Starting phenix.real_space_refine on Fri Sep 11 22:55:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lcr_0873/09_2026/6lcr_0873.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lcr_0873/09_2026/6lcr_0873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lcr_0873/09_2026/6lcr_0873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lcr_0873/09_2026/6lcr_0873.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6lcr_0873/09_2026/6lcr_0873.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lcr_0873/09_2026/6lcr_0873.cif" model { file = "/net/cci-nas-00/data/ceres_data/6lcr_0873/09_2026/6lcr_0873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lcr_0873/09_2026/6lcr_0873.cif" } resolution = 3.4 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 7395 2.51 5 N 1931 2.21 5 O 2168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11561 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8280 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 35, 'TRANS': 1008} Chain breaks: 4 Chain: "B" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3061 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 26, 'TRANS': 349} 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 chiralities: 2 Chain: "D" 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 chiralities: 3 Chain: "E" 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 chiralities: 2 Chain: "F" 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 chiralities: 3 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.23, per 1000 atoms: 0.19 Number of scatterers: 11561 At special positions: 0 Unit cell: (143.48, 118.16, 128.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 4 15.00 Mg 1 11.99 O 2168 8.00 N 1931 7.00 C 7395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG B 508 " - " ASN B 241 " " NAG E 1 " - " ASN B 189 " " NAG F 1 " - " ASN B 314 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 530.9 milliseconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 46.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 162 through 184 removed outlier: 4.365A pdb=" N ILE A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 488 through 514 removed outlier: 3.873A pdb=" N ILE A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 removed outlier: 4.168A pdb=" N TRP A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 548 removed outlier: 3.935A pdb=" N PHE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 553 through 573 removed outlier: 3.582A pdb=" N TYR A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 562 " --> pdb=" O ILE A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.771A pdb=" N ILE A 593 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 594 " --> pdb=" O TRP A 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 590 through 594' Processing helix chain 'A' and resid 595 through 600 removed outlier: 4.081A pdb=" N ILE A 600 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 642 Processing helix chain 'A' and resid 648 through 671 removed outlier: 4.319A pdb=" N ARG A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.911A pdb=" N GLY A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 713 removed outlier: 3.785A pdb=" N GLN A 704 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 748 removed outlier: 4.189A pdb=" N LEU A 743 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 751 No H-bonds generated for 'chain 'A' and resid 749 through 751' Processing helix chain 'A' and resid 806 through 811 removed outlier: 3.703A pdb=" N ILE A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 837 removed outlier: 4.179A pdb=" N GLU A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 865 removed outlier: 4.276A pdb=" N GLU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 878 removed outlier: 4.123A pdb=" N GLU A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU A 876 " --> pdb=" O GLU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 883 removed outlier: 3.835A pdb=" N GLU A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 883 " --> pdb=" O ASP A 879 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 878 through 883' Processing helix chain 'A' and resid 900 through 911 removed outlier: 3.978A pdb=" N ALA A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 933 removed outlier: 3.516A pdb=" N ALA A 926 " --> pdb=" O LYS A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 972 removed outlier: 3.625A pdb=" N TYR A 958 " --> pdb=" O THR A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 986 Processing helix chain 'A' and resid 1003 through 1009 removed outlier: 3.618A pdb=" N TRP A1007 " --> pdb=" O PHE A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1024 removed outlier: 3.601A pdb=" N CYS A1024 " --> pdb=" O LEU A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1047 removed outlier: 4.152A pdb=" N ALA A1038 " --> pdb=" O PRO A1034 