Starting phenix.real_space_refine on Thu Mar 5 08:00:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q3y_13797/03_2026/7q3y_13797_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q3y_13797/03_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_13797/03_2026/7q3y_13797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q3y_13797/03_2026/7q3y_13797.map" model { file = "/net/cci-nas-00/data/ceres_data/7q3y_13797/03_2026/7q3y_13797_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q3y_13797/03_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-5986/lib/python3.9/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, 61 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.59, per 1000 atoms: 0.18 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: 2.09 Conformation dependent library (CDL) restraints added in 555.0 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: 0.43 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: 4.83 Time building geometry restraints manager: 2.80 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: 1.380 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.570 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 covalent geometry : bond 0.00676 (10537) covalent geometry : angle 0.90445 (14348) SS BOND : bond 0.00254 ( 6) SS BOND : angle 2.19553 ( 12) hydrogen bonds : bond 0.21457 ( 570) hydrogen bonds : angle 8.24563 ( 1626) metal coordination : bond 0.01407 ( 2) link_ALPHA1-3 : bond 0.00387 ( 2) link_ALPHA1-3 : angle 3.30613 ( 6) link_ALPHA1-6 : bond 0.00583 ( 3) link_ALPHA1-6 : angle 1.57515 ( 9) link_BETA1-4 : bond 0.00716 ( 16) link_BETA1-4 : angle 3.20314 ( 48) link_BETA1-6 : bond 0.00738 ( 1) link_BETA1-6 : angle 2.64788 ( 3) link_NAG-ASN : bond 0.00578 ( 13) link_NAG-ASN : angle 4.70395 ( 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 : 0.537 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: 0.2635 time to fit residues: 68.9741 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 : 0.504 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3589 r_free = 0.3589 target = 0.084551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.067005 restraints weight = 98678.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.070862 restraints weight = 45108.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073408 restraints weight = 26511.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.075065 restraints weight = 18233.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.076190 restraints weight = 13950.138| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2408 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= 0.178 Angle : 0.722 6.171 14465 Z= 0.373 Chirality : 0.042 0.260 1603 Planarity : 0.005 0.062 1808 Dihedral : 12.106 72.800 2021 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.24 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: 0.15 (0.23), residues: 1199 helix: 0.32 (0.17), residues: 740 sheet: 0.05 (1.73), residues: 10 loop : -0.05 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 350 TYR 0.024 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 covalent geometry : bond 0.00368 (10537) covalent geometry : angle 0.69651 (14348) SS BOND : bond 0.00175 ( 6) SS BOND : angle 1.38397 ( 12) hydrogen bonds : bond 0.06720 ( 570) hydrogen bonds : angle 5.79587 ( 1626) metal coordination : bond 0.00325 ( 2) link_ALPHA1-3 : bond 0.00418 ( 2) link_ALPHA1-3 : angle 2.32173 ( 6) link_ALPHA1-6 : bond 0.00594 ( 3) link_ALPHA1-6 : angle 1.80246 ( 9) link_BETA1-4 : bond 0.00462 ( 16) link_BETA1-4 : angle 2.44126 ( 48) link_BETA1-6 : bond 0.00338 ( 1) link_BETA1-6 : angle 1.90468 ( 3) link_NAG-ASN : bond 0.00281 ( 13) link_NAG-ASN : angle 2.26940 ( 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 144 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.510 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: A 182 SER cc_start: 0.9050 (t) cc_final: 0.8823 (m) REVERT: A 183 ASN cc_start: 0.8469 (m-40) cc_final: 0.7338 (t0) REVERT: A 293 MET cc_start: 0.8903 (mtp) cc_final: 0.8461 (mmm) REVERT: A 428 MET cc_start: 0.7990 (tpp) cc_final: 0.7769 (tpp) REVERT: A 489 LYS cc_start: 0.8077 (tptt) cc_final: 0.7871 (tptp) REVERT: A 826 TYR cc_start: 0.8848 (t80) cc_final: 0.8415 (t80) REVERT: A 916 MET cc_start: 0.9021 (ttp) cc_final: 0.8588 (tmm) REVERT: A 1017 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7864 (mp0) REVERT: A 1020 ILE cc_start: 0.8933 (mm) cc_final: 0.8610 (tp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2742 time to fit residues: 53.8630 Evaluate side-chains 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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: 0.8980 chunk 86 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3590 r_free = 0.3590 target = 0.085215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.067506 restraints weight = 96723.