Starting phenix.real_space_refine on Thu Jul 2 22:52:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hel_52080/07_2026/9hel_52080.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hel_52080/07_2026/9hel_52080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hel_52080/07_2026/9hel_52080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hel_52080/07_2026/9hel_52080.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hel_52080/07_2026/9hel_52080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hel_52080/07_2026/9hel_52080.map" } resolution = 3.1 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= 0.014 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: 5 Type Number sf(0) Gaussians Ca 7 9.91 5 S 115 5.16 5 C 6507 2.51 5 N 1904 2.21 5 O 2083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10616 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5650 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 23, 'TRANS': 723} Chain breaks: 1 Chain: "B" Number of atoms: 4811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 4811 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 19, 'TRANS': 615} Chain breaks: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 14 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.09, per 1000 atoms: 0.20 Number of scatterers: 10616 At special positions: 0 Unit cell: (80.704, 133.952, 167.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 7 19.99 S 115 16.00 O 2083 8.00 N 1904 7.00 C 6507 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 258 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 462 " distance=2.04 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 442 " - pdb=" SG CYS A 452 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 577 " distance=2.04 Simple disulfide: pdb=" SG CYS A 547 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 869 " distance=2.03 Simple disulfide: pdb=" SG CYS A 864 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A 938 " - pdb=" SG CYS A 972 " distance=2.02 Simple disulfide: pdb=" SG CYS A 954 " - pdb=" SG CYS A1018 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A1028 " distance=2.02 Simple disulfide: pdb=" SG CYS A 998 " - pdb=" SG CYS A1008 " distance=2.03 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 355 " distance=2.04 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 365 " distance=2.02 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 462 " distance=2.03 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 442 " - pdb=" SG CYS B 452 " distance=2.03 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 547 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 728 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 808 " distance=2.03 Simple disulfide: pdb=" SG CYS B 757 " - pdb=" SG CYS B 818 " distance=2.02 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 869 " distance=2.03 Simple disulfide: pdb=" SG CYS B 864 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B 895 " - pdb=" SG CYS B 905 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1201 " - " ASN A 445 " " NAG A1202 " - " ASN A1027 " " NAG B1201 " - " ASN B 445 " " NAG C 1 " - " ASN A 320 " " NAG D 1 " - " ASN B 320 " " NAG E 1 " - " ASN B 767 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 405.9 milliseconds 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 29 sheets defined 17.3% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 189 through 200 removed outlier: 3.765A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 200 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 removed outlier: 4.293A pdb=" N PHE A 214 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.590A pdb=" N CYS A 238 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 403 through 415 removed outlier: 3.939A pdb=" N VAL A 409 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.544A pdb=" N CYS A 452 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.820A pdb=" N ARG A 571 " --> pdb=" O SER A 568 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP A 572 " --> pdb=" O HIS A 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 568 through 572' Processing helix chain 'A' and resid 613 through 624 Processing helix chain 'A' and resid 658 through 662 removed outlier: 3.549A pdb=" N CYS A 662 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 868 Processing helix chain 'A' and resid 901 through 905 removed outlier: 3.738A pdb=" N GLN A 904 " --> pdb=" O THR A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'A' and resid 1019 through 1023 removed outlier: 3.586A pdb=" N GLU A1022 " --> pdb=" O GLY A1019 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP A1023 " --> pdb=" O HIS A1020 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1019 through 1023' Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.538A pdb=" N GLN B 344 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS B 345 " --> pdb=" O ILE B 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 341 through 345' Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.851A pdb=" N ASP B 360 " --> pdb=" O HIS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 removed outlier: 4.344A pdb=" N VAL B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 613 through 624 removed outlier: 3.886A pdb=" N VAL B 619 " --> pdb=" O GLU B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 removed outlier: 3.580A pdb=" N VAL B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 798 Processing helix chain 'B' and resid 809 through 813 removed outlier: 3.990A pdb=" N ASP B 813 " --> pdb=" O HIS B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 868 Processing helix chain 'B' and resid 901 through 905 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 3.874A pdb=" N GLU A 158 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 162 removed outlier: 3.874A pdb=" N GLU A 158 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 255 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 269 Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 269 removed outlier: 7.028A pdb=" N LEU A 279 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE A 290 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A 328 " --> pdb=" O TRP A 287 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THR A 289 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 330 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 377 removed outlier: 7.071A pdb=" N THR A 471 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 420 " --> pdb=" O