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A1041 " --> pdb=" O LYS A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1060 No H-bonds generated for 'chain 'A' and resid 1058 through 1060' Processing helix chain 'A' and resid 1061 through 1067 Processing helix chain 'A' and resid 1092 through 1094 No H-bonds generated for 'chain 'A' and resid 1092 through 1094' Processing helix chain 'A' and resid 1095 through 1100 Processing helix chain 'A' and resid 1102 through 1134 removed outlier: 3.600A pdb=" N LEU A1111 " --> pdb=" O SER A1107 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A1122 " --> pdb=" O PHE A1118 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A1128 " --> pdb=" O ILE A1124 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A1132 " --> pdb=" O SER A1128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS A1134 " --> pdb=" O PHE A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1152 Processing helix chain 'A' and resid 1158 through 1167 Processing helix chain 'A' and resid 1174 through 1179 Processing helix chain 'A' and resid 1180 through 1182 No H-bonds generated for 'chain 'A' and resid 1180 through 1182' Processing helix chain 'A' and resid 1183 through 1188 Processing helix chain 'A' and resid 1193 through 1220 removed outlier: 3.877A pdb=" N PHE A1197 " --> pdb=" O THR A1193 " (cutoff:3.500A) Proline residue: A1215 - end of helix removed outlier: 4.051A pdb=" N VAL A1219 " --> pdb=" O PRO A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1257 Proline residue: A1245 - end of helix removed outlier: 3.745A pdb=" N ASN A1251 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A1257 " --> pdb=" O TYR A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1285 removed outlier: 3.851A pdb=" N ILE A1276 " --> pdb=" O SER A1272 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A1285 " --> pdb=" O GLY A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1301 removed outlier: 3.685A pdb=" N GLN A1301 " --> pdb=" O PRO A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1331 Proline residue: A1313 - end of helix Proline residue: A1319 - end of helix removed outlier: 3.924A pdb=" N VAL A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1345 removed outlier: 3.918A pdb=" N ILE A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A1344 " --> pdb=" O GLU A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1356 Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 56 through 75 removed outlier: 3.616A pdb=" N VAL B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 removed outlier: 3.612A pdb=" N ALA B 89 " --> pdb=" O CYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 4.263A pdb=" N ASN B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 334 through 338 removed outlier: 3.599A pdb=" N LYS B 338 " --> pdb=" O THR B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 327 through 330 removed outlier: 3.738A pdb=" N PHE A 339 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 356 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL A 460 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 354 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.549A pdb=" N ASP A 346 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 943 through 945 removed outlier: 3.910A pdb=" N ASP A1001 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE A 603 " --> pdb=" O TRP A 916 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR A1052 " --> pdb=" O VAL A1070 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL A1072 " --> pdb=" O THR A1052 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER A1054 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE A1074 " --> pdb=" O SER A1054 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY A1056 " --> pdb=" O ILE A1074 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A1088 " --> pdb=" O GLY A1071 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628 removed outlier: 3.657A pdb=" N ALA A 621 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N MET A 616 " --> pdb=" O ARG A 896 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ARG A 896 " --> pdb=" O MET A 616 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N PHE A 618 " --> pdb=" O GLU A 894 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU A 894 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 843 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG A 793 " --> pdb=" O VAL A 775 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL A 775 " --> pdb=" O ARG A 793 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 720 through 723 Processing sheet with id=AA6, first strand: chain 'A' and resid 763 through 766 Processing sheet with id=AA7, first strand: chain 'A' and resid 1260 through 1262 Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.733A pdb=" N ARG B 340 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 153 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS