Starting phenix.real_space_refine on Thu Jul 2 17:45:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gsd_51544/07_2026/9gsd_51544.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gsd_51544/07_2026/9gsd_51544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gsd_51544/07_2026/9gsd_51544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gsd_51544/07_2026/9gsd_51544.map" model { file = "/net/cci-nas-00/data/ceres_data/9gsd_51544/07_2026/9gsd_51544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gsd_51544/07_2026/9gsd_51544.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 55 5.16 5 Be 1 3.05 5 C 5854 2.51 5 N 1533 2.21 5 O 1732 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9182 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 7349 Classifications: {'peptide': 947} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 899} Chain breaks: 3 Chain: "B" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1703 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'BEF': 1, 'KXP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'KXP:plan-1': 1, 'KXP:plan-3': 1, 'KXP:plan-4': 1, 'KXP:plan-5': 1, 'KXP:plan-6': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.28, per 1000 atoms: 0.25 Number of scatterers: 9182 At special positions: 0 Unit cell: (92.82, 92.82, 181.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 55 16.00 P 3 15.00 Mg 1 11.99 F 3 9.00 O 1732 8.00 N 1533 7.00 C 5854 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 315 " 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=1, symmetry=0 Links applied NAG-ASN " NAG B 501 " - " ASN B 283 " " NAG B 502 " - " ASN B 316 " " NAG B 503 " - " ASN B 295 " " NAG B 504 " - " ASN B 170 " " NAG B 505 " - " ASN B 228 " " NAG B 506 " - " ASN B 196 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 325.2 milliseconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 11 sheets defined 45.7% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.608A pdb=" N GLU A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.764A pdb=" N GLN A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 123 removed outlier: 3.734A pdb=" N ILE A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 183 removed outlier: 3.593A pdb=" N GLY A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.699A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 379 removed outlier: 3.605A pdb=" N GLY A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 344 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 378 " --> pdb=" O ASP A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 410 removed outlier: 4.431A pdb=" N VAL A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 392 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.871A pdb=" N LYS A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 487 through 501 removed outlier: 4.178A pdb=" N GLU A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.303A pdb=" N LEU A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.861A pdb=" N MET A 546 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 607 through 622 removed outlier: 4.035A pdb=" N MET A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Proline residue: A 618 - end of helix Processing helix chain 'A' and resid 644 through 650 removed outlier: 4.053A pdb=" N ILE A 648 " --> pdb=" O ASN A 644 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 650 " --> pdb=" O ASN A 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 644 through 650' Processing helix chain 'A' and resid 667 through 678 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.527A pdb=" N ALA A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 747 through 761 Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 786 Processing helix chain 'A' and resid 797 through 803 Processing helix chain 'A' and resid 812 through 815 Processing helix chain 'A' and resid 816 through 854 removed outlier: 3.531A pdb=" N TYR A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 833 " --> pdb=" O SER A 829 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 839 " --> pdb=" O GLN A 835 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 842 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 870 removed outlier: 3.570A pdb=" N MET A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 882 removed outlier: 3.643A pdb=" N THR A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 892 removed outlier: 3.667A pdb=" N ARG A 892 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 933 removed outlier: 3.505A pdb=" N TYR A 916 " --> pdb=" O GLY A 912 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS A 930 " --> pdb=" O PHE A 926 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET A 931 " --> pdb=" O VAL A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 968 removed outlier: 3.808A pdb=" N ILE A 953 " --> pdb=" O HIS A 949 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A 