Starting phenix.real_space_refine on Sat Jul 4 11:41:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q3y_13797/07_2026/7q3y_13797_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q3y_13797/07_2026/7q3y_13797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q3y_13797/07_2026/7q3y_13797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q3y_13797/07_2026/7q3y_13797.map" model { file = "/net/cci-nas-00/data/ceres_data/7q3y_13797/07_2026/7q3y_13797_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q3y_13797/07_2026/7q3y_13797_trim.cif" } resolution = 4.34 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= 0.048 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 S 43 5.16 5 Cl 1 4.86 5 C 6531 2.51 5 N 1695 2.21 5 O 1970 1.98 5 H 9386 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 19627 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 19172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1201, 19172 Classifications: {'peptide': 1201} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 68, 'TRANS': 1129} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 60 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.43, per 1000 atoms: 0.17 Number of scatterers: 19627 At special positions: 0 Unit cell: (84.8, 90.1, 153.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 43 16.00 O 1970 8.00 N 1695 7.00 C 6531 6.00 H 9386 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 734 " distance=2.03 Simple disulfide: pdb=" SG CYS A 928 " - pdb=" SG CYS A 946 " distance=2.03 Simple disulfide: pdb=" SG CYS A1114 " - pdb=" SG CYS A1126 " 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA B 3 " - " MAN B 4 " " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " BETA1-6 " NAG J 1 " - " FUC J 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1303 " - " ASN A 666 " " NAG A1304 " - " ASN A 913 " " NAG A1305 " - " ASN A 416 " " NAG A1306 " - " ASN A 82 " " NAG B 1 " - " ASN A 648 " " NAG C 1 " - " ASN A 685 " " NAG D 1 " - " ASN A 731 " " NAG E 1 " - " ASN A 9 " " NAG F 1 " - " ASN A 25 " " NAG G 1 " - " ASN A 117 " " NAG H 1 " - " ASN A 480 " " NAG I 1 " - " ASN A 45 " " NAG J 1 " - " ASN A 289 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 472.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 361 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 365 " 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 6 sheets defined 70.7% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.711A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 77 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 104 through 125 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 152 through 190 Proline residue: A 170 - end of helix Proline residue: A 173 - end of helix removed outlier: 3.719A pdb=" N GLU A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.702A pdb=" N TRP A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 238 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 251 through 254 removed outlier: 4.216A pdb=" N GLY A 254 " --> pdb=" O HIS A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.535A pdb=" N VAL A 268 " --> pdb=" O ILE A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.510A pdb=" N ARG A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.822A pdb=" N TRP A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 373 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 386 through 401 removed outlier: 3.619A pdb=" N ALA A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 392 " --> pdb=" O HIS A 388 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 417 through 433 Processing helix chain 'A' and resid 434 through 452 removed outlier: 4.505A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 498 through 519 removed outlier: 3.830A pdb=" N PHE A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 533 through 546 Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'A' and resid 616 through 648 removed outlier: 3.923A pdb=" N ALA A 620 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 676 Processing helix chain 'A' and resid 677 through 678 No H-bonds generated for 'chain 'A' and resid 677 through 678' Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.718A pdb=" N GLN A 682 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 725 Processing helix chain 'A' and resid 739 through 748 Processing helix chain 'A' and resid 750 through 769 removed outlier: 3.897A pdb=" N ARG A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 769 " --> pdb=" O ALA A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 787 Processing helix chain 'A' and resid 791 through 799 removed outlier: 3.848A pdb=" N MET A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 836 removed outlier: 3.505A pdb=" N LEU A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Proline residue: A 818 - end of helix removed outlier: 3.600A pdb=" N HIS A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 861 No H-bonds generated for 'chain 'A' and resid 859 through 861' Processing helix chain 'A' and resid 862 through 867 Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 887 through 902 Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 950 through 970 removed outlier: 3.627A pdb=" N TYR A 970 " --> pdb=" O TYR A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 978 Processing helix chain 'A' and resid 982 through 996 removed outlier: 3.608A pdb=" N HIS A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 990 " --> pdb=" O HIS A 986 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 994 " --> pdb=" O GLY A 990 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER A 996 " --> pdb=" O VAL A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1006 Processing helix chain 'A' and resid 1015 through 1031 removed outlier: 3.691A pdb=" N ASP A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP A1029 " --> pdb=" O LYS A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1049 removed outlier: 3.870A pdb=" N PHE A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1056 through 1070 Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1096 through 1117 removed outlier: 3.887A pdb=" N PHE A1100 " --> pdb=" O TYR A1096 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A1108 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 3.571A pdb=" N GLN A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A1141 " --> pdb=" O ARG A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1159 removed outlier: 3.961A pdb=" N ALA A1153 " --> pdb=" O PRO A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1186 Proline residue: A1174 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 removed outlier: 5.988A pdb=" N ILE A 248 " --> pdb=" O CYS A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 335 Processing sheet with id=AA4, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA5, first strand: chain 'A' and resid 846 through 847 removed outlier: 6.356A pdb=" N ILE A 846 " --> pdb=" O CYS A1072 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 931 through 934 570 hydrogen bonds defined for protein. 1626 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: 4.10 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9384 1.03 - 1.23: 286 1.23 - 1.43: 4409 1.43 - 1.63: 5772 1.63 - 1.83: 72 Bond restraints: 19923 Sorted by residual: bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sigma weight residual 1.417 1.456 -0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.564 -0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" CB TRP A1062 " pdb=" CG TRP A1062 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.21e+00 bond pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.417 1.452 -0.035 2.00e-02 2.50e+03 3.03e+00 ... (remaining 19918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 33542 1.39 - 2.79: 1826 2.79 - 4.18: 248 4.18 - 5.58: 55 5.58 - 6.97: 23 Bond angle restraints: 35694 Sorted by residual: angle pdb=" C CYS A 928 " pdb=" N HIS A 929 " pdb=" CA HIS A 929 " ideal model delta sigma weight residual 121.24 116.55 4.69 1.44e+00 4.82e-01 1.06e+01 angle pdb=" N ASN A1196 " pdb=" CA ASN A1196 " pdb=" C ASN A1196 " ideal model delta sigma weight residual 107.41 113.66 -6.25 2.02e+00 2.45e-01 9.57e+00 angle pdb=" C LYS A 341 " pdb=" N ASP A 342 " pdb=" CA ASP A 342 " ideal model delta sigma weight residual 121.62 116.09 5.53 1.83e+00 2.99e-01 9.14e+00 angle pdb=" CA CYS A 928 " pdb=" C CYS A 928 " pdb=" N HIS A 929 " ideal model delta sigma weight residual 118.59 123.49 -4.90 1.63e+00 3.76e-01 9.05e+00 angle pdb=" CA TRP A1062 " pdb=" CB TRP A1062 " pdb=" CG TRP A1062 " ideal model delta sigma weight residual 113.60 108.00 5.60 1.90e+00 2.77e-01 8.70e+00 ... (remaining 35689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.49: 9277 21.49 - 42.97: 445 42.97 - 64.46: 153 64.46 - 85.95: 72 85.95 - 107.43: 32 Dihedral angle restraints: 9979 sinusoidal: 5598 harmonic: 4381 Sorted by residual: dihedral pdb=" CB CYS A 928 " pdb=" SG CYS A 928 " pdb=" SG CYS A 946 " pdb=" CB CYS A 946 " ideal model delta sinusoidal sigma weight residual 93.00 168.62 -75.62 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.72 107.43 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C3 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.12 105.74 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 9976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1409 0.070 - 0.141: 169 0.141 - 0.211: 15 0.211 - 0.282: 5 0.282 - 0.352: 5 Chirality restraints: 1603 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 666 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1600 not shown) Planarity restraints: 