B 313 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE B 155 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.518A pdb=" N THR B 221 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 95 through 96 502 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1898 1.31 - 1.44: 3230 1.44 - 1.56: 6586 1.56 - 1.69: 9 1.69 - 1.81: 100 Bond restraints: 11823 Sorted by residual: bond pdb=" C17 P5S A2003 " pdb=" O19 P5S A2003 " ideal model delta sigma weight residual 1.328 1.449 -0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C38 P5S A2003 " pdb=" O37 P5S A2003 " ideal model delta sigma weight residual 1.331 1.451 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" O2B ACP A2002 " pdb=" PB ACP A2002 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O15 P5S A2003 " pdb=" P12 P5S A2003 " ideal model delta sigma weight residual 1.502 1.600 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" O3A ACP A2002 " pdb=" PB ACP A2002 " ideal model delta sigma weight residual 1.698 1.610 0.088 2.00e-02 2.50e+03 1.96e+01 ... (remaining 11818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 15781 3.11 - 6.22: 230 6.22 - 9.34: 27 9.34 - 12.45: 9 12.45 - 15.56: 5 Bond angle restraints: 16052 Sorted by residual: angle pdb=" C GLN A 408 " pdb=" N PRO A 409 " pdb=" CA PRO A 409 " ideal model delta sigma weight residual 119.84 127.83 -7.99 1.25e+00 6.40e-01 4.09e+01 angle pdb=" C4 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sigma weight residual 112.02 96.46 15.56 3.00e+00 1.11e-01 2.69e+01 angle pdb=" C4 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" C6 NAG F 1 " ideal model delta sigma weight residual 113.89 99.50 14.39 3.00e+00 1.11e-01 2.30e+01 angle pdb=" C ALA A 952 " pdb=" CA ALA A 952 " pdb=" CB ALA A 952 " ideal model delta sigma weight residual 116.54 111.05 5.49 1.15e+00 7.56e-01 2.28e+01 angle pdb=" N PHE A 548 " pdb=" CA PHE A 548 " pdb=" C PHE A 548 " ideal model delta sigma weight residual 112.97 108.13 4.84 1.06e+00 8.90e-01 2.08e+01 ... (remaining 16047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.08: 6636 29.08 - 58.16: 276 58.16 - 87.24: 22 87.24 - 116.32: 2 116.32 - 145.39: 2 Dihedral angle restraints: 6938 sinusoidal: 2790 harmonic: 4148 Sorted by residual: dihedral pdb=" CA SER A1233 " pdb=" C SER A1233 " pdb=" N GLU A1234 " pdb=" CA GLU A1234 " ideal model delta harmonic sigma weight residual 180.00 152.35 27.65 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA ASP A1231 " pdb=" C ASP A1231 " pdb=" N VAL A1232 " pdb=" CA VAL A1232 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ASN A 990 " pdb=" C ASN A 990 " pdb=" N ALA A 991 " pdb=" CA ALA A 991 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 6935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 1800 0.223 - 0.446: 4 0.446 - 0.670: 3 0.670 - 0.893: 1 0.893 - 1.116: 2 Chirality restraints: 1810 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.31 -1.09 2.00e-02 2.50e+03 2.98e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.87 0.47 2.00e-02 2.50e+03 5.60e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-02 2.50e+03 3.72e+02 ... (remaining 1807 not shown) Planarity restraints: 2039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.255 2.00e-02 2.50e+03 2.14e-01 5.70e+02 pdb=" C7 NAG E 2 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.359 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.230 2.00e-02 2.50e+03 1.85e-01 4.29e+02 pdb=" C7 NAG E 1 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.289 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.181 2.00e-02 2.50e+03 1.52e-01 2.87e+02 pdb=" C7 NAG D 1 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.131 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.250 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.014 2.00e-02 2.50e+03 ... (remaining 2036 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 116 2.51 - 3.11: 9169 3.11 - 3.71: 17852 3.71 - 4.30: 26005 4.30 - 4.90: 43443 Nonbonded interactions: 96585 Sorted by model distance: nonbonded pdb=" OD2 ASP A 606 " pdb="MG MG A2001 " model vdw 1.914 2.170 nonbonded pdb=" O3 NAG E 1 " pdb=" O7 NAG E 1 " model vdw 2.035 3.040 nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.044 3.040 nonbonded pdb=" O3 NAG F 1 " pdb=" O7 NAG F 1 " model vdw 2.103 3.040 nonbonded pdb=" OE1 GLU A1234 " pdb=" OG1 THR A1236 " model vdw 2.105 3.040 ... (remaining 96580 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 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.580 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.009 0.194 11832 Z= 0.395 Angle : 1.069 24.958 16079 Z= 0.515 Chirality : 0.070 1.116 1810 Planarity : 0.009 0.214 2036 Dihedral : 15.548 145.395 4262 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.58 % Favored : 88.21 % Rotamer: Outliers : 0.49 % Allowed : 10.33 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.30 (0.19), residues: 1408 helix: -2.74 (0.17), residues: 578 sheet: -1.82 (0.37), residues: 174 loop : -3.22 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1260 TYR 0.025 0.002 TYR B 132 PHE 0.023 0.002 PHE A1017 TRP 0.038 0.002 TRP B 120 HIS 0.003 0.001 HIS A 717 Details of bonding type rmsd/Z covalent geometry : bond 0.00875 / 0.38 (11823) covalent geometry : angle 0.98388 / 0.50 (16052) hydrogen bonds : bond 0.15897 / 10.57 ( 484) hydrogen bonds : angle 7.66913 / 5.28 ( 1425) link_BETA1-4 : bond 0.02944 / 1.88 ( 6) link_BETA1-4 : angle 8.27416 / 5.29 ( 18) link_NAG-ASN : bond 0.11615 / 7.17 ( 3) link_NAG-ASN : angle 13.37580 / 6.