967 " --> pdb=" O PHE A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1005 removed outlier: 3.865A pdb=" N CYS A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1039 removed outlier: 3.673A pdb=" N TRP A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A1029 " --> pdb=" O ILE A1025 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A1035 " --> pdb=" O VAL A1031 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A1039 " --> pdb=" O VAL A1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 360 removed outlier: 3.614A pdb=" N PHE B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194 removed outlier: 3.515A pdb=" N VAL A 194 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.817A pdb=" N ARG A 270 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 250 removed outlier: 3.907A pdb=" N LEU A 234 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP A 237 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL A 264 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 434 through 436 removed outlier: 6.017A pdb=" N GLY A 789 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU A 808 " --> pdb=" O GLY A 789 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA A 791 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 770 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N PHE A 790 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 772 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N MET A 792 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N GLY A 774 " --> pdb=" O MET A 792 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA A 450 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N THR A 773 " --> pdb=" O ALA A 450 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS A 452 " --> pdb=" O THR A 773 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG A 741 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU A 710 " --> pdb=" O ARG A 741 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 743 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 712 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 476 removed outlier: 6.940A pdb=" N GLY A 659 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA A 469 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL A 657 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL A 471 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N ILE A 655 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N CYS A 654 " --> pdb=" O TYR A 631 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR A 631 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS A 656 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 575 " --> pdb=" O PHE A 634 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 476 removed outlier: 6.940A pdb=" N GLY A 659 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA A 469 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL A 657 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL A 471 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N ILE A 655 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LYS A 592 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N CYS A 656 " --> pdb=" O LYS A 592 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 152 removed outlier: 6.682A pdb=" N ARG B 149 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 169 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET B 200 " --> pdb=" O CYS B 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 158 removed outlier: 4.030A pdb=" N VAL B 156 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 245 through 249 removed outlier: 5.035A pdb=" N GLU B 312 " --> pdb=" O LYS B 273 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 254 through 258 441 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1512 1.31 - 1.44: 2310 1.44 - 1.56: 5440 1.56 - 1.69: 4 1.69 - 1.82: 86 Bond restraints: 9352 Sorted by residual: bond pdb=" F2 BEF A1303 " pdb="BE BEF A1303 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" O41 KXP A1302 " pdb=" P42 KXP A1302 " ideal model delta sigma weight residual 1.725 1.648 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C18 KXP A1302 " pdb=" O20 KXP A1302 " ideal model delta sigma weight residual 1.323 1.399 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O36 KXP A1302 " pdb=" P37 KXP A1302 " ideal model delta sigma weight residual 1.722 1.646 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" F3 BEF A1303 " pdb="BE BEF A1303 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 9347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 12612 3.61 - 7.23: 59 7.23 - 10.84: 14 10.84 - 14.46: 1 14.46 - 18.07: 1 Bond angle restraints: 12687 Sorted by residual: angle pdb=" O24 KXP A1302 " pdb=" P25 KXP A1302 " pdb=" O28 KXP A1302 " ideal model delta sigma weight residual 90.95 109.02 -18.07 3.00e+00 1.11e-01 3.63e+01 angle pdb=" F2 BEF