2950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 508 " -0.037 2.00e-02 2.50e+03 4.25e-02 2.71e+01 pdb=" CD GLN A 508 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN A 508 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 508 " 0.061 2.00e-02 2.50e+03 pdb="HE21 GLN A 508 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 508 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 446 " -0.090 9.50e-02 1.11e+02 3.77e-02 1.27e+01 pdb=" NE ARG A 446 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 446 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 446 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 446 " 0.043 2.00e-02 2.50e+03 pdb="HH11 ARG A 446 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 446 " 0.009 2.00e-02 2.50e+03 pdb="HH21 ARG A 446 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 446 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 371 " 0.024 2.00e-02 2.50e+03 2.85e-02 1.22e+01 pdb=" CD GLN A 371 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 371 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 371 " -0.044 2.00e-02 2.50e+03 pdb="HE21 GLN A 371 " 0.000 2.00e-02 2.50e+03 pdb="HE22 GLN A 371 " 0.043 2.00e-02 2.50e+03 ... (remaining 2947 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 290 2.05 - 2.69: 29670 2.69 - 3.32: 59137 3.32 - 3.96: 72516 3.96 - 4.60: 115764 Nonbonded interactions: 277377 Sorted by model distance: nonbonded pdb=" OD2 ASP A1041 " pdb=" H ILE A1097 " model vdw 1.411 2.450 nonbonded pdb=" H THR A 948 " pdb=" OD2 ASP A 953 " model vdw 1.500 2.450 nonbonded pdb=" HG1 THR A 454 " pdb=" OD2 ASP A 462 " model vdw 1.514 2.450 nonbonded pdb=" OD2 ASP A 443 " pdb=" H ILE A 499 " model vdw 1.515 2.450 nonbonded pdb=" HG1 THR A 468 " pdb=" O ILE A 473 " model vdw 1.566 2.450 ... (remaining 277372 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.150 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.450 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 0.056 10580 Z= 0.331 Angle : 0.957 14.066 14465 Z= 0.490 Chirality : 0.050 0.352 1603 Planarity : 0.008 0.095 1808 Dihedral : 17.139 107.431 4371 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.19 % Allowed : 2.31 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: -1.33 (0.22), residues: 1199 helix: -0.73 (0.16), residues: 715 sheet: -0.82 (1.11), residues: 20 loop : -0.89 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG A 199 TYR 0.026 0.004 TYR A 501 PHE 0.032 0.003 PHE A1107 TRP 0.036 0.004 TRP A 552 HIS 0.013 0.003 HIS A 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.33 (10537) covalent geometry : angle 0.90445 / 0.48 (14348) SS BOND : bond 0.00254 / 0.13 ( 6) SS BOND : angle 2.19553 / 1.10 ( 12) hydrogen bonds : bond 0.21457 / 14.68 ( 570) hydrogen bonds : angle 8.24563 / 6.11 ( 1626) metal coordination : bond 0.01407 / 0.67 ( 2) link_ALPHA1-3 : bond 0.00387 / 0.18 ( 2) link_ALPHA1-3 : angle 3.30613 / 1.50 ( 6) link_ALPHA1-6 : bond 0.00583 / 0.28 ( 3) link_ALPHA1-6 : angle 1.57515 / 0.74 ( 9) link_BETA1-4 : bond 0.00716 / 0.39 ( 16) link_BETA1-4 : angle 3.20314 / 1.93 ( 48) link_BETA1-6 : bond 0.00738 / 0.35 ( 1) link_BETA1-6 : angle 2.64788 / 1.16 ( 3) link_NAG-ASN : bond 0.00578 / 0.30 ( 13) link_NAG-ASN : angle 4.70395 / 2.90 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8547 (m-10) cc_final: 0.8198 (m-80) REVERT: A 182 SER cc_start: 0.9071 (t) cc_final: 0.8858 (m) REVERT: A 183 ASN cc_start: 0.8527 (m-40) cc_final: 0.7534 (t0) REVERT: A 293 MET cc_start: 0.8985 (mtp) cc_final: 0.8549 (mmm) REVERT: A 606 ASN cc_start: 0.9013 (m-40) cc_final: 0.8374 (m-40) REVERT: A 779 LEU cc_start: 0.9500 (mt) cc_final: 0.9094 (mt) REVERT: A 916 MET cc_start: 0.9011 (ttp) cc_final: 0.8615 (tmm) REVERT: A 943 ILE cc_start: 0.9536 (mt) cc_final: 0.9290 (tp) REVERT: A 968 MET cc_start: 0.9401 (mtm) cc_final: 0.9184 (mtp) outliers start: 2 outliers final: 2 residues processed: 192 average time/residue: 0.2180 time to fit residues: 58.1479 Evaluate side-chains 120 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN A 832 HIS ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 GLN ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.085420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.066995 restraints weight = 102603.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.070883 restraints weight = 48099.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073491 restraints weight = 28941.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.075176 restraints weight = 20279.