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 GLN cc_start: 0.3650 (OUTLIER) cc_final: 0.0395 (pt0) REVERT: A 683 MET cc_start: 0.1248 (mtt) cc_final: 0.1020 (mtt) REVERT: A 1019 LEU cc_start: 0.7888 (mt) cc_final: 0.7641 (mp) REVERT: B 188 ILE cc_start: 0.8628 (tp) cc_final: 0.8392 (tp) outliers start: 6 outliers final: 4 residues processed: 157 average time/residue: 0.1232 time to fit residues: 26.5809 Evaluate side-chains 123 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 1304 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 HIS A 466 HIS A 489 ASN A 510 ASN A 550 ASN A 626 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 ASN A 898 GLN A 965 GLN A 990 ASN A1023 GLN A1092 GLN A1133 GLN A1251 ASN B 73 HIS B 144 ASN B 161 ASN B 166 HIS B 312 GLN B 323 GLN B 398 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.189753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146468 restraints weight = 13982.963| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.87 r_work: 0.3264 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11832 Z= 0.150 Angle : 0.740 12.562 16079 Z= 0.373 Chirality : 0.047 0.331 1810 Planarity : 0.005 0.057 2036 Dihedral : 7.819 94.518 1584 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.96 % Favored : 92.97 % Rotamer: Outliers : 2.21 % Allowed : 14.67 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.14 (0.21), residues: 1408 helix: -1.69 (0.19), residues: 610 sheet: -1.26 (0.38), residues: 175 loop : -2.68 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 944 TYR 0.021 0.002 TYR A1183 PHE 0.019 0.002 PHE A1197 TRP 0.022 0.001 TRP B 120 HIS 0.012 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (11823) covalent geometry : angle 0.72482 / 0.37 (16052) hydrogen bonds : bond 0.04596 / 3.00 ( 484) hydrogen bonds : angle 5.86476 / 3.93 ( 1425) link_BETA1-4 : bond 0.00736 / 0.54 ( 6) link_BETA1-4 : angle 4.41227 / 3.30 ( 18) link_NAG-ASN : bond 0.00626 / 0.36 ( 3) link_NAG-ASN : angle 1.89926 / 0.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 GLN cc_start: 0.2763 (OUTLIER) cc_final: 0.2404 (mt0) REVERT: A 944 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7656 (ttt180) REVERT: A 975 MET cc_start: 0.7044 (tmm) cc_final: 0.6744 (tmm) REVERT: A 1183 TYR cc_start: 0.8762 (t80) cc_final: 0.8348 (t80) REVERT: B 78 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8756 (tt) REVERT: B 94 PHE cc_start: 0.8527 (m-80) cc_final: 0.8277 (m-10) REVERT: B 142 ARG cc_start: 0.7606 (mtm180) cc_final: 0.7239 (mtm180) REVERT: B 161 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8533 (t0) outliers start: 27 outliers final: 15 residues processed: 164 average time/residue: 0.1029 time to fit residues: 24.3130 Evaluate side-chains 141 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN ** A 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 GLN ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1117 ASN A1257 ASN B 99 GLN B 323 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.187379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143378 restraints weight = 14113.893| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.91 r_work: 0.3228 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11832 Z= 0.203 Angle : 0.725 9.648 16079 Z= 0.367 Chirality : 0.047 0.322 1810 Planarity : 0.005 0.060 2036 Dihedral : 7.448 93.430 1582 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.81 % Favored : 92.12 % Rotamer: Outliers : 3.28 % Allowed : 17.87 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.67 (0.21), residues: 1408 helix: -1.22 (0.20), residues: 586 sheet: -1.06 (0.40), residues: 172 loop : -2.48 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 787 TYR 0.020 0.002 TYR B 375 PHE 0.018 0.002 PHE A1197 TRP 0.022 0.002 TRP B 120 HIS 0.014 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (11823) covalent geometry : angle 0.71190 / 0.36 (16052) hydrogen bonds : bond 0.04718 / 3.03 ( 484) hydrogen bonds : angle 5.68846 / 3.81 ( 1425) link_BETA1-4 : bond 0.00593 / 0.43 ( 6) link_BETA1-4 : angle 3.90325 / 2.72 ( 18) link_NAG-ASN : bond 0.00282 / 0.17 ( 3) link_NAG-ASN : angle 2.21935 / 1.24 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 GLN cc_start: 0.2785 (OUTLIER) cc_final: 