A1303 " pdb="BE BEF A1303 " pdb=" F3 BEF A1303 " ideal model delta sigma weight residual 119.96 108.15 11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C1 KXP A1302 " pdb=" C18 KXP A1302 " pdb=" O20 KXP A1302 " ideal model delta sigma weight residual 110.71 121.51 -10.80 3.00e+00 1.11e-01 1.29e+01 angle pdb=" O26 KXP A1302 " pdb=" P25 KXP A1302 " pdb=" O27 KXP A1302 " ideal model delta sigma weight residual 119.47 108.99 10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C GLU A 667 " pdb=" N VAL A 668 " pdb=" CA VAL A 668 " ideal model delta sigma weight residual 120.33 123.11 -2.78 8.00e-01 1.56e+00 1.21e+01 ... (remaining 12682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.64: 5525 31.64 - 63.28: 242 63.28 - 94.92: 17 94.92 - 126.56: 4 126.56 - 158.20: 1 Dihedral angle restraints: 5789 sinusoidal: 2436 harmonic: 3353 Sorted by residual: dihedral pdb=" O20 KXP A1302 " pdb=" C21 KXP A1302 " pdb=" C22 KXP A1302 " pdb=" O48 KXP A1302 " ideal model delta sinusoidal sigma weight residual 51.71 -106.49 158.20 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C29 KXP A1302 " pdb=" C30 KXP A1302 " pdb=" C31 KXP A1302 " pdb=" C32 KXP A1302 " ideal model delta sinusoidal sigma weight residual 55.03 -52.61 107.64 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C32 KXP A1302 " pdb=" C30 KXP A1302 " pdb=" C31 KXP A1302 " pdb=" O47 KXP A1302 " ideal model delta sinusoidal sigma weight residual 66.56 173.60 -107.04 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 5786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 865 0.031 - 0.062: 444 0.062 - 0.093: 112 0.093 - 0.124: 75 0.124 - 0.155: 8 Chirality restraints: 1504 Sorted by residual: chirality pdb=" C1 NAG B 504 " pdb=" ND2 ASN B 170 " pdb=" C2 NAG B 504 " pdb=" O5 NAG B 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" C1 NAG B 503 " pdb=" ND2 ASN B 295 " pdb=" C2 NAG B 503 " pdb=" O5 NAG B 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA TRP A 737 " pdb=" N TRP A 737 " pdb=" C TRP A 737 " pdb=" CB TRP A 737 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 1501 not shown) Planarity restraints: 1601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 222 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 223 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 780 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 781 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 781 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 781 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 811 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" CG ASP A 811 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP A 811 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 811 " 0.009 2.00e-02 2.50e+03 ... (remaining 1598 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 4 2.53 - 3.12: 6818 3.12 - 3.71: 13517 3.71 - 4.31: 18705 4.31 - 4.90: 31647 Nonbonded interactions: 70691 Sorted by model distance: nonbonded pdb="MG MG A1301 " pdb=" F3 BEF A1303 " model vdw 1.936 2.120 nonbonded pdb=" OD2 ASP A 454 " pdb="MG MG A1301 " model vdw 2.004 2.170 nonbonded pdb=" O THR A 456 " pdb="MG MG A1301 " model vdw 2.425 2.170 nonbonded pdb=" O28 KXP A1302 " pdb=" O47 KXP A1302 " model vdw 2.452 2.432 nonbonded pdb=" O ASP A 810 " pdb=" OD1 ASP A 811 " model vdw 2.537 3.040 ... (remaining 70686 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.256 9361 Z= 0.314 Angle : 0.692 18.069 12709 Z= 0.320 Chirality : 0.043 0.155 1504 Planarity : 0.004 0.040 1595 Dihedral : 16.768 158.205 3615 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.17 % Favored : 95.74 % Rotamer: Outliers : 0.79 % Allowed : 22.18 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.25), residues: 1151 helix: 0.39 (0.25), residues: 475 sheet: 1.05 (0.43), residues: 155 loop : -1.26 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 983 TYR 0.019 0.001 TYR A 218 PHE 0.017 0.001 PHE A1024 TRP 0.015 0.001 TRP A 867 HIS 0.003 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 ( 9352) covalent geometry : angle 0.68907 / 0.32 (12687) SS BOND : bond 0.00269 / 0.16 ( 2) SS BOND : angle 0.17348 / 0.08 ( 4) hydrogen bonds : bond 0.20782 / 13.76 ( 434) hydrogen bonds : angle 7.07453 / 4.98 ( 1239) Misc. bond : bond 0.25569 / 15.98 ( 1) link_NAG-ASN : bond 0.00356 / 0.22 ( 6) link_NAG-ASN : angle 1.87104 / 1.