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.076339 restraints weight = 15766.004| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10580 Z= 0.179 Angle : 0.722 6.091 14465 Z= 0.373 Chirality : 0.042 0.261 1603 Planarity : 0.005 0.062 1808 Dihedral : 12.000 72.295 2021 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.16 (0.23), residues: 1199 helix: 0.34 (0.17), residues: 740 sheet: 0.07 (1.74), residues: 10 loop : -0.04 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 350 TYR 0.025 0.002 TYR A 368 PHE 0.018 0.002 PHE A 83 TRP 0.018 0.002 TRP A 552 HIS 0.010 0.002 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (10537) covalent geometry : angle 0.69617 / 0.37 (14348) SS BOND : bond 0.00175 / 0.09 ( 6) SS BOND : angle 1.37948 / 0.75 ( 12) hydrogen bonds : bond 0.06624 / 4.46 ( 570) hydrogen bonds : angle 5.78050 / 4.31 ( 1626) metal coordination : bond 0.00341 / 0.16 ( 2) link_ALPHA1-3 : bond 0.00344 / 0.16 ( 2) link_ALPHA1-3 : angle 2.29400 / 1.11 ( 6) link_ALPHA1-6 : bond 0.00655 / 0.31 ( 3) link_ALPHA1-6 : angle 1.81758 / 0.83 ( 9) link_BETA1-4 : bond 0.00373 / 0.21 ( 16) link_BETA1-4 : angle 2.46416 / 1.69 ( 48) link_BETA1-6 : bond 0.00312 / 0.15 ( 1) link_BETA1-6 : angle 1.91046 / 0.78 ( 3) link_NAG-ASN : bond 0.00289 / 0.16 ( 13) link_NAG-ASN : angle 2.24279 / 1.36 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 SER cc_start: 0.9048 (t) cc_final: 0.8833 (m) REVERT: A 183 ASN cc_start: 0.8477 (m-40) cc_final: 0.7374 (t0) REVERT: A 293 MET cc_start: 0.8908 (mtp) cc_final: 0.8456 (mmm) REVERT: A 428 MET cc_start: 0.7995 (tpp) cc_final: 0.7775 (tpp) REVERT: A 916 MET cc_start: 0.9024 (ttp) cc_final: 0.8586 (tmm) REVERT: A 1017 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7876 (mp0) REVERT: A 1020 ILE cc_start: 0.8935 (mm) cc_final: 0.8620 (tp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2140 time to fit residues: 43.3818 Evaluate side-chains 108 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 97 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.084312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.066644 restraints weight = 97280.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.070530 restraints weight = 43050.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073109 restraints weight = 24963.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.074793 restraints weight = 16971.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.075967 restraints weight = 12904.262| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10580 Z= 0.164 Angle : 0.653 5.689 14465 Z= 0.331 Chirality : 0.040 0.241 1603 Planarity : 0.005 0.055 1808 Dihedral : 9.550 61.290 2021 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 (0.24), residues: 1199 helix: 0.56 (0.18), residues: 741 sheet: 0.04 (1.83), residues: 10 loop : 0.22 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 236 TYR 0.013 0.002 TYR A 111 PHE 0.022 0.002 PHE A 505 TRP 0.023 0.002 TRP A1062 HIS 0.004 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (10537) covalent geometry : angle 0.63051 / 0.33 (14348) SS BOND : bond 0.00136 / 0.07 ( 6) SS BOND : angle 1.02719 / 0.56 ( 12) hydrogen bonds : bond 0.05818 / 3.93 ( 570) hydrogen bonds : angle 5.38753 / 4.02 ( 1626) metal coordination : bond 0.00159 / 0.08 ( 2) link_ALPHA1-3 : bond 0.00784 / 0.37 ( 2) link_ALPHA1-3 : angle 1.83900 / 0.87 ( 6) link_ALPHA1-6 : bond 0.00567 / 0.27 ( 3) link_ALPHA1-6 : angle 1.67222 / 0.78 ( 9) link_BETA1-4 : bond 0.00399 / 0.22 ( 16) link_BETA1-4 : angle 2.26470 / 1.56 ( 48) link_BETA1-6 : bond 0.00139 / 0.07 ( 1) link_BETA1-6 : angle 1.61510 / 0.73 ( 3) link_NAG-ASN : bond 0.00210 / 0.11 ( 13) link_NAG-ASN : angle 1.92004 / 1.14 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 SER cc_start: 0.9062 (t) cc_final: 0.8854 (m) REVERT: A 183 ASN cc_start: 0.8399 (m-40) cc_final: 0.7333 (t0) REVERT: A 293 MET cc_start: 0.8901 (mtp) cc_final: 0.8664 (mtp) REVERT: A 309 MET cc_start: 0.8231 (mmt) cc_final: 0.7841 (mmt) REVERT: A 428 MET cc_start: 0.8051 (tpp) cc_final: 0.7824 (tpp) REVERT: A 443 ASP cc_start: 0.7834 (m-30) cc_final: 0.7352 (t0) REVERT: A 826 TYR cc_start: 0.8816 (t80) cc_final: 0.8407 (t80) REVERT: A 916 MET cc_start: 0.8897 (ttp) cc_final: 0.8523 (tmm) REVERT: A 1017 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7812 (mp0) REVERT: A 1020 ILE cc_start: 0.8914 (mm) cc_final: 0.8595 (tp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2184 time to fit residues: 43.5086 Evaluate side-chains 112 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 782 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.083301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.064897 restraints weight = 98180.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.068766 restraints weight = 43635.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.071342 restraints weight = 25655.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.073030 restraints weight = 17718.