Starting phenix.real_space_refine on Thu Sep 26 06:02:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp7_33995/09_2024/7yp7_33995.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp7_33995/09_2024/7yp7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp7_33995/09_2024/7yp7_33995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp7_33995/09_2024/7yp7_33995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp7_33995/09_2024/7yp7_33995.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp7_33995/09_2024/7yp7_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-5461/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: 4.75, per 1000 atoms: 0.60 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: 1.80 Conformation dependent library (CDL) restraints added in 915.9 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: 0.83 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: 2.04 Time building geometry restraints manager: 2.12 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 19.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- 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 8074 Z= 0.442 Angle : 0.950 12.086 10941 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 0.921 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: 0.2729 time to fit residues: 65.3853 Evaluate side-chains 157 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 8074 Z= 0.179 Angle : 0.572 6.193 10941 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 *********************** 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 fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.7804 (ptm160) cc_final: 0.7521 (ptm160) REVERT: B 84 SER cc_start: 0.9187 (p) cc_final: 0.8967 (p) REVERT: B 262 MET cc_start: 0.8589 (tpp) cc_final: 0.8317 (tpp) REVERT: B 264 TYR cc_start: 0.8961 (m-80) cc_final: 0.8760 (m-80) REVERT: G 32 LYS cc_start: 0.8638 (tppt) cc_final: 0.8359 (tppt) REVERT: G 53 PRO cc_start: 0.7365 (Cg_exo) cc_final: 0.7060 (Cg_endo) REVERT: N 50 ASP cc_start: 0.8127 (p0) cc_final: 0.7758 (p0) REVERT: R 646 GLU cc_start: 0.7552 (tm-30) cc_final: 0.6675 (tm-30) REVERT: R 650 ARG cc_start: 0.7326 (mtt180) cc_final: 0.6712 (mtt180) REVERT: R 670 ILE cc_start: 0.9342 (tt) cc_final: 0.9032 (tt) REVERT: R 785 TYR cc_start: 0.8662 (t80) cc_final: 0.8197 (t80) REVERT: R 849 ASN cc_start: 0.6780 (OUTLIER) cc_final: 0.6376 (t0) REVERT: R 856 PHE cc_start: 0.8646 (t80) cc_final: 0.8403 (t80) outliers start: 16 outliers final: 10 residues processed: 201 average time/residue: 0.2439 time to fit residues: 63.0639 Evaluate side-chains 161 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0870 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8074 Z= 0.174 Angle : 0.539 6.833 10941 Z= 0.295 Chirality : 0.042 0.197 1229 Planarity : 0.004 0.064 1397 Dihedral : 5.434 41.962 1109 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.36 % Favored : 94.34 % Rotamer: Outliers : 2.52 % Allowed : 15.35 % 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: -2.35 (0.26), residues: 989 helix: -1.36 (0.27), residues: 326 sheet: -0.95 (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 0.009 0.001 PHE A 340 TYR 0.010 0.001 TYR R 625 ARG 0.007 0.000 ARG R 825 *********************** 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 187 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 SER cc_start: 0.9171 (p) cc_final: 0.8970 (p) REVERT: B 262 MET cc_start: 0.8559 (tpp) cc_final: 0.8306 (tpp) REVERT: G 15 LEU cc_start: 0.9090 (tp) cc_final: 0.8890 (mt) REVERT: N 50 ASP cc_start: 0.8074 (p0) cc_final: 0.7771 (p0) REVERT: R 646 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7047 (tm-30) REVERT: R 650 ARG cc_start: 0.7214 (mtt180) cc_final: 0.6711 (mtt180) REVERT: R 670 ILE cc_start: 0.9380 (tt) cc_final: 0.9091 (tt) REVERT: R 785 TYR cc_start: 0.8629 (t80) cc_final: 0.8185 (t80) REVERT: R 825 ARG cc_start: 0.7484 (ttp-110) cc_final: 0.7273 (ptt90) REVERT: R 849 ASN cc_start: 0.6592 (OUTLIER) cc_final: 0.6222 (t0) outliers start: 21 outliers final: 15 residues processed: 178 average time/residue: 0.2229 time to fit residues: 51.9395 Evaluate side-chains 167 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 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 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 88 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.0170 chunk 84 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8074 Z= 0.170 Angle : 0.521 5.997 10941 Z= 0.285 Chirality : 0.042 0.190 1229 Planarity : 0.004 0.062 1397 Dihedral : 5.024 38.924 1104 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.45 % Favored : 95.25 % Rotamer: Outliers : 3.00 % Allowed : 16.07 % Favored : 80.94 % 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: -1.90 (0.26), residues: 989 helix: -0.78 (0.29), residues: 328 sheet: -0.85 (0.34), residues: 228 loop : -1.78 (0.29), residues: 433 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 0.024 0.001 PHE R 856 TYR 0.014 0.001 TYR R 625 ARG 0.003 0.000 ARG B 256 *********************** 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 177 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 152 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.7171 (m-80) REVERT: B 228 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: N 50 ASP cc_start: 0.8077 (p0) cc_final: 0.7770 (p0) REVERT: R 625 TYR cc_start: 0.6781 (m-80) cc_final: 0.6188 (m-10) REVERT: R 646 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7031 (tm-30) REVERT: R 650 ARG cc_start: 0.7185 (mtt180) cc_final: 0.6669 (mtt180) REVERT: R 670 ILE cc_start: 0.9372 (tt) cc_final: 0.9079 (tt) REVERT: R 785 TYR cc_start: 0.8616 (t80) cc_final: 0.8158 (t80) REVERT: R 881 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7834 (mp10) outliers start: 25 outliers final: 19 residues processed: 169 average time/residue: 0.2219 time to fit residues: 49.0405 Evaluate side-chains 168 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain B residue 228 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 83 MET 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 831 THR 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 53 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8074 Z= 0.178 Angle : 0.524 6.824 10941 Z= 0.284 Chirality : 0.042 0.189 1229 Planarity : 0.004 0.062 1397 Dihedral : 4.850 37.475 1102 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.65 % Favored : 95.05 % Rotamer: Outliers : 3.24 % Allowed : 16.79 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.27), residues: 989 helix: -0.34 (0.29), residues: 325 sheet: -0.57 (0.34), residues: 229 loop : -1.81 (0.30), residues: 435 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 0.019 0.001 PHE R 856 TYR 0.012 0.001 TYR R 625 ARG 0.003 0.000 ARG B 256 *********************** 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 184 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8588 (tp40) cc_final: 0.7923 (tp40) REVERT: B 59 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: B 228 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: N 50 ASP cc_start: 0.8110 (p0) cc_final: 0.7797 (p0) REVERT: R 625 TYR cc_start: 0.6905 (m-80) cc_final: 0.6421 (m-10) REVERT: R 646 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7015 (tm-30) REVERT: R 650 ARG cc_start: 0.7289 (mtt180) cc_final: 0.6750 (mtt180) REVERT: R 670 ILE cc_start: 0.9360 (tt) cc_final: 0.9075 (tt) REVERT: R 785 TYR cc_start: 0.8602 (t80) cc_final: 0.8094 (t80) REVERT: R 881 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7849 (mp10) outliers start: 27 outliers final: 21 residues processed: 175 average time/residue: 0.2398 time to fit residues: 54.5547 Evaluate side-chains 168 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 30 LEU 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 228 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 53 GLN 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 745 VAL Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 809 LYS Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 831 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 0.0060 chunk 23 optimal weight: 0.0770 chunk 94 optimal weight: 0.0370 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 7 optimal weight: 0.0060 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 91 optimal weight: 0.0770 overall best weight: 0.0406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN ** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.002 0.053 8074 Z= 0.135 Angle : 0.510 10.227 10941 Z= 0.271 Chirality : 0.041 0.188 1229 Planarity : 0.004 0.058 1397 Dihedral : 4.385 33.568 1102 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.25 % Favored : 95.45 % Rotamer: Outliers : 2.04 % Allowed : 19.18 % Favored : 78.78 % 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: -1.13 (0.27), residues: 989 helix: 0.22 (0.31), residues: 320 sheet: -0.31 (0.34), residues: 228 loop : -1.69 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.000 HIS R 694 PHE 0.007 0.001 PHE B 241 TYR 0.015 0.001 TYR R 625 ARG 0.010 0.000 ARG A 283 *********************** 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 184 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8619 (m110) cc_final: 0.8290 (p0) REVERT: B 59 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: B 209 LYS cc_start: 0.8800 (mttt) cc_final: 0.8586 (mttt) REVERT: B 228 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: B 303 ASP cc_start: 0.7850 (m-30) cc_final: 0.7639 (m-30) REVERT: N 50 ASP cc_start: 0.8034 (p0) cc_final: 0.7691 (p0) REVERT: R 646 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7017 (tm-30) REVERT: R 650 ARG cc_start: 0.7211 (mtt180) cc_final: 0.6648 (mtt180) REVERT: R 670 ILE cc_start: 