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 503 TYR cc_start: 0.7199 (p90) cc_final: 0.5758 (m-10) REVERT: A 546 MET cc_start: 0.7226 (mmm) cc_final: 0.6628 (mmm) REVERT: A 670 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7119 (tp30) REVERT: B 252 GLN cc_start: 0.7267 (mt0) cc_final: 0.7061 (mt0) outliers start: 8 outliers final: 8 residues processed: 100 average time/residue: 0.0904 time to fit residues: 13.1581 Evaluate side-chains 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 383 TRP Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 291 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0010 chunk 100 optimal weight: 9.9990 overall best weight: 0.5546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.221888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123819 restraints weight = 9532.913| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.30 r_work: 0.3065 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9361 Z= 0.111 Angle : 0.551 8.001 12709 Z= 0.279 Chirality : 0.043 0.159 1504 Planarity : 0.004 0.036 1595 Dihedral : 8.817 153.600 1434 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.26 % Rotamer: Outliers : 2.77 % Allowed : 19.80 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1151 helix: 0.94 (0.25), residues: 485 sheet: 0.98 (0.42), residues: 164 loop : -1.24 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 208 TYR 0.012 0.001 TYR B 180 PHE 0.014 0.001 PHE A1024 TRP 0.010 0.001 TRP A 173 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 9352) covalent geometry : angle 0.54723 / 0.28 (12687) SS BOND : bond 0.00232 / 0.14 ( 2) SS BOND : angle 0.39526 / 0.23 ( 4) hydrogen bonds : bond 0.04713 / 3.13 ( 434) hydrogen bonds : angle 4.71672 / 3.35 ( 1239) Misc. bond : bond 0.00048 / 0.03 ( 1) link_NAG-ASN : bond 0.00279 / 0.17 ( 6) link_NAG-ASN : angle 1.76433 / 1.15 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.8941 (tpp) cc_final: 0.8677 (mmp) REVERT: A 289 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6770 (mp) REVERT: A 369 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.6087 (tt) REVERT: A 546 MET cc_start: 0.7115 (mmm) cc_final: 0.6884 (mmm) REVERT: A 892 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8101 (ptp-170) outliers start: 28 outliers final: 16 residues processed: 119 average time/residue: 0.0974 time to fit residues: 16.5816 Evaluate side-chains 104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 383 TRP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 291 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 8.9990 chunk 20 optimal weight: 0.0870 chunk 110 optimal weight: 0.0770 chunk 98 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 GLN A 984 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.218064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119289 restraints weight = 9550.804| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.26 r_work: 0.2984 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9361 Z= 0.173 Angle : 0.574 8.801 12709 Z= 0.292 Chirality : 0.045 0.154 1504 Planarity : 0.004 0.043 1595 Dihedral : 8.282 159.132 1434 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 3.17 % Allowed : 19.01 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1151 helix: 0.75 (0.24), residues: 493 sheet: 0.88 (0.42), residues: 169 loop : -1.24 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 331 TYR 0.015 0.001 TYR A 827 PHE 0.019 0.002 PHE A1024 TRP 0.011 0.001 TRP A 173 HIS 0.003 0.001 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.17 ( 9352) covalent geometry : angle 0.57004 / 0.29 (12687) SS BOND : bond 0.00249 / 0.15 ( 2) SS BOND : angle 0.33058 / 0.20 ( 4) hydrogen bonds : bond 0.05680 / 3.77 ( 434) hydrogen bonds : angle 4.59380 / 3.27 ( 1239) Misc. bond : bond 0.00099 / 0.06 ( 1) link_NAG-ASN : bond 0.00312 / 0.20 ( 6) link_NAG-ASN : angle 1.78482 / 1.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.8953 (tpp) cc_final: 0.8728 (mmp) REVERT: A 289 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6784 (mp) REVERT: A 476 TYR cc_start: 0.7002 (m-80) cc_final: 0.6770 (m-10) REVERT: A 546 MET cc_start: 0.7089 (mmm) cc_final: 0.6676 (mmm) REVERT: A 892 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8055 (ptp-170) outliers start: 32 outliers final: 23 residues processed: 113 average time/residue: 0.1001 time to fit residues: 16.2121 Evaluate side-chains 108 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 383 TRP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 944 SER Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 335 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 52 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 94 optimal weight: 0.0060 chunk 59 optimal weight: 0.1980 chunk 112 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.218357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126654 restraints weight = 9555.133| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.04 r_work: 0.3144 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9361 Z= 0.153 Angle : 0.545 8.457 12709 Z= 0.278 Chirality : 0.044 0.154 1504 Planarity : 0.004 0.043 1595 Dihedral : 8.173 161.299 1434 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.27 % Allowed : 19.60 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.25), residues: 1151 helix: 0.84 (0.24), residues: 494 sheet: 1.03 (0.42), residues: 177 loop : -1.27 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 331 TYR 0.013 0.001 TYR A 827 PHE 0.019 0.001 PHE A1024 TRP 0.009 0.001 TRP A 173 HIS 0.004 0.001 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 ( 9352) covalent geometry : angle 0.54164 / 0.28 (12687) SS BOND : bond 0.00275 / 0.17 ( 2) SS BOND : angle 0.29194 / 0.18 ( 4) hydrogen bonds : bond 0.05263 / 3.49 ( 434) hydrogen bonds : angle 4.45027 / 3.18 ( 1239) Misc. bond : bond 0.00101 / 0.06 ( 1) link_NAG-ASN : bond 0.00296 / 0.18 ( 6) link_NAG-ASN : angle 1.73322 / 1.