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.074191 restraints weight = 13646.567| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10580 Z= 0.188 Angle : 0.622 5.773 14465 Z= 0.319 Chirality : 0.039 0.225 1603 Planarity : 0.004 0.050 1808 Dihedral : 7.141 49.006 2021 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.24), residues: 1199 helix: 0.70 (0.18), residues: 745 sheet: -0.56 (1.69), residues: 10 loop : 0.39 (0.33), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 500 TYR 0.015 0.002 TYR A1068 PHE 0.016 0.002 PHE A 892 TRP 0.015 0.001 TRP A 758 HIS 0.005 0.001 HIS A 963 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (10537) covalent geometry : angle 0.60028 / 0.32 (14348) SS BOND : bond 0.00235 / 0.12 ( 6) SS BOND : angle 1.24206 / 0.69 ( 12) hydrogen bonds : bond 0.05056 / 3.38 ( 570) hydrogen bonds : angle 5.16294 / 3.84 ( 1626) metal coordination : bond 0.00384 / 0.18 ( 2) link_ALPHA1-3 : bond 0.00807 / 0.38 ( 2) link_ALPHA1-3 : angle 2.09456 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00608 / 0.30 ( 3) link_ALPHA1-6 : angle 2.20950 / 1.01 ( 9) link_BETA1-4 : bond 0.00344 / 0.19 ( 16) link_BETA1-4 : angle 2.05673 / 1.43 ( 48) link_BETA1-6 : bond 0.00280 / 0.13 ( 1) link_BETA1-6 : angle 1.76488 / 0.75 ( 3) link_NAG-ASN : bond 0.00271 / 0.14 ( 13) link_NAG-ASN : angle 1.74011 / 0.97 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 SER cc_start: 0.9149 (t) cc_final: 0.8889 (m) REVERT: A 183 ASN cc_start: 0.8498 (m-40) cc_final: 0.7420 (t0) REVERT: A 256 MET cc_start: 0.9013 (tpp) cc_final: 0.8756 (tpp) REVERT: A 363 MET cc_start: 0.8496 (ttt) cc_final: 0.8273 (ttt) REVERT: A 662 MET cc_start: 0.8509 (ttt) cc_final: 0.8020 (tmm) REVERT: A 916 MET cc_start: 0.9011 (ttp) cc_final: 0.8531 (tmm) REVERT: A 961 MET cc_start: 0.8633 (mmm) cc_final: 0.8336 (mmm) REVERT: A 1017 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7900 (mp0) REVERT: A 1020 ILE cc_start: 0.9001 (mm) cc_final: 0.8676 (tp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2285 time to fit residues: 43.2996 Evaluate side-chains 109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 49 optimal weight: 0.0980 chunk 56 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 782 GLN A 834 HIS ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.084007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.064692 restraints weight = 103058.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.068588 restraints weight = 48466.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.071214 restraints weight = 29566.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.072929 restraints weight = 21028.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.074090 restraints weight = 16510.019| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10580 Z= 0.159 Angle : 0.584 5.866 14465 Z= 0.300 Chirality : 0.037 0.218 1603 Planarity : 0.004 0.048 1808 Dihedral : 6.417 40.436 2021 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.09 (0.25), residues: 1199 helix: 0.97 (0.18), residues: 740 sheet: -0.63 (1.69), residues: 10 loop : 0.58 (0.33), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.013 0.001 TYR A 372 PHE 0.017 0.002 PHE A 892 TRP 0.014 0.001 TRP A 758 HIS 0.004 0.001 HIS A 963 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (10537) covalent geometry : angle 0.56624 / 0.30 (14348) SS BOND : bond 0.00161 / 0.08 ( 6) SS BOND : angle 1.57942 / 0.78 ( 12) hydrogen bonds : bond 0.04761 / 3.21 ( 570) hydrogen bonds : angle 4.96547 / 3.69 ( 1626) metal coordination : bond 0.00274 / 0.13 ( 2) link_ALPHA1-3 : bond 0.00902 / 0.43 ( 2) link_ALPHA1-3 : angle 2.01673 / 0.96 ( 6) link_ALPHA1-6 : bond 0.00603 / 0.30 ( 3) link_ALPHA1-6 : angle 1.71249 / 0.85 ( 9) link_BETA1-4 : bond 0.00317 / 0.18 ( 16) link_BETA1-4 : angle 1.77391 / 1.22 ( 48) link_BETA1-6 : bond 0.00247 / 0.12 ( 1) link_BETA1-6 : angle 1.66305 / 0.72 ( 3) link_NAG-ASN : bond 0.00225 / 0.12 ( 13) link_NAG-ASN : angle 1.54481 / 0.83 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8740 (m-10) cc_final: 0.8335 (m-80) REVERT: A 183 ASN cc_start: 0.8348 (m-40) cc_final: 0.7355 (t0) REVERT: A 428 MET cc_start: 0.7965 (tpp) cc_final: 0.7692 (tpp) REVERT: A 662 MET cc_start: 0.8435 (ttt) cc_final: 0.8053 (tmm) REVERT: A 961 MET cc_start: 0.8601 (mmm) cc_final: 0.8338 (mmm) REVERT: A 1017 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7869 (mp0) REVERT: A 1020 ILE cc_start: 0.8931 (mm) cc_final: 0.8626 (tp) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2207 time to fit residues: 39.2242 Evaluate side-chains 103 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 119 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.082836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.063408 restraints weight = 104219.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.067170 restraints weight = 49580.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.069741 restraints weight = 30543.