0.1948 (pt0) REVERT: A 466 HIS cc_start: 0.4955 (OUTLIER) cc_final: 0.4738 (t70) REVERT: A 1019 LEU cc_start: 0.7998 (mt) cc_final: 0.7667 (mt) REVERT: A 1183 TYR cc_start: 0.8755 (t80) cc_final: 0.8052 (t80) REVERT: B 78 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8759 (tt) REVERT: B 94 PHE cc_start: 0.8495 (m-80) cc_final: 0.8269 (m-10) REVERT: B 142 ARG cc_start: 0.7634 (mtm180) cc_final: 0.7232 (mtm180) REVERT: B 188 ILE cc_start: 0.8523 (tp) cc_final: 0.8308 (tp) outliers start: 40 outliers final: 25 residues processed: 156 average time/residue: 0.1028 time to fit residues: 23.1429 Evaluate side-chains 143 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 811 TYR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 0.0970 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.190560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145441 restraints weight = 14088.455| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.13 r_work: 0.3268 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11832 Z= 0.143 Angle : 0.656 8.338 16079 Z= 0.333 Chirality : 0.044 0.248 1810 Planarity : 0.005 0.062 2036 Dihedral : 6.947 85.685 1582 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.39 % Rotamer: Outliers : 4.10 % Allowed : 19.02 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.24 (0.22), residues: 1408 helix: -0.78 (0.21), residues: 588 sheet: -0.84 (0.39), residues: 176 loop : -2.35 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 813 TYR 0.020 0.001 TYR B 375 PHE 0.022 0.002 PHE A 833 TRP 0.014 0.001 TRP A1279 HIS 0.018 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (11823) covalent geometry : angle 0.64428 / 0.33 (16052) hydrogen bonds : bond 0.04221 / 2.72 ( 484) hydrogen bonds : angle 5.37850 / 3.59 ( 1425) link_BETA1-4 : bond 0.00509 / 0.37 ( 6) link_BETA1-4 : angle 3.48277 / 2.43 ( 18) link_NAG-ASN : bond 0.00444 / 0.27 ( 3) link_NAG-ASN : angle 2.26090 / 1.14 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 GLN cc_start: 0.1897 (OUTLIER) cc_final: 0.1371 (pt0) REVERT: A 828 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6622 (pp30) REVERT: A 1183 TYR cc_start: 0.8735 (t80) cc_final: 0.7971 (t80) REVERT: B 78 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8693 (tt) REVERT: B 86 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8191 (mm) REVERT: B 142 ARG cc_start: 0.7579 (mtm180) cc_final: 0.7214 (mtm180) REVERT: B 161 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8427 (t0) outliers start: 50 outliers final: 28 residues processed: 169 average time/residue: 0.0976 time to fit residues: 24.4376 Evaluate side-chains 153 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 811 TYR Chi-restraints excluded: chain A residue 828 GLN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 989 HIS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 106 optimal weight: 0.0270 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 HIS ** 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 = 0.4238 r_free = 0.4238 target = 0.196286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.154711 restraints weight = 13995.698| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.68 r_work: 0.3336 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11832 Z= 0.157 Angle : 0.666 7.805 16079 Z= 0.338 Chirality : 0.045 0.240 1810 Planarity : 0.005 0.060 2036 Dihedral : 6.632 79.975 1581 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.24 % Favored : 92.68 % Rotamer: Outliers : 5.16 % Allowed : 18.85 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.08 (0.22), residues: 1408 helix: -0.61 (0.21), residues: 589 sheet: -1.07 (0.38), residues: 185 loop : -2.20 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 142 TYR 0.019 0.002 TYR B 375 PHE 0.033 0.002 PHE B 94 TRP 0.012 0.001 TRP A1279 HIS 0.021 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (11823) covalent geometry : angle 0.65447 / 0.34 (16052) hydrogen bonds : bond 0.04223 / 2.70 ( 484) hydrogen bonds : angle 5.30054 / 3.53 ( 1425) link_BETA1-4 : bond 0.00504 / 0.36 ( 6) link_BETA1-4 : angle 3.38777 / 2.35 ( 18) link_NAG-ASN : bond 0.00374 / 0.23 ( 3) link_NAG-ASN : angle 2.15483 / 1.