0.9292 (tt) cc_final: 0.9029 (tt) REVERT: R 785 TYR cc_start: 0.8546 (t80) cc_final: 0.8078 (t80) outliers start: 17 outliers final: 12 residues processed: 179 average time/residue: 0.2292 time to fit residues: 53.6642 Evaluate side-chains 172 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 228 ASP 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 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 777 VAL Chi-restraints excluded: chain R residue 792 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 0.0060 chunk 43 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN B 340 ASN N 53 GLN ** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8074 Z= 0.171 Angle : 0.531 8.114 10941 Z= 0.284 Chirality : 0.042 0.185 1229 Planarity : 0.004 0.059 1397 Dihedral : 4.356 20.776 1098 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.25 % Favored : 95.45 % Rotamer: Outliers : 2.52 % Allowed : 20.14 % Favored : 77.34 % 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: 0.29 (0.30), residues: 327 sheet: -0.36 (0.34), residues: 222 loop : -1.69 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.008 0.001 PHE B 241 TYR 0.014 0.001 TYR R 625 ARG 0.010 0.000 ARG A 283 *********************** 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 fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8613 (m110) cc_final: 0.8321 (p0) REVERT: A 368 ASP cc_start: 0.6605 (p0) cc_final: 0.6057 (p0) REVERT: B 59 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: B 209 LYS cc_start: 0.8895 (mttt) cc_final: 0.8658 (mttt) REVERT: B 228 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: N 50 ASP cc_start: 0.8057 (p0) cc_final: 0.7736 (p0) REVERT: N 85 SER cc_start: 0.9466 (m) cc_final: 0.8847 (p) REVERT: R 650 ARG cc_start: 0.7381 (mtt180) cc_final: 0.6998 (mtt180) REVERT: R 670 ILE cc_start: 0.9326 (tt) cc_final: 0.9040 (tt) REVERT: R 785 TYR cc_start: 0.8568 (t80) cc_final: 0.8028 (t80) REVERT: R 809 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7899 (pptt) outliers start: 21 outliers final: 16 residues processed: 169 average time/residue: 0.2304 time to fit residues: 50.9189 Evaluate side-chains 172 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain B residue 228 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 53 GLN 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 777 VAL Chi-restraints excluded: chain R residue 792 LEU Chi-restraints excluded: chain R residue 809 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN N 53 GLN ** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 8074 Z= 0.144 Angle : 0.538 10.301 10941 Z= 0.281 Chirality : 0.041 0.184 1229 Planarity : 0.004 0.059 1397 Dihedral : 4.234 19.462 1098 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.94 % Favored : 95.75 % Rotamer: Outliers : 2.28 % Allowed : 21.10 % Favored : 76.62 % 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: -1.00 (0.27), residues: 989 helix: 0.42 (0.30), residues: 326 sheet: -0.27 (0.35), residues: 219 loop : -1.69 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.007 0.001 PHE B 241 TYR 0.016 0.001 TYR R 625 ARG 0.008 0.000 ARG A 283 *********************** 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 174 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8576 (m110) cc_final: 0.8351 (p0) REVERT: A 368 ASP cc_start: 0.6611 (p0) cc_final: 0.6089 (p0) REVERT: B 59 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: B 209 LYS cc_start: 0.8864 (mttt) cc_final: 0.8633 (mttt) REVERT: B 228 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: B 234 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.7871 (t80) REVERT: B 312 ASP cc_start: 0.7833 (m-30) cc_final: 0.7534 (m-30) REVERT: N 50 ASP cc_start: 0.7954 (p0) cc_final: 0.7643 (p0) REVERT: N 85 SER cc_start: 0.9492 (m) cc_final: 0.8824 (p) REVERT: R 670 ILE cc_start: 0.9259 (tt) cc_final: 0.8965 (tt) REVERT: R 785 TYR cc_start: 0.8592 (t80) cc_final: 0.8038 (t80) REVERT: R 809 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7913 (pptt) outliers start: 19 outliers final: 14 residues processed: 168 average time/residue: 0.2696 time to fit residues: 60.1254 Evaluate side-chains 172 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 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 777 VAL Chi-restraints excluded: chain R residue 792 LEU Chi-restraints excluded: chain R residue 809 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 0.2980 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 0.0050 chunk 57 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN B 340 ASN N 53 GLN ** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 8074 Z= 0.158 Angle : 0.545 8.791 10941 Z= 0.284 Chirality : 0.042 0.183 1229 Planarity : 0.004 0.059 1397 Dihedral : 4.234 20.091 1098 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.25 % Favored : 95.45 % Rotamer: Outliers : 