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.071438 restraints weight = 21876.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072597 restraints weight = 17311.454| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10580 Z= 0.207 Angle : 0.599 5.949 14465 Z= 0.312 Chirality : 0.038 0.208 1603 Planarity : 0.004 0.048 1808 Dihedral : 6.161 39.682 2021 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.03 (0.25), residues: 1199 helix: 0.95 (0.18), residues: 742 sheet: -0.63 (1.63), residues: 10 loop : 0.51 (0.33), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 500 TYR 0.015 0.002 TYR A 372 PHE 0.015 0.001 PHE A 892 TRP 0.013 0.001 TRP A 552 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (10537) covalent geometry : angle 0.58189 / 0.31 (14348) SS BOND : bond 0.00161 / 0.08 ( 6) SS BOND : angle 1.29586 / 0.65 ( 12) hydrogen bonds : bond 0.04678 / 3.15 ( 570) hydrogen bonds : angle 4.95766 / 3.68 ( 1626) metal coordination : bond 0.00397 / 0.19 ( 2) link_ALPHA1-3 : bond 0.00806 / 0.38 ( 2) link_ALPHA1-3 : angle 2.03594 / 0.97 ( 6) link_ALPHA1-6 : bond 0.00677 / 0.34 ( 3) link_ALPHA1-6 : angle 1.74184 / 0.87 ( 9) link_BETA1-4 : bond 0.00366 / 0.20 ( 16) link_BETA1-4 : angle 1.76221 / 1.20 ( 48) link_BETA1-6 : bond 0.00416 / 0.20 ( 1) link_BETA1-6 : angle 1.81669 / 0.77 ( 3) link_NAG-ASN : bond 0.00262 / 0.14 ( 13) link_NAG-ASN : angle 1.58709 / 0.85 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8825 (m-10) cc_final: 0.8395 (m-80) REVERT: A 183 ASN cc_start: 0.8275 (m-40) cc_final: 0.7321 (t0) REVERT: A 256 MET cc_start: 0.8992 (tpp) cc_final: 0.8741 (tpp) REVERT: A 606 ASN cc_start: 0.8687 (m-40) cc_final: 0.8410 (m110) REVERT: A 662 MET cc_start: 0.8550 (ttt) cc_final: 0.8135 (tmm) REVERT: A 961 MET cc_start: 0.8622 (mmm) cc_final: 0.8362 (mmm) REVERT: A 1017 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7880 (mp0) REVERT: A 1020 ILE cc_start: 0.8933 (mm) cc_final: 0.8629 (tp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2082 time to fit residues: 34.5866 Evaluate side-chains 98 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.082828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.064517 restraints weight = 98370.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.068260 restraints weight = 44013.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.070797 restraints weight = 26035.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.072525 restraints weight = 18111.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.073665 restraints weight = 13943.407| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10580 Z= 0.171 Angle : 0.576 5.919 14465 Z= 0.297 Chirality : 0.037 0.203 1603 Planarity : 0.004 0.047 1808 Dihedral : 5.873 38.129 2021 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.10 % Allowed : 0.48 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.24 (0.25), residues: 1199 helix: 1.11 (0.18), residues: 739 sheet: -0.53 (1.66), residues: 10 loop : 0.59 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 231 TYR 0.014 0.001 TYR A 372 PHE 0.013 0.001 PHE A 505 TRP 0.013 0.001 TRP A 552 HIS 0.004 0.001 HIS A 963 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (10537) covalent geometry : angle 0.56072 / 0.29 (14348) SS BOND : bond 0.00151 / 0.07 ( 6) SS BOND : angle 1.11657 / 0.56 ( 12) hydrogen bonds : bond 0.04486 / 3.01 ( 570) hydrogen bonds : angle 4.83646 / 3.59 ( 1626) metal coordination : bond 0.00296 / 0.14 ( 2) link_ALPHA1-3 : bond 0.00852 / 0.41 ( 2) link_ALPHA1-3 : angle 1.98872 / 0.95 ( 6) link_ALPHA1-6 : bond 0.00689 / 0.34 ( 3) link_ALPHA1-6 : angle 1.67883 / 0.86 ( 9) link_BETA1-4 : bond 0.00357 / 0.20 ( 16) link_BETA1-4 : angle 1.64943 / 1.12 ( 48) link_BETA1-6 : bond 0.00358 / 0.17 ( 1) link_BETA1-6 : angle 1.74410 / 0.73 ( 3) link_NAG-ASN : bond 0.00235 / 0.12 ( 13) link_NAG-ASN : angle 1.48940 / 0.79 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8818 (m-10) cc_final: 0.8389 (m-80) REVERT: A 183 ASN cc_start: 0.8235 (m-40) cc_final: 0.7365 (t0) REVERT: A 256 MET cc_start: 0.8963 (tpp) cc_final: 0.8733 (tpp) REVERT: A 320 GLU cc_start: 0.8535 (pm20) cc_final: 0.8186 (pm20) REVERT: A 363 MET cc_start: 0.8683 (ttt) cc_final: 0.8460 (ttt) REVERT: A 606 ASN cc_start: 0.8625 (m-40) cc_final: 0.8348 (m110) REVERT: A 662 MET cc_start: 0.8458 (ttt) cc_final: 0.8075 (tmm) REVERT: A 961 MET cc_start: 0.8613 (mmm) cc_final: 0.8351 (mmm) REVERT: A 1017 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7878 (mp0) REVERT: A 1020 ILE cc_start: 0.8947 (mm) cc_final: 0.8635 (tp) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.2112 time to fit residues: 34.7507 Evaluate side-chains 101 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 782 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.083521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.064083 restraints weight = 103435.