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 124 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 ASP cc_start: 0.6516 (m-30) cc_final: 0.6305 (m-30) REVERT: A 408 GLN cc_start: 0.2141 (OUTLIER) cc_final: 0.1630 (pt0) REVERT: A 828 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6658 (pp30) REVERT: A 832 MET cc_start: 0.6599 (mmp) cc_final: 0.6137 (mmt) REVERT: A 1155 PHE cc_start: 0.8495 (m-80) cc_final: 0.8280 (m-80) REVERT: A 1183 TYR cc_start: 0.8754 (t80) cc_final: 0.7991 (t80) REVERT: B 78 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8725 (tt) REVERT: B 86 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8226 (mm) REVERT: B 94 PHE cc_start: 0.8548 (m-10) cc_final: 0.7383 (m-10) REVERT: B 142 ARG cc_start: 0.7498 (mtm180) cc_final: 0.7297 (mtm180) outliers start: 63 outliers final: 42 residues processed: 174 average time/residue: 0.0937 time to fit residues: 24.2871 Evaluate side-chains 166 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 811 TYR Chi-restraints excluded: chain A residue 828 GLN Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 989 HIS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 128 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 38 optimal weight: 0.0030 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 HIS ** 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 = 0.4261 r_free = 0.4261 target = 0.198420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158793 restraints weight = 13953.058| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.70 r_work: 0.3360 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11832 Z= 0.132 Angle : 0.644 7.312 16079 Z= 0.326 Chirality : 0.044 0.225 1810 Planarity : 0.005 0.060 2036 Dihedral : 6.270 72.775 1581 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.61 % Favored : 93.32 % Rotamer: Outliers : 4.26 % Allowed : 20.25 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.85 (0.22), residues: 1408 helix: -0.39 (0.22), residues: 588 sheet: -0.97 (0.38), residues: 185 loop : -2.09 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 870 TYR 0.021 0.001 TYR B 375 PHE 0.029 0.002 PHE A 833 TRP 0.014 0.001 TRP A1279 HIS 0.022 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11823) covalent geometry : angle 0.63277 / 0.32 (16052) hydrogen bonds : bond 0.04048 / 2.61 ( 484) hydrogen bonds : angle 5.18331 / 3.45 ( 1425) link_BETA1-4 : bond 0.00469 / 0.34 ( 6) link_BETA1-4 : angle 3.27542 / 2.25 ( 18) link_NAG-ASN : bond 0.00347 / 0.21 ( 3) link_NAG-ASN : angle 2.13309 / 1.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ASP cc_start: 0.6664 (m-30) cc_final: 0.6408 (m-30) REVERT: A 597 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8396 (t) REVERT: A 731 MET cc_start: 0.4386 (ttm) cc_final: 0.4077 (ttm) REVERT: A 828 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.6870 (pp30) REVERT: A 832 MET cc_start: 0.6706 (mmp) cc_final: 0.6277 (mmt) REVERT: A 1183 TYR cc_start: 0.8752 (t80) cc_final: 0.7946 (t80) REVERT: A 1265 MET cc_start: 0.8482 (tpp) cc_final: 0.8055 (tpt) REVERT: A 1351 ASP cc_start: 0.5465 (m-30) cc_final: 0.5056 (m-30) REVERT: B 78 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8721 (tt) REVERT: B 91 LYS cc_start: 0.8833 (tptp) cc_final: 0.7888 (mmtm) outliers start: 52 outliers final: 41 residues processed: 179 average time/residue: 0.0890 time to fit residues: 24.1845 Evaluate side-chains 175 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 811 TYR Chi-restraints excluded: chain A residue 828 GLN Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 989 HIS Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 0.0570 chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 HIS ** 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 = 0.4275 r_free = 0.4275 target = 0.199806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158676 restraints weight = 13880.768| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.71 r_work: 0.3378 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11832 Z= 0.122 Angle : 0.631 7.002 16079 Z= 0.318 Chirality : 0.044 0.216 1810 Planarity : 0.005 0.059 2036 Dihedral : 6.010 64.965 1581 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.82 % Favored : 93.11 % Rotamer: Outliers : 4.59 % Allowed : 20.33 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.67 (0.22), residues: 1408 helix: -0.16 (0.22), residues: 588 sheet: -0.93 (0.38), residues: 188 loop : -2.08 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1094 TYR 0.021 0.001 TYR B 375 PHE 0.027 0.001 PHE A 833 TRP 0.014 0.001 TRP A1279 HIS 0.022 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (11823) covalent geometry : angle 0.62033 / 0.32 (16052) hydrogen bonds : bond 0.03888 / 2.51 ( 484) hydrogen bonds : angle 5.05905 / 3.37 ( 1425) link_BETA1-4 : bond 0.00472 / 0.34 ( 6) link_BETA1-4 : angle 3.17422 / 2.18 ( 18) link_NAG-ASN : bond 0.00345 / 0.21 ( 3) link_NAG-ASN : angle 2.11194 / 1.04 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 134 time to evaluate : 0.369 Fit side-chains REVERT: A 329 ASP cc_start: 0.6454 (m-30) cc_final: 0.6183 (m-30) REVERT: A 597 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8364 (t) REVERT: A 731 MET cc_start: 0.4617 (ttm) cc_final: 0.4350 (ttm) REVERT: A 803 CYS cc_start: 0.4257 (OUTLIER) cc_final: 0.2988 (m) REVERT: A 828 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.6750 (pp30) REVERT: A 832 MET cc_start: 0.6695 (mmp) cc_final: 0.6240 (mmm) REVERT: A 1078 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7764 (mt-10) REVERT: A 1135 TYR cc_start: 0.8853 (m-80) cc_final: 0.8485 (m-80) REVERT: A 