6462 (p0) REVERT: A 386 MET cc_start: 0.9121 (tmm) cc_final: 0.8873 (ttp) REVERT: B 10 GLU cc_start: 0.7582 (tp30) cc_final: 0.7356 (tp30) REVERT: B 59 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: B 228 ASP cc_start: 0.8711 (m-30) cc_final: 0.8362 (m-30) REVERT: G 15 LEU cc_start: 0.9115 (tp) cc_final: 0.8887 (mt) REVERT: N 76 LYS cc_start: 0.9138 (mttt) cc_final: 0.8937 (mtmm) REVERT: N 85 SER cc_start: 0.9556 (m) cc_final: 0.8981 (p) REVERT: R 646 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7820 (tm-30) REVERT: R 650 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7431 (mtt180) REVERT: R 670 ILE cc_start: 0.9343 (tt) cc_final: 0.9103 (tt) REVERT: R 785 TYR cc_start: 0.8674 (t80) cc_final: 0.8220 (t80) outliers start: 23 outliers final: 22 residues processed: 162 average time/residue: 0.2430 time to fit residues: 51.3409 Evaluate side-chains 167 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 681 ASN Chi-restraints excluded: chain R residue 745 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 791 LEU Chi-restraints excluded: chain R residue 792 LEU Chi-restraints excluded: chain R residue 809 LYS Chi-restraints excluded: chain R residue 831 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.0060 chunk 25 optimal weight: 1.9990 overall best weight: 0.4934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN ** R 863 GLN ** 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 = 0.3551 r_free = 0.3551 target = 0.112679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.091937 restraints weight = 14306.074| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.40 r_work: 0.3131 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8076 Z= 0.110 Angle : 0.584 12.372 10945 Z= 0.304 Chirality : 0.043 0.276 1229 Planarity : 0.004 0.060 1397 Dihedral : 4.440 24.516 1098 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.65 % Favored : 95.05 % Rotamer: Outliers : 2.76 % Allowed : 21.82 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.27), residues: 989 helix: 0.41 (0.30), residues: 326 sheet: -0.25 (0.34), residues: 218 loop : -1.74 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.009 0.001 PHE B 241 TYR 0.019 0.001 TYR R 625 ARG 0.004 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 272) hydrogen bonds : angle 4.16419 ( 780) SS BOND : bond 0.00081 ( 2) SS BOND : angle 0.62639 ( 4) covalent geometry : bond 0.00255 ( 8074) covalent geometry : angle 0.58380 (10941) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4899.51 seconds wall clock time: 85 minutes 54.45 seconds (5154.45 seconds total)