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.071499 restraints weight = 42538.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.074116 restraints weight = 24453.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.075840 restraints weight = 16540.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.076991 restraints weight = 12451.949| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10580 Z= 0.143 Angle : 0.642 5.563 14465 Z= 0.323 Chirality : 0.040 0.241 1603 Planarity : 0.004 0.054 1808 Dihedral : 9.380 60.201 2021 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 0.72 (0.24), residues: 1199 helix: 0.68 (0.18), residues: 736 sheet: 0.19 (1.82), residues: 10 loop : 0.39 (0.32), residues: 453 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 0.020 0.002 PHE A 505 TRP 0.018 0.001 TRP A 40 HIS 0.004 0.001 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00297 (10537) covalent geometry : angle 0.61962 (14348) SS BOND : bond 0.00127 ( 6) SS BOND : angle 1.13631 ( 12) hydrogen bonds : bond 0.05703 ( 570) hydrogen bonds : angle 5.30998 ( 1626) metal coordination : bond 0.00082 ( 2) link_ALPHA1-3 : bond 0.00860 ( 2) link_ALPHA1-3 : angle 1.80345 ( 6) link_ALPHA1-6 : bond 0.00597 ( 3) link_ALPHA1-6 : angle 1.65063 ( 9) link_BETA1-4 : bond 0.00373 ( 16) link_BETA1-4 : angle 2.22410 ( 48) link_BETA1-6 : bond 0.00019 ( 1) link_BETA1-6 : angle 1.47399 ( 3) link_NAG-ASN : bond 0.00434 ( 13) link_NAG-ASN : angle 1.90777 ( 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 139 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.583 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 183 ASN cc_start: 0.8377 (m-40) cc_final: 0.7314 (t0) REVERT: A 293 MET cc_start: 0.8910 (mtp) cc_final: 0.8670 (mtp) REVERT: A 309 MET cc_start: 0.8176 (mmt) cc_final: 0.7790 (mmt) REVERT: A 428 MET cc_start: 0.8014 (tpp) cc_final: 0.7771 (tpp) REVERT: A 443 ASP cc_start: 0.7790 (m-30) cc_final: 0.7301 (t0) REVERT: A 826 TYR cc_start: 0.8817 (t80) cc_final: 0.8413 (t80) REVERT: A 916 MET cc_start: 0.8929 (ttp) cc_final: 0.8520 (tmm) REVERT: A 1020 ILE cc_start: 0.8888 (mm) cc_final: 0.8562 (tp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2353 time to fit residues: 46.1723 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 : 0.507 ------------------------------------------------------------------------------- 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: 4.9990 chunk 28 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.084531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.065897 restraints weight = 96914.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.069810 restraints weight = 43319.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.072437 restraints weight = 25404.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.074136 restraints weight = 17509.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.075315 restraints weight = 13484.760| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10580 Z= 0.159 Angle : 0.604 5.690 14465 Z= 0.307 Chirality : 0.038 0.226 1603 Planarity : 0.004 0.051 1808 Dihedral : 7.500 52.278 2021 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 0.95 (0.24), residues: 1199 helix: 0.85 (0.18), residues: 739 sheet: -0.12 (1.65), residues: 10 loop : 0.51 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.014 0.001 TYR A 498 PHE 0.015 0.001 PHE A 505 TRP 0.014 0.001 TRP A 758 HIS 0.004 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00333 (10537) covalent geometry : angle 0.58310 (14348) SS BOND : bond 0.00150 ( 6) SS BOND : angle 1.04565 ( 12) hydrogen bonds : bond 0.05132 ( 570) hydrogen bonds : angle 5.14379 ( 1626) metal coordination : bond 0.00284 ( 2) link_ALPHA1-3 : bond 0.00846 ( 2) link_ALPHA1-3 : angle 2.05282 ( 6) link_ALPHA1-6 : bond 0.00594 ( 3) link_ALPHA1-6 : angle 1.83736 ( 9) link_BETA1-4 : bond 0.00367 ( 16) link_BETA1-4 : angle 2.11765 ( 48) link_BETA1-6 : bond 0.00131 ( 1) link_BETA1-6 : angle 1.60755 ( 3) link_NAG-ASN : bond 0.00260 ( 13) link_NAG-ASN : angle 1.71393 ( 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 : 0.360 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: A 183 ASN cc_start: 0.8363 (m-40) cc_final: 0.7392 (t0) REVERT: A 428 MET cc_start: 0.8045 (tpp) cc_final: 0.7831 (tpp) REVERT: A 662 MET cc_start: 0.8495 (ttt) cc_final: 0.8119 (tmm) REVERT: A 961 MET cc_start: 0.8565 (mmm) cc_final: 0.8219 (mmm) REVERT: A 1017 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7903 (mp0) REVERT: A 1020 ILE cc_start: 0.8985 (mm) cc_final: 0.8658 (tp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2334 time to fit residues: 42.8429 Evaluate side-chains 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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: 0.0770 chunk 41 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.084418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.066466 restraints weight = 98415.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.070354 restraints weight = 44511.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.072907 restraints weight = 26226.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.074586 restraints weight = 18160.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.075712 restraints weight = 13956.647| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10580 Z= 0.138 Angle : 0.580 5.764 14465 Z= 0.295 Chirality : 0.037 0.218 1603 Planarity : 0.004 0.049 1808 Dihedral : 6.593 44.485 2021 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: 1.22 (0.24), residues: 1199 helix: 1.06 (0.18), residues: 741 sheet: -0.30 (1.55), residues: 10 loop : 0.64 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.013 0.001 TYR A 372 PHE 0.016 0.001 PHE A 892 TRP 0.013 0.001 TRP A 758 HIS 0.004 0.001 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00287 (10537) covalent geometry : angle 0.56189 (14348) SS BOND : bond 0.00744 ( 6) SS BOND : angle 1.22850 ( 12) hydrogen bonds : bond 0.04802 ( 570) hydrogen bonds : angle 4.96676 ( 1626) metal coordination : bond 0.00180 ( 2) link_ALPHA1-3 : bond 0.00941 ( 2) link_ALPHA1-3 : angle 2.04128 ( 6) link_ALPHA1-6 : bond 0.00539 ( 3) link_ALPHA1-6 : angle 1.71673 ( 9) link_BETA1-4 : bond 0.00333 ( 16) link_BETA1-4 : angle 1.88073 ( 48) link_BETA1-6 : bond 0.00085 ( 1) link_BETA1-6 : angle 1.52173 ( 3) link_NAG-ASN : bond 0.00226 ( 13) link_NAG-ASN : angle 1.48906 ( 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 124 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.500 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: 0.8620 (m-10) cc_final: 0.8209 (m-80) REVERT: A 183 ASN cc_start: 0.8349 (m-40) cc_final: 0.7328 (t0) REVERT: A 256 MET cc_start: 0.9128 (tpp) cc_final: 0.8746 (tpp) REVERT: A 662 MET cc_start: 0.8408 (ttt) cc_final: 0.8036 (tmm) REVERT: A 961 MET cc_start: 0.8547 (mmm) cc_final: 0.8231 (mmm) REVERT: A 1017 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7856 (mp0) REVERT: A 1020 ILE cc_start: 0.8934 (mm) cc_final: 0.8621 (tp) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2424 time to fit residues: 41.7558 Evaluate side-chains 102 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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: 0.9980 chunk 52 optimal weight: 6.9990 chunk 101 optimal weight: 0.0970 chunk 59 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3575 r_free = 0.3575 target = 0.084175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.064919 restraints weight = 104716.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.068846 restraints weight = 49566.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071440 restraints weight = 30265.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073132 restraints weight = 21594.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.074147 restraints weight = 17017.632| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10580 Z= 0.165 Angle : 0.578 8.035 14465 Z= 0.296 Chirality : 0.037 0.207 1603 Planarity : 0.004 0.048 1808 Dihedral : 5.985 39.374 2021 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: 1.38 (0.25), residues: 1199 helix: 1.19 (0.18), residues: 740 sheet: 0.05 (1.67), residues: 10 loop : 0.69 (0.33), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 890 TYR 0.014 0.001 TYR A 372 PHE 0.018 0.001 PHE A 301 TRP 0.014 0.001 TRP A 758 HIS 0.004 0.001 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00346 (10537) covalent geometry : angle 0.56211 (14348) SS BOND : bond 0.00318 ( 6) SS BOND : angle 1.33594 ( 12) hydrogen bonds : bond 0.04540 ( 570) hydrogen bonds : angle 4.84055 ( 1626) metal coordination : bond 0.00271 ( 2) link_ALPHA1-3 : bond 0.00870 ( 2) link_ALPHA1-3 : angle 1.99343 ( 6) link_ALPHA1-6 : bond 0.00577 ( 3) link_ALPHA1-6 : angle 