1183 TYR cc_start: 0.8733 (t80) cc_final: 0.7939 (t80) REVERT: A 1351 ASP cc_start: 0.5361 (m-30) cc_final: 0.4955 (m-30) REVERT: B 78 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8728 (tt) outliers start: 56 outliers final: 40 residues processed: 180 average time/residue: 0.0917 time to fit residues: 24.7272 Evaluate side-chains 169 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 828 GLN Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 989 HIS Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 8 optimal weight: 0.0570 chunk 90 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 HIS ** 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 = 0.4270 r_free = 0.4270 target = 0.199325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.161541 restraints weight = 13975.116| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.59 r_work: 0.3373 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11832 Z= 0.138 Angle : 0.656 10.806 16079 Z= 0.328 Chirality : 0.045 0.234 1810 Planarity : 0.005 0.060 2036 Dihedral : 5.731 56.715 1578 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.89 % Favored : 93.04 % Rotamer: Outliers : 4.43 % Allowed : 20.57 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.65 (0.22), residues: 1408 helix: -0.19 (0.22), residues: 601 sheet: -0.89 (0.38), residues: 188 loop : -2.05 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 142 TYR 0.021 0.001 TYR B 375 PHE 0.031 0.002 PHE A 833 TRP 0.012 0.001 TRP A1279 HIS 0.022 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (11823) covalent geometry : angle 0.64645 / 0.33 (16052) hydrogen bonds : bond 0.03932 / 2.53 ( 484) hydrogen bonds : angle 5.05975 / 3.37 ( 1425) link_BETA1-4 : bond 0.00403 / 0.29 ( 6) link_BETA1-4 : angle 3.14748 / 2.15 ( 18) link_NAG-ASN : bond 0.00280 / 0.17 ( 3) link_NAG-ASN : angle 2.13351 / 1.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 0.388 Fit side-chains REVERT: A 329 ASP cc_start: 0.6602 (m-30) cc_final: 0.6365 (m-30) REVERT: A 597 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8419 (t) REVERT: A 803 CYS cc_start: 0.4411 (OUTLIER) cc_final: 0.3227 (m) REVERT: A 828 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6798 (pp30) REVERT: A 832 MET cc_start: 0.6555 (mmp) cc_final: 0.6193 (mmm) REVERT: A 960 GLN cc_start: 0.8053 (mp10) cc_final: 0.7834 (mp10) REVERT: A 1135 TYR cc_start: 0.8862 (m-80) cc_final: 0.8471 (m-80) REVERT: A 1183 TYR cc_start: 0.8746 (t80) cc_final: 0.7920 (t80) REVERT: A 1265 MET cc_start: 0.8518 (tpp) cc_final: 0.8103 (tpt) REVERT: A 1351 ASP cc_start: 0.5486 (m-30) cc_final: 0.5116 (m-30) REVERT: B 78 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8734 (tt) REVERT: B 119 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8148 (mt0) outliers start: 54 outliers final: 39 residues processed: 172 average time/residue: 0.0890 time to fit residues: 23.3082 Evaluate side-chains 166 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 828 GLN Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 989 HIS Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 54 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 133 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 HIS ** 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 = 0.4260 r_free = 0.4260 target = 0.198199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.152117 restraints weight = 13784.760| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.86 r_work: 0.3375 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11832 Z= 0.148 Angle : 0.671 10.687 16079 Z= 0.332 Chirality : 0.045 0.278 1810 Planarity : 0.005 0.060 2036 Dihedral : 5.713 54.244 1578 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.03 % Favored : 92.90 % Rotamer: Outliers : 4.02 % Allowed : 21.31 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.22), residues: 1408 helix: -0.16 (0.22), residues: 598 sheet: -0.89 (0.38), residues: 188 loop : -2.04 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 142 TYR 0.021 0.002 TYR B 375 PHE 0.031 0.002 PHE A 833 TRP 0.011 0.001 TRP A1279 HIS 0.024 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (11823) covalent geometry : angle 0.66155 / 0.33 (16052) hydrogen bonds : bond 0.03983 / 2.56 ( 484) hydrogen bonds : angle 5.04091 / 3.36 ( 1425) link_BETA1-4 : bond 0.00391 / 0.28 ( 6) link_BETA1-4 : angle 3.14687 / 2.14 ( 18) link_NAG-ASN : bond 0.00254 / 0.16 ( 3) link_NAG-ASN : angle 2.11511 / 1.09 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 123 time to evaluate : 0.367 Fit side-chains REVERT: A 329 ASP cc_start: 0.5553 (m-30) cc_final: 0.5320 (m-30) REVERT: A 597 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8351 (t) REVERT: A 731 MET cc_start: 0.5018 (ttm) cc_final: 0.4635 (ttm) REVERT: A 803 CYS cc_start: 0.4046 (OUTLIER) cc_final: 0.2621 (m) REVERT: A 828 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6638 (pp30) REVERT: A 832 