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.8857 (tpp) cc_final: 0.8499 (mmp) REVERT: A 263 HIS cc_start: 0.7459 (t70) cc_final: 0.6162 (m90) REVERT: A 289 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6985 (mp) REVERT: A 546 MET cc_start: 0.7099 (mmm) cc_final: 0.6665 (mmm) REVERT: A 892 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8246 (ptp-170) outliers start: 33 outliers final: 21 residues processed: 113 average time/residue: 0.0871 time to fit residues: 14.4914 Evaluate side-chains 107 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 383 TRP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 944 SER Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 335 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 43 optimal weight: 7.9990 chunk 96 optimal weight: 40.0000 chunk 94 optimal weight: 0.0170 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 47 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.218827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128424 restraints weight = 9576.076| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.52 r_work: 0.3164 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9361 Z= 0.140 Angle : 0.534 8.106 12709 Z= 0.272 Chirality : 0.043 0.149 1504 Planarity : 0.004 0.041 1595 Dihedral : 8.020 160.122 1434 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.96 % Allowed : 19.11 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.25), residues: 1151 helix: 1.00 (0.24), residues: 490 sheet: 1.22 (0.42), residues: 166 loop : -1.29 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 331 TYR 0.012 0.001 TYR A 827 PHE 0.018 0.001 PHE A1024 TRP 0.009 0.001 TRP A 173 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 9352) covalent geometry : angle 0.53034 / 0.27 (12687) SS BOND : bond 0.00225 / 0.14 ( 2) SS BOND : angle 0.38245 / 0.20 ( 4) hydrogen bonds : bond 0.04983 / 3.31 ( 434) hydrogen bonds : angle 4.37789 / 3.12 ( 1239) Misc. bond : bond 0.00077 / 0.05 ( 1) link_NAG-ASN : bond 0.00237 / 0.14 ( 6) link_NAG-ASN : angle 1.65844 / 1.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8172 (tt) REVERT: A 257 MET cc_start: 0.8849 (tpp) cc_final: 0.8537 (mmp) REVERT: A 289 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6981 (mp) REVERT: A 546 MET cc_start: 0.7132 (mmm) cc_final: 0.6676 (mmm) REVERT: A 792 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.7636 (mmt) REVERT: A 811 ASP cc_start: 0.8558 (p0) cc_final: 0.8063 (p0) REVERT: A 892 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8322 (ptp-170) outliers start: 40 outliers final: 28 residues processed: 121 average time/residue: 0.0820 time to fit residues: 14.3401 Evaluate side-chains 116 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 383 TRP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 944 SER Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 335 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.219295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120820 restraints weight = 9595.165| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.26 r_work: 0.3006 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9361 Z= 0.130 Angle : 0.523 7.764 12709 Z= 0.266 Chirality : 0.043 0.157 1504 Planarity : 0.004 0.040 1595 Dihedral : 7.884 158.671 1434 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.06 % Allowed : 19.60 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1151 helix: 1.12 (0.24), residues: 490 sheet: 1.03 (0.41), residues: 176 loop : -1.20 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 331 TYR 0.011 0.001 TYR A 827 PHE 0.018 0.001 PHE A1024 TRP 0.009 0.001 TRP A 173 HIS 0.002 0.001 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 9352) covalent geometry : angle 0.51962 / 0.27 (12687) SS BOND : bond 0.00327 / 0.20 ( 2) SS BOND : angle 0.57449 / 0.24 ( 4) hydrogen bonds : bond 0.04748 / 3.15 ( 434) hydrogen bonds : angle 4.27223 / 3.05 ( 1239) Misc. bond : bond 0.00061 / 0.04 ( 1) link_NAG-ASN : bond 0.00302 / 0.18 ( 6) link_NAG-ASN : angle 1.63334 / 1.