1.65776 ( 9) link_BETA1-4 : bond 0.00343 ( 16) link_BETA1-4 : angle 1.71401 ( 48) link_BETA1-6 : bond 0.00207 ( 1) link_BETA1-6 : angle 1.64623 ( 3) link_NAG-ASN : bond 0.00233 ( 13) link_NAG-ASN : angle 1.46276 ( 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 120 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.536 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: A 83 PHE cc_start: 0.8764 (m-10) cc_final: 0.8324 (m-80) REVERT: A 183 ASN cc_start: 0.8245 (m-40) cc_final: 0.7307 (t0) REVERT: A 256 MET cc_start: 0.9106 (tpp) cc_final: 0.8702 (tpp) REVERT: A 320 GLU cc_start: 0.8452 (pm20) cc_final: 0.8091 (pm20) REVERT: A 662 MET cc_start: 0.8442 (ttt) cc_final: 0.8047 (tmm) REVERT: A 961 MET cc_start: 0.8571 (mmm) cc_final: 0.8265 (mmm) REVERT: A 1017 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7891 (mp0) REVERT: A 1020 ILE cc_start: 0.8949 (mm) cc_final: 0.8632 (tp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2368 time to fit residues: 39.7308 Evaluate side-chains 102 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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: 6.9990 chunk 103 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.082010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.063837 restraints weight = 98982.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.067533 restraints weight = 45534.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.070047 restraints weight = 27274.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.071726 restraints weight = 19110.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.072874 restraints weight = 14835.753| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10580 Z= 0.202 Angle : 0.596 5.980 14465 Z= 0.311 Chirality : 0.037 0.199 1603 Planarity : 0.004 0.049 1808 Dihedral : 5.756 37.782 2021 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: 1.30 (0.25), residues: 1199 helix: 1.17 (0.18), residues: 747 sheet: 0.30 (1.83), residues: 10 loop : 0.57 (0.34), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 500 TYR 0.015 0.002 TYR A 372 PHE 0.017 0.002 PHE A 387 TRP 0.015 0.001 TRP A 758 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00425 (10537) covalent geometry : angle 0.58087 (14348) SS BOND : bond 0.00159 ( 6) SS BOND : angle 1.16300 ( 12) hydrogen bonds : bond 0.04513 ( 570) hydrogen bonds : angle 4.85589 ( 1626) metal coordination : bond 0.00353 ( 2) link_ALPHA1-3 : bond 0.00847 ( 2) link_ALPHA1-3 : angle 1.99659 ( 6) link_ALPHA1-6 : bond 0.00649 ( 3) link_ALPHA1-6 : angle 1.63835 ( 9) link_BETA1-4 : bond 0.00347 ( 16) link_BETA1-4 : angle 1.65512 ( 48) link_BETA1-6 : bond 0.00371 ( 1) link_BETA1-6 : angle 1.78377 ( 3) link_NAG-ASN : bond 0.00239 ( 13) link_NAG-ASN : angle 1.50689 ( 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 116 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.496 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: A 83 PHE cc_start: 0.8780 (m-10) cc_final: 0.8346 (m-80) REVERT: A 183 ASN cc_start: 0.8265 (m-40) cc_final: 0.7342 (t0) REVERT: A 256 MET cc_start: 0.9084 (tpp) cc_final: 0.8708 (tpp) REVERT: A 320 GLU cc_start: 0.8538 (pm20) cc_final: 0.8228 (pm20) REVERT: A 606 ASN cc_start: 0.8642 (m-40) cc_final: 0.8360 (m110) REVERT: A 662 MET cc_start: 0.8397 (ttt) cc_final: 0.8006 (tmm) REVERT: A 961 MET cc_start: 0.8605 (mmm) cc_final: 0.8335 (mmm) REVERT: A 1017 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7852 (mp0) REVERT: A 1020 ILE cc_start: 0.8917 (mm) cc_final: 0.8614 (tp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2354 time to fit residues: 38.2247 Evaluate side-chains 97 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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: 4.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3556 r_free = 0.3556 target = 0.083005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063563 restraints weight = 104399.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.067353 restraints weight = 49313.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069959 restraints weight = 30365.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.071665 restraints weight = 21777.