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.067918 restraints weight = 48924.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.070485 restraints weight = 29993.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.072218 restraints weight = 21467.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.073402 restraints weight = 16926.436| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10580 Z= 0.128 Angle : 0.546 5.896 14465 Z= 0.278 Chirality : 0.037 0.204 1603 Planarity : 0.004 0.046 1808 Dihedral : 5.538 37.278 2021 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.10 % Allowed : 0.58 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.50 (0.25), residues: 1199 helix: 1.34 (0.19), residues: 741 sheet: -0.08 (1.82), residues: 10 loop : 0.64 (0.34), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 231 TYR 0.030 0.001 TYR A 122 PHE 0.034 0.001 PHE A 967 TRP 0.013 0.001 TRP A1062 HIS 0.004 0.001 HIS A 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (10537) covalent geometry : angle 0.53231 / 0.28 (14348) SS BOND : bond 0.00167 / 0.08 ( 6) SS BOND : angle 0.99537 / 0.49 ( 12) hydrogen bonds : bond 0.04228 / 2.83 ( 570) hydrogen bonds : angle 4.70510 / 3.49 ( 1626) metal coordination : bond 0.00144 / 0.07 ( 2) link_ALPHA1-3 : bond 0.00870 / 0.41 ( 2) link_ALPHA1-3 : angle 1.90842 / 0.91 ( 6) link_ALPHA1-6 : bond 0.00707 / 0.35 ( 3) link_ALPHA1-6 : angle 1.62685 / 0.83 ( 9) link_BETA1-4 : bond 0.00277 / 0.15 ( 16) link_BETA1-4 : angle 1.54996 / 1.05 ( 48) link_BETA1-6 : bond 0.00206 / 0.10 ( 1) link_BETA1-6 : angle 1.58982 / 0.67 ( 3) link_NAG-ASN : bond 0.00210 / 0.11 ( 13) link_NAG-ASN : angle 1.35633 / 0.73 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8822 (m-10) cc_final: 0.8377 (m-80) REVERT: A 183 ASN cc_start: 0.8188 (m-40) cc_final: 0.7311 (t0) REVERT: A 293 MET cc_start: 0.8815 (mtp) cc_final: 0.8598 (mtt) REVERT: A 320 GLU cc_start: 0.8550 (pm20) cc_final: 0.8286 (pm20) REVERT: A 363 MET cc_start: 0.8651 (ttt) cc_final: 0.8412 (ttt) REVERT: A 428 MET cc_start: 0.7932 (tpp) cc_final: 0.7723 (tpp) REVERT: A 606 ASN cc_start: 0.8616 (m-40) cc_final: 0.8346 (m110) REVERT: A 662 MET cc_start: 0.8486 (ttt) cc_final: 0.7984 (tmm) REVERT: A 854 MET cc_start: 0.9096 (tpt) cc_final: 0.8633 (tpp) REVERT: A 858 THR cc_start: 0.9212 (p) cc_final: 0.8891 (t) REVERT: A 961 MET cc_start: 0.8483 (mmm) cc_final: 0.8188 (mmm) REVERT: A 1017 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7804 (mp0) REVERT: A 1020 ILE cc_start: 0.8920 (mm) cc_final: 0.8623 (tp) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.2290 time to fit residues: 37.8632 Evaluate side-chains 101 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 4 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.082573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.063705 restraints weight = 102429.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.067376 restraints weight = 49131.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.069885 restraints weight = 30254.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.071551 restraints weight = 21672.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072700 restraints weight = 17106.270| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10580 Z= 0.192 Angle : 0.579 6.030 14465 Z= 0.300 Chirality : 0.037 0.197 1603 Planarity : 0.004 0.049 1808 Dihedral : 5.489 37.259 2021 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.33 (0.25), residues: 1199 helix: 1.22 (0.18), residues: 741 sheet: -0.34 (1.81), residues: 10 loop : 0.54 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 762 TYR 0.022 0.002 TYR A 776 PHE 0.026 0.001 PHE A 967 TRP 0.014 0.001 TRP A 758 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (10537) covalent geometry : angle 0.56441 / 0.30 (14348) SS BOND : bond 0.00162 / 0.08 ( 6) SS BOND : angle 1.00729 / 0.50 ( 12) hydrogen bonds : bond 0.04326 / 2.91 ( 570) hydrogen bonds : angle 4.78515 / 3.55 ( 1626) metal coordination : bond 0.00350 / 0.17 ( 2) link_ALPHA1-3 : bond 0.00802 / 0.38 ( 2) link_ALPHA1-3 : angle 1.88690 / 0.89 ( 6) link_ALPHA1-6 : bond 0.00680 / 0.34 ( 3) link_ALPHA1-6 : angle 1.58220 / 0.81 ( 9) link_BETA1-4 : bond 0.00346 / 0.19 ( 16) link_BETA1-4 : angle 1.60286 / 1.07 ( 48) link_BETA1-6 : bond 0.00394 / 0.19 ( 1) link_BETA1-6 : angle 1.76301 / 0.74 ( 3) link_NAG-ASN : bond 0.00274 / 0.15 ( 13) link_NAG-ASN : angle 1.45311 / 0.78 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASN cc_start: 0.8213 (m-40) cc_final: 0.7336 (t0) REVERT: A 363 MET cc_start: 0.8679 (ttt) cc_final: 0.8429 (ttt) REVERT: A 606 ASN cc_start: 0.8607 (m-40) cc_final: 0.8330 (m110) REVERT: A 662 MET cc_start: 0.8263 (ttt) cc_final: 0.7918 (tmm) REVERT: A 961 MET cc_start: 0.8513 (mmm) cc_final: 0.8216 (mmm) REVERT: A 1017 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7806 (mp0) REVERT: A 1020 ILE cc_start: 0.8930 (mm) cc_final: 0.8609 (tp) outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.2227 time to fit residues: 35.4698 Evaluate side-chains 96 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.083220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.064165 restraints weight = 102928.