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7880 (tt) REVERT: A 289 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6759 (mp) REVERT: A 625 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.5822 (ttm-80) REVERT: A 792 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.7255 (mmt) REVERT: A 805 ASP cc_start: 0.8302 (m-30) cc_final: 0.8068 (m-30) REVERT: A 811 ASP cc_start: 0.8425 (p0) cc_final: 0.7833 (p0) REVERT: A 892 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8072 (ptp-170) outliers start: 41 outliers final: 32 residues processed: 124 average time/residue: 0.0902 time to fit residues: 15.9965 Evaluate side-chains 121 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 383 TRP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 944 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 98 optimal weight: 30.0000 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.218203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120150 restraints weight = 9542.956| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.39 r_work: 0.2969 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9361 Z= 0.164 Angle : 0.552 8.142 12709 Z= 0.282 Chirality : 0.044 0.152 1504 Planarity : 0.004 0.054 1595 Dihedral : 7.920 158.673 1434 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.06 % Allowed : 20.50 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.25), residues: 1151 helix: 1.01 (0.24), residues: 490 sheet: 1.03 (0.41), residues: 172 loop : -1.24 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 331 TYR 0.013 0.001 TYR A 827 PHE 0.035 0.002 PHE A 192 TRP 0.009 0.001 TRP A 173 HIS 0.003 0.001 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.16 ( 9352) covalent geometry : angle 0.54947 / 0.28 (12687) SS BOND : bond 0.00253 / 0.16 ( 2) SS BOND : angle 0.46872 / 0.22 ( 4) hydrogen bonds : bond 0.05277 / 3.50 ( 434) hydrogen bonds : angle 4.35865 / 3.12 ( 1239) Misc. bond : bond 0.00111 / 0.07 ( 1) link_NAG-ASN : bond 0.00295 / 0.18 ( 6) link_NAG-ASN : angle 1.61637 / 1.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7898 (tt) REVERT: A 289 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6740 (mp) REVERT: A 625 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.5941 (ttm-80) REVERT: A 792 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.7319 (mmt) REVERT: A 892 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8150 (ptp-170) REVERT: B 255 MET cc_start: 0.8062 (pp-130) cc_final: 0.7605 (pp-130) outliers start: 41 outliers final: 30 residues processed: 123 average time/residue: 0.0908 time to fit residues: 16.1426 Evaluate side-chains 120 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 383 TRP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 944 SER Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 335 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 0.0370 chunk 21 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.221504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125040 restraints weight = 9545.013| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.61 r_work: 0.3016 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9361 Z= 0.103 Angle : 0.503 7.301 12709 Z= 0.255 Chirality : 0.042 0.158 1504 Planarity : 0.004 0.048 1595 Dihedral : 7.716 157.261 1434 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.37 % Allowed : 20.99 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1151 helix: 1.35 (0.24), residues: 494 sheet: 1.02 (0.41), residues: 172 loop : -1.19 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 331 TYR 0.009 0.001 TYR A 827 PHE 0.017 0.001 PHE A 192 TRP 0.008 0.001 TRP B 183 HIS 0.002 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 9352) covalent geometry : angle 0.49983 / 0.25 (12687) SS BOND : bond 0.00281 / 0.17 ( 2) SS BOND : angle 0.46901 / 0.22 ( 4) hydrogen bonds : bond 0.04071 / 2.71 ( 434) hydrogen bonds : angle 4.12182 / 2.94 ( 1239) Misc. bond : bond 0.00026 / 0.02 ( 1) link_NAG-ASN : bond 0.00285 / 0.17 ( 6) link_NAG-ASN : angle 1.53996 / 0.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6325 (pt0) REVERT: A 289 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6762 (mp) REVERT: A 670 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7140 (tp30) REVERT: A 792 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7292 (mmt) REVERT: A 811 ASP cc_start: 0.8378 (p0) cc_final: 0.7821 (p0) REVERT: A 892 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8116 (ptp-170) REVERT: B 255 MET cc_start: 0.8081 (pp-130) cc_final: 0.7598 (pp-130) outliers start: 34 outliers final: 27 residues processed: 122 average time/residue: 0.0805 time to fit residues: 14.3674 Evaluate side-chains 124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 383 TRP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 944 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 335 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 0.0010 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.219575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122964 restraints weight = 9349.617| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.16 r_work: 0.3026 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9361 Z= 0.121 Angle : 0.532 8.621 