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.072839 restraints weight = 17231.662| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4326 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= 0.168 Angle : 0.571 5.891 14465 Z= 0.294 Chirality : 0.037 0.198 1603 Planarity : 0.004 0.049 1808 Dihedral : 5.586 36.871 2021 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.10 % Allowed : 0.38 % 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: 1.31 (0.25), residues: 1199 helix: 1.19 (0.18), residues: 745 sheet: 0.27 (1.91), residues: 10 loop : 0.53 (0.34), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.016 0.002 TYR A 607 PHE 0.018 0.002 PHE A 772 TRP 0.014 0.001 TRP A 758 HIS 0.004 0.001 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00353 (10537) covalent geometry : angle 0.55667 (14348) SS BOND : bond 0.00189 ( 6) SS BOND : angle 1.10032 ( 12) hydrogen bonds : bond 0.04374 ( 570) hydrogen bonds : angle 4.75412 ( 1626) metal coordination : bond 0.00313 ( 2) link_ALPHA1-3 : bond 0.00833 ( 2) link_ALPHA1-3 : angle 1.93484 ( 6) link_ALPHA1-6 : bond 0.00626 ( 3) link_ALPHA1-6 : angle 1.60040 ( 9) link_BETA1-4 : bond 0.00329 ( 16) link_BETA1-4 : angle 1.59812 ( 48) link_BETA1-6 : bond 0.00337 ( 1) link_BETA1-6 : angle 1.71955 ( 3) link_NAG-ASN : bond 0.00229 ( 13) link_NAG-ASN : angle 1.43060 ( 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 114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.517 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 183 ASN cc_start: 0.8212 (m-40) cc_final: 0.7332 (t0) REVERT: A 320 GLU cc_start: 0.8538 (pm20) cc_final: 0.8302 (pm20) REVERT: A 606 ASN cc_start: 0.8677 (m-40) cc_final: 0.8398 (m110) REVERT: A 662 MET cc_start: 0.8513 (ttt) cc_final: 0.8011 (tmm) REVERT: A 961 MET cc_start: 0.8585 (mmm) cc_final: 0.8299 (mmm) REVERT: A 1017 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7824 (mp0) REVERT: A 1020 ILE cc_start: 0.8918 (mm) cc_final: 0.8621 (tp) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.2539 time to fit residues: 39.4341 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 : 0.639 ------------------------------------------------------------------------------- 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: 7.9990 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.082279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.063788 restraints weight = 97638.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.067541 restraints weight = 44176.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070039 restraints weight = 26271.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071709 restraints weight = 18418.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072888 restraints weight = 14360.914| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4466 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= 0.191 Angle : 0.585 5.950 14465 Z= 0.305 Chirality : 0.037 0.194 1603 Planarity : 0.004 0.051 1808 Dihedral : 5.480 37.031 2021 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 0.10 % Allowed : 0.38 % 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: 1.25 (0.25), residues: 1199 helix: 1.18 (0.18), residues: 749 sheet: -0.01 (1.89), residues: 10 loop : 0.43 (0.34), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 500 TYR 0.016 0.002 TYR A 372 PHE 0.034 0.002 PHE A 967 TRP 0.014 0.001 TRP A 758 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00401 (10537) covalent geometry : angle 0.57123 (14348) SS BOND : bond 0.00169 ( 6) SS BOND : angle 1.02596 ( 12) hydrogen bonds : bond 0.04376 ( 570) hydrogen bonds : angle 4.77512 ( 1626) metal coordination : bond 0.00355 ( 2) link_ALPHA1-3 : bond 0.00789 ( 2) link_ALPHA1-3 : angle 1.88104 ( 6) link_ALPHA1-6 : bond 0.00696 ( 3) link_ALPHA1-6 : angle 1.59801 ( 9) link_BETA1-4 : bond 0.00339 ( 16) link_BETA1-4 : angle 1.59457 ( 48) link_BETA1-6 : bond 0.00430 ( 1) link_BETA1-6 : angle 1.77747 ( 3) link_NAG-ASN : bond 0.00260 ( 13) link_NAG-ASN : angle 1.44807 ( 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 109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.501 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: A 183 ASN cc_start: 0.8256 (m-40) cc_final: 0.7398 (t0) REVERT: A 259 GLN cc_start: 0.8990 (pt0) cc_final: 0.8754 (pt0) REVERT: A 606 ASN cc_start: 0.8658 (m-40) cc_final: 0.8367 (m110) REVERT: A 662 MET cc_start: 0.8285 (ttt) cc_final: 0.7932 (tmm) REVERT: A 961 MET cc_start: 0.8539 (mmm) cc_final: 0.8231 (mmm) REVERT: A 1017 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7806 (mp0) REVERT: A 1020 ILE cc_start: 0.8961 (mm) cc_final: 0.8651 (tp) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.2403 time to fit residues: 36.6462 Evaluate side-chains 94 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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: 6.9990 chunk 48 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.0570 chunk 76 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3550 r_free = 0.3550 target = 0.082819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063509 restraints weight = 103750.