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.067863 restraints weight = 49234.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.070388 restraints weight = 30369.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.072068 restraints weight = 21802.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.073074 restraints weight = 17237.499| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10580 Z= 0.135 Angle : 0.561 8.175 14465 Z= 0.284 Chirality : 0.038 0.411 1603 Planarity : 0.004 0.050 1808 Dihedral : 5.365 36.980 2021 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.25 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.51 (0.25), residues: 1199 helix: 1.39 (0.18), residues: 747 sheet: -0.09 (1.91), residues: 10 loop : 0.53 (0.34), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 541 TYR 0.015 0.001 TYR A 122 PHE 0.026 0.001 PHE A 967 TRP 0.013 0.001 TRP A1062 HIS 0.006 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10537) covalent geometry : angle 0.54372 / 0.28 (14348) SS BOND : bond 0.00165 / 0.08 ( 6) SS BOND : angle 0.93318 / 0.46 ( 12) hydrogen bonds : bond 0.04169 / 2.80 ( 570) hydrogen bonds : angle 4.66276 / 3.45 ( 1626) metal coordination : bond 0.00204 / 0.10 ( 2) link_ALPHA1-3 : bond 0.00779 / 0.37 ( 2) link_ALPHA1-3 : angle 1.80402 / 0.84 ( 6) link_ALPHA1-6 : bond 0.00508 / 0.25 ( 3) link_ALPHA1-6 : angle 1.48868 / 0.78 ( 9) link_BETA1-4 : bond 0.00310 / 0.17 ( 16) link_BETA1-4 : angle 1.53138 / 1.04 ( 48) link_BETA1-6 : bond 0.00245 / 0.12 ( 1) link_BETA1-6 : angle 1.66170 / 0.69 ( 3) link_NAG-ASN : bond 0.00479 / 0.24 ( 13) link_NAG-ASN : angle 1.87116 / 1.15 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASN cc_start: 0.8216 (m-40) cc_final: 0.7324 (t0) REVERT: A 363 MET cc_start: 0.8725 (ttt) cc_final: 0.8487 (ttt) REVERT: A 606 ASN cc_start: 0.8652 (m-40) cc_final: 0.8368 (m110) REVERT: A 662 MET cc_start: 0.8232 (ttt) cc_final: 0.7902 (tmm) REVERT: A 854 MET cc_start: 0.9092 (tpt) cc_final: 0.8587 (tpp) REVERT: A 858 THR cc_start: 0.9215 (p) cc_final: 0.8876 (t) REVERT: A 961 MET cc_start: 0.8511 (mmm) cc_final: 0.8194 (mmm) REVERT: A 1017 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7808 (mp0) REVERT: A 1020 ILE cc_start: 0.8942 (mm) cc_final: 0.8613 (tp) outliers start: 1 outliers final: 1 residues processed: 111 average time/residue: 0.2431 time to fit residues: 38.4621 Evaluate side-chains 98 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 57 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.083363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.064183 restraints weight = 103046.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.067937 restraints weight = 49212.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.070499 restraints weight = 30202.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.072196 restraints weight = 21574.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.073362 restraints weight = 17045.294| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10580 Z= 0.141 Angle : 0.565 7.677 14465 Z= 0.287 Chirality : 0.037 0.317 1603 Planarity : 0.004 0.049 1808 Dihedral : 5.255 36.610 2021 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.91 % Rotamer: Outliers : 0.10 % Allowed : 0.00 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.50 (0.25), residues: 1199 helix: 1.42 (0.18), residues: 744 sheet: -0.06 (1.91), residues: 10 loop : 0.46 (0.33), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 380 TYR 0.015 0.001 TYR A 122 PHE 0.025 0.001 PHE A 967 TRP 0.016 0.001 TRP A 163 HIS 0.006 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (10537) covalent geometry : angle 0.54912 / 0.28 (14348) SS BOND : bond 0.00172 / 0.09 ( 6) SS BOND : angle 0.91352 / 0.46 ( 12) hydrogen bonds : bond 0.04119 / 2.76 ( 570) hydrogen bonds : angle 4.63932 / 3.44 ( 1626) metal coordination : bond 0.00198 / 0.09 ( 2) link_ALPHA1-3 : bond 0.00820 / 0.39 ( 2) link_ALPHA1-3 : angle 1.76863 / 0.83 ( 6) link_ALPHA1-6 : bond 0.00685 / 0.34 ( 3) link_ALPHA1-6 : angle 1.51297 / 0.78 ( 9) link_BETA1-4 : bond 0.00316 / 0.18 ( 16) link_BETA1-4 : angle 1.52080 / 1.03 ( 48) link_BETA1-6 : bond 0.00236 / 0.11 ( 1) link_BETA1-6 : angle 1.62728 / 0.68 ( 3) link_NAG-ASN : bond 0.00473 / 0.24 ( 13) link_NAG-ASN : angle 1.78794 / 1.09 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3021.87 seconds wall clock time: 52 minutes 27.82 seconds (3147.82 seconds total)