12709 Z= 0.267 Chirality : 0.042 0.158 1504 Planarity : 0.004 0.050 1595 Dihedral : 7.698 156.822 1434 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.27 % Allowed : 21.29 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1151 helix: 1.30 (0.24), residues: 496 sheet: 0.98 (0.41), residues: 177 loop : -1.13 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 331 TYR 0.011 0.001 TYR A 827 PHE 0.017 0.001 PHE A1024 TRP 0.008 0.001 TRP B 183 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 9352) covalent geometry : angle 0.52896 / 0.27 (12687) SS BOND : bond 0.00249 / 0.15 ( 2) SS BOND : angle 0.43439 / 0.20 ( 4) hydrogen bonds : bond 0.04414 / 2.94 ( 434) hydrogen bonds : angle 4.13776 / 2.96 ( 1239) Misc. bond : bond 0.00049 / 0.03 ( 1) link_NAG-ASN : bond 0.00279 / 0.17 ( 6) link_NAG-ASN : angle 1.55137 / 0.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: A 148 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6346 (pt0) REVERT: A 289 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6868 (mp) REVERT: A 670 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7119 (tp30) REVERT: A 792 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7253 (mmt) REVERT: A 892 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8087 (ptp-170) REVERT: B 255 MET cc_start: 0.8045 (pp-130) cc_final: 0.7579 (pp-130) outliers start: 33 outliers final: 26 residues processed: 119 average time/residue: 0.0799 time to fit residues: 13.9934 Evaluate side-chains 120 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 383 TRP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 944 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 85 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.221379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123775 restraints weight = 9558.949| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.47 r_work: 0.3245 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9361 Z= 0.103 Angle : 0.519 8.594 12709 Z= 0.260 Chirality : 0.042 0.159 1504 Planarity : 0.004 0.045 1595 Dihedral : 7.609 156.336 1434 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.67 % Allowed : 22.08 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 1151 helix: 1.45 (0.24), residues: 497 sheet: 0.99 (0.41), residues: 176 loop : -1.12 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 331 TYR 0.009 0.001 TYR A 827 PHE 0.017 0.001 PHE A1024 TRP 0.008 0.001 TRP B 183 HIS 0.002 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 9352) covalent geometry : angle 0.51651 / 0.26 (12687) SS BOND : bond 0.00259 / 0.15 ( 2) SS BOND : angle 0.40914 / 0.19 ( 4) hydrogen bonds : bond 0.03949 / 2.63 ( 434) hydrogen bonds : angle 4.04279 / 2.88 ( 1239) Misc. bond : bond 0.00031 / 0.02 ( 1) link_NAG-ASN : bond 0.00280 / 0.17 ( 6) link_NAG-ASN : angle 1.50514 / 0.96 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6561 (pt0) REVERT: A 289 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7162 (mp) REVERT: A 670 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7567 (tp30) REVERT: A 792 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.7512 (mmt) REVERT: B 255 MET cc_start: 0.8225 (pp-130) cc_final: 0.7793 (pp-130) outliers start: 27 outliers final: 24 residues processed: 118 average time/residue: 0.0769 time to fit residues: 13.5113 Evaluate side-chains 118 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 383 TRP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 944 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 291 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 99 optimal weight: 0.0670 chunk 19 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.221281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129061 restraints weight = 9523.430| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.46 r_work: 0.3220 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9361 Z= 0.105 Angle : 0.516 8.936 12709 Z= 0.260 Chirality : 0.042 0.159 1504 Planarity : 0.004 0.045 1595 Dihedral : 7.533 155.328 1434 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.07 % Allowed : 21.39 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 1151 helix: 1.49 (0.24), residues: 497 sheet: 0.83 (0.42), residues: 164 loop : -1.06 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 331 TYR 0.009 0.001 TYR A 827 PHE 0.016 0.001 PHE A1024 TRP 0.008 0.001 TRP B 183 HIS 0.003 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 9352) covalent geometry : angle 0.51362 / 0.26 (12687) SS BOND : bond 0.00248 / 0.15 ( 2) SS BOND : angle 0.41873 / 0.19 ( 4) hydrogen bonds : bond 0.03981 / 2.66 ( 434) hydrogen bonds : angle 4.00176 / 2.85 ( 1239) Misc. bond : bond 0.00033 / 0.02 ( 1) link_NAG-ASN : bond 0.00283 / 0.17 ( 6) link_NAG-ASN : angle 1.48371 / 0.95 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3487.98 seconds wall clock time: 60 minutes 7.42 seconds (3607.42 seconds total)