2.28 % Allowed : 21.10 % Favored : 76.62 % 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: -0.93 (0.27), residues: 989 helix: 0.47 (0.30), residues: 328 sheet: -0.30 (0.35), residues: 222 loop : -1.61 (0.30), residues: 439 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 B 241 TYR 0.015 0.001 TYR R 625 ARG 0.007 0.000 ARG A 283 *********************** 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 176 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.7896 (ptm160) cc_final: 0.7566 (ptm160) REVERT: A 368 ASP cc_start: 0.6623 (p0) cc_final: 0.6101 (p0) REVERT: B 59 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: B 209 LYS cc_start: 0.8884 (mttt) cc_final: 0.8643 (mttt) REVERT: B 228 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: B 234 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.7846 (t80) REVERT: N 50 ASP cc_start: 0.7960 (p0) cc_final: 0.7641 (p0) REVERT: N 85 SER cc_start: 0.9491 (m) cc_final: 0.8822 (p) REVERT: R 670 ILE cc_start: 0.9281 (tt) cc_final: 0.9004 (tt) REVERT: R 785 TYR cc_start: 0.8591 (t80) cc_final: 0.8020 (t80) REVERT: R 809 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7916 (pptt) outliers start: 19 outliers final: 14 residues processed: 171 average time/residue: 0.2312 time to fit residues: 51.2056 Evaluate side-chains 172 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE 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 792 LEU Chi-restraints excluded: chain R residue 809 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.0040 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 0.0670 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.0370 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN N 53 GLN ** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 8074 Z= 0.148 Angle : 0.552 8.732 10941 Z= 0.289 Chirality : 0.042 0.197 1229 Planarity : 0.004 0.058 1397 Dihedral : 4.175 19.190 1098 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.35 % Favored : 95.35 % Rotamer: Outliers : 2.04 % Allowed : 21.82 % Favored : 76.14 % 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: -0.85 (0.27), residues: 989 helix: 0.56 (0.30), residues: 326 sheet: -0.15 (0.35), residues: 219 loop : -1.63 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 771 HIS 0.004 0.001 HIS A 220 PHE 0.007 0.001 PHE B 241 TYR 0.017 0.001 TYR R 625 ARG 0.007 0.000 ARG A 283 ********************** 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 176 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8619 (m110) cc_final: 0.8289 (p0) REVERT: A 333 ARG cc_start: 0.7870 (ptm160) cc_final: 0.7544 (ptm160) REVERT: A 368 ASP cc_start: 0.6599 (p0) cc_final: 0.6078 (p0) REVERT: B 59 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.7138 (m-80) REVERT: B 209 LYS cc_start: 0.8857 (mttt) cc_final: 0.8624 (mttt) REVERT: B 228 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: B 234 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.7861 (t80) REVERT: B 303 ASP cc_start: 0.7907 (m-30) cc_final: 0.7673 (m-30) REVERT: N 50 ASP cc_start: 0.7891 (p0) cc_final: 0.7564 (p0) REVERT: N 76 LYS cc_start: 0.8810 (mttt) cc_final: 0.8559 (mtmm) REVERT: N 85 SER cc_start: 0.9485 (m) cc_final: 0.8766 (p) REVERT: R 670 ILE cc_start: 0.9248 (tt) cc_final: 0.8982 (tt) REVERT: R 785 TYR cc_start: 0.8587 (t80) cc_final: 0.8073 (t80) REVERT: R 809 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7935 (pptt) outliers start: 17 outliers final: 13 residues processed: 173 average time/residue: 0.2347 time to fit residues: 52.4698 Evaluate side-chains 173 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 228 ASP Chi-restraints excluded: chain B residue 234 PHE 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 792 LEU Chi-restraints excluded: chain R residue 809 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN N 53 GLN N 120 GLN ** 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 = 0.3545 r_free = 0.3545 target = 0.112071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.091351 restraints weight = 14101.116| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.37 r_work: 0.3133 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8074 Z= 0.185 Angle : 0.581 11.463 10941 Z= 0.305 Chirality : 0.043 0.189 1229 Planarity : 0.004 0.059 1397 Dihedral : 4.362 21.065 1098 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.65 % Favored : 95.05 % Rotamer: Outliers : 2.64 % Allowed : 20.86 % 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: -0.91 (0.27), residues: 989 helix: 0.50 (0.30), residues: 330 sheet: -0.24 (0.34), residues: 224 loop : -1.66 (0.30), residues: 435 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 0.010 0.001 PHE R 622 TYR 0.017 0.001 TYR R 625 ARG 0.007 0.000 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2201.01 seconds wall clock time: 39 minutes 30.27 seconds (2370.27 seconds total)