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.067271 restraints weight = 49210.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.069790 restraints weight = 30391.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.071502 restraints weight = 21907.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.072677 restraints weight = 17358.482| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10580 Z= 0.168 Angle : 0.572 6.019 14465 Z= 0.296 Chirality : 0.037 0.193 1603 Planarity : 0.004 0.052 1808 Dihedral : 5.369 37.086 2021 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.84 % Favored : 97.08 % 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: 1.30 (0.25), residues: 1199 helix: 1.25 (0.18), residues: 745 sheet: -0.24 (1.88), residues: 10 loop : 0.40 (0.34), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.029 0.002 TYR A 776 PHE 0.027 0.002 PHE A 967 TRP 0.013 0.001 TRP A 758 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00354 (10537) covalent geometry : angle 0.55844 (14348) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.95931 ( 12) hydrogen bonds : bond 0.04244 ( 570) hydrogen bonds : angle 4.73145 ( 1626) metal coordination : bond 0.00297 ( 2) link_ALPHA1-3 : bond 0.00818 ( 2) link_ALPHA1-3 : angle 1.86167 ( 6) link_ALPHA1-6 : bond 0.00661 ( 3) link_ALPHA1-6 : angle 1.53918 ( 9) link_BETA1-4 : bond 0.00323 ( 16) link_BETA1-4 : angle 1.55606 ( 48) link_BETA1-6 : bond 0.00290 ( 1) link_BETA1-6 : angle 1.80296 ( 3) link_NAG-ASN : bond 0.00240 ( 13) link_NAG-ASN : angle 1.38455 ( 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 : 0.515 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 29 GLU cc_start: 0.8913 (pt0) cc_final: 0.8248 (pt0) REVERT: A 183 ASN cc_start: 0.8226 (m-40) cc_final: 0.7361 (t0) REVERT: A 606 ASN cc_start: 0.8701 (m-40) cc_final: 0.8420 (m110) REVERT: A 662 MET cc_start: 0.8257 (ttt) cc_final: 0.7910 (tmm) REVERT: A 961 MET cc_start: 0.8545 (mmm) cc_final: 0.8233 (mmm) REVERT: A 1017 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7781 (mp0) REVERT: A 1020 ILE cc_start: 0.8942 (mm) cc_final: 0.8612 (tp) outliers start: 1 outliers final: 1 residues processed: 111 average time/residue: 0.2408 time to fit residues: 37.3253 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 : 0.459 ------------------------------------------------------------------------------- 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: 3.9990 chunk 82 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 782 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.083005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.064105 restraints weight = 96169.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.067983 restraints weight = 43409.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.070601 restraints weight = 25786.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.072327 restraints weight = 18001.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.073476 restraints weight = 13945.198| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10580 Z= 0.126 Angle : 0.541 6.285 14465 Z= 0.276 Chirality : 0.036 0.195 1603 Planarity : 0.004 0.048 1808 Dihedral : 5.109 36.455 2021 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.16 % 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: 1.56 (0.25), residues: 1199 helix: 1.47 (0.19), residues: 748 sheet: -0.02 (1.90), residues: 10 loop : 0.46 (0.34), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 380 TYR 0.014 0.001 TYR A 372 PHE 0.026 0.001 PHE A 967 TRP 0.015 0.001 TRP A1062 HIS 0.004 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00272 (10537) covalent geometry : angle 0.52854 (14348) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.87085 ( 12) hydrogen bonds : bond 0.04075 ( 570) hydrogen bonds : angle 4.58564 ( 1626) metal coordination : bond 0.00167 ( 2) link_ALPHA1-3 : bond 0.00820 ( 2) link_ALPHA1-3 : angle 1.74594 ( 6) link_ALPHA1-6 : bond 0.00635 ( 3) link_ALPHA1-6 : angle 1.50484 ( 9) link_BETA1-4 : bond 0.00309 ( 16) link_BETA1-4 : angle 1.50223 ( 48) link_BETA1-6 : bond 0.00258 ( 1) link_BETA1-6 : angle 1.62848 ( 3) link_NAG-ASN : bond 0.00216 ( 13) link_NAG-ASN : angle 1.26243 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3095.71 seconds wall clock time: 53 minutes 35.08 seconds (3215.08 seconds total)