MET cc_start: 0.6707 (mmp) cc_final: 0.6177 (mmm) REVERT: A 1096 LEU cc_start: 0.8897 (mm) cc_final: 0.8645 (mm) REVERT: A 1135 TYR cc_start: 0.8919 (m-80) cc_final: 0.8531 (m-80) REVERT: A 1183 TYR cc_start: 0.8760 (t80) cc_final: 0.7874 (t80) REVERT: A 1265 MET cc_start: 0.8538 (tpp) cc_final: 0.8049 (tpt) REVERT: A 1351 ASP cc_start: 0.5376 (m-30) cc_final: 0.4997 (m-30) REVERT: B 119 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8023 (mt0) REVERT: B 317 HIS cc_start: 0.7699 (m90) cc_final: 0.7475 (m90) outliers start: 49 outliers final: 40 residues processed: 159 average time/residue: 0.0797 time to fit residues: 19.5953 Evaluate side-chains 165 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 828 GLN Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 989 HIS Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 137 optimal weight: 0.2980 chunk 46 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 0.0570 chunk 64 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 HIS ** A 829 HIS ** 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 = 0.4279 r_free = 0.4279 target = 0.200142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162345 restraints weight = 13872.563| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.67 r_work: 0.3378 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11832 Z= 0.127 Angle : 0.653 11.112 16079 Z= 0.323 Chirality : 0.044 0.281 1810 Planarity : 0.005 0.060 2036 Dihedral : 5.572 53.445 1578 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.89 % Favored : 93.04 % Rotamer: Outliers : 3.20 % Allowed : 22.38 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.22), residues: 1408 helix: -0.06 (0.22), residues: 603 sheet: -0.87 (0.38), residues: 188 loop : -2.04 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 142 TYR 0.021 0.001 TYR B 375 PHE 0.031 0.002 PHE A 833 TRP 0.014 0.001 TRP A1279 HIS 0.024 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (11823) covalent geometry : angle 0.64372 / 0.32 (16052) hydrogen bonds : bond 0.03804 / 2.45 ( 484) hydrogen bonds : angle 4.95432 / 3.31 ( 1425) link_BETA1-4 : bond 0.00406 / 0.29 ( 6) link_BETA1-4 : angle 3.06456 / 2.08 ( 18) link_NAG-ASN : bond 0.00300 / 0.18 ( 3) link_NAG-ASN : angle 2.13299 / 1.07 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.427 Fit side-chains REVERT: A 329 ASP cc_start: 0.6487 (m-30) cc_final: 0.6201 (m-30) REVERT: A 581 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8752 (mmtm) REVERT: A 597 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8381 (t) REVERT: A 731 MET cc_start: 0.4260 (ttm) cc_final: 0.3949 (ttm) REVERT: A 803 CYS cc_start: 0.4327 (OUTLIER) cc_final: 0.3005 (m) REVERT: A 822 MET cc_start: 0.2338 (ttp) cc_final: 0.2127 (tpt) REVERT: A 832 MET cc_start: 0.6558 (mmp) cc_final: 0.6356 (mmm) REVERT: A 960 GLN cc_start: 0.8101 (mp10) cc_final: 0.7896 (mp10) REVERT: A 1096 LEU cc_start: 0.8862 (mm) cc_final: 0.8640 (mm) REVERT: A 1135 TYR cc_start: 0.8847 (m-80) cc_final: 0.8499 (m-80) REVERT: A 1183 TYR cc_start: 0.8741 (t80) cc_final: 0.7916 (t80) REVERT: A 1265 MET cc_start: 0.8549 (tpp) cc_final: 0.8113 (tpt) REVERT: A 1351 ASP cc_start: 0.5370 (m-30) cc_final: 0.5021 (m-30) REVERT: B 119 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8052 (mt0) outliers start: 39 outliers final: 35 residues processed: 159 average time/residue: 0.0863 time to fit residues: 21.1031 Evaluate side-chains 158 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 989 HIS Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 GLN A 708 HIS A 782 ASN ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.194903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153708 restraints weight = 13954.352| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.86 r_work: 0.3298 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11832 Z= 0.210 Angle : 0.716 10.349 16079 Z= 0.358 Chirality : 0.047 0.263 1810 Planarity : 0.005 0.060 2036 Dihedral : 5.847 58.832 1577 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.95 % Favored : 91.97 % Rotamer: Outliers : 3.28 % Allowed : 22.70 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.73 (0.22), residues: 1408 helix: -0.29 (0.22), residues: 596 sheet: -0.88 (0.39), residues: 187 loop : -2.06 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1260 TYR 0.020 0.002 TYR B 157 PHE 0.030 0.002 PHE A 833 TRP 0.013 0.001 TRP A1198 HIS 0.030 0.002 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (11823) covalent geometry : angle 0.70670 / 0.36 (16052) hydrogen bonds : bond 0.04374 / 2.80 ( 484) hydrogen bonds : angle 5.13986 / 3.43 ( 1425) link_BETA1-4 : bond 0.00400 / 0.28 ( 6) link_BETA1-4 : angle 3.18975 / 2.15 ( 18) link_NAG-ASN : bond 0.00222 / 0.13 ( 3) link_NAG-ASN : angle 2.17738 / 1.19 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.04 seconds wall clock time: 46 minutes 53.97 seconds (2813.97 seconds total)