THR A 471 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 377 removed outlier: 6.443A pdb=" N VAL A 386 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 397 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU A 437 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS A 396 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 477 through 481 Processing sheet with id=AA8, first strand: chain 'A' and resid 477 through 481 Processing sheet with id=AA9, first strand: chain 'A' and resid 543 through 545 Processing sheet with id=AB1, first strand: chain 'A' and resid 582 through 586 removed outlier: 4.621A pdb=" N GLU A 582 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 582 through 586 removed outlier: 4.621A pdb=" N GLU A 582 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 649 through 650 Processing sheet with id=AB4, first strand: chain 'A' and resid 823 through 827 removed outlier: 3.572A pdb=" N SER A 823 " --> pdb=" O PHE A 842 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 823 through 827 removed outlier: 3.572A pdb=" N SER A 823 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 839 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A 850 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TRP A 889 " --> pdb=" O TRP A 847 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR A 849 " --> pdb=" O TRP A 889 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 929 through 932 removed outlier: 3.715A pdb=" N ALA A1025 " --> pdb=" O PHE A 979 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A1027 " --> pdb=" O LYS A 977 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 977 " --> pdb=" O ASN A1027 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 929 through 932 removed outlier: 6.565A pdb=" N VAL A 942 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 953 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N TRP A 992 " --> pdb=" O TRP A 950 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR A 952 " --> pdb=" O TRP A 992 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 265 through 269 removed outlier: 3.831A pdb=" N SER B 265 " --> pdb=" O ARG B 282 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 265 through 269 removed outlier: 3.831A pdb=" N SER B 265 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU B 279 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE B 290 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TRP B 329 " --> pdb=" O TRP B 287 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR B 289 " --> pdb=" O TRP B 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 371 through 376 removed outlier: 7.392A pdb=" N THR B 471 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 420 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 371 through 376 removed outlier: 6.435A pdb=" N VAL B 386 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 397 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N LEU B 437 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS B 396 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU B 439 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 476 through 480 removed outlier: 3.750A pdb=" N GLU B 477 " --> pdb=" O LYS B 494 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 476 through 480 removed outlier: 3.750A pdb=" N GLU B 477 " --> pdb=" O LYS B 494 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 491 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 502 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TRP B 499 " --> pdb=" O GLN B 539 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N TRP B 541 " --> pdb=" O TRP B 499 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER B 501 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 582 through 586 removed outlier: 4.472A pdb=" N GLU B 582 " --> pdb=" O LYS B 599 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 606 through 607 removed outlier: 6.109A pdb=" N SER B 606 " --> pdb=" O TRP B 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 649 through 650 Processing sheet with id=AC8, first strand: chain 'B' and resid 719 through 722 removed outlier: 6.322A pdb=" N GLY B 815 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA B 768 " --> pdb=" O GLY B 815 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 817 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 719 through 722 removed outlier: 6.735A pdb=" N VAL B 732 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE B 743 " --> pdb=" O VAL B 732 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TRP B 782 " --> pdb=" O TRP B 740 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR B 742 " --> pdb=" O TRP B 782 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 823 through 827 removed outlier: 3.608A pdb=" N SER B 823 " --> pdb=" O PHE B 842 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP B 922 " --> pdb=" O ASN B 876 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 823 through 827 removed outlier: 3.608A pdb=" N SER B 823 " --> pdb=" O PHE B 842 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 839 " --> pdb=" O VAL B 850 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL B 850 " --> pdb=" O LEU B 839 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TRP B 889 " --> pdb=" O TRP B 847 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR B 849 " --> pdb=" O TRP B 889 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3614 1.34 - 1.46: 2558 1.46 - 1.58: 4546 1.58 - 1.70: 0 1.70 - 1.82: 130 Bond restraints: 10848 Sorted by residual: bond pdb=" N ASP A 900 " pdb=" CA ASP A 900 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.29e-02 6.01e+03 7.04e+00 bond pdb=" N GLN A 969 " pdb=" CA GLN A 969 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.42e+00 bond pdb=" N ASP A1007 " pdb=" CA ASP A1007 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.29e-02 6.01e+03 5.35e+00 bond pdb=" N LEU A1005 " pdb=" CA LEU A1005 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.62e+00 bond pdb=" N TRP A1006 " pdb=" CA TRP A1006 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.44e-02 4.82e+03 4.29e+00 ... (remaining 10843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 14283 1.72 - 3.45: 344 3.45 - 5.17: 54 5.17 - 6.89: 11 6.89 - 8.62: 4 Bond angle restraints: 14696 Sorted by residual: angle pdb=" N ASP A1007 " pdb=" CA ASP A1007 " pdb=" C ASP A1007 " ideal model delta sigma weight residual 113.97 105.90 8.07 1.28e+00 6.10e-01 3.97e+01 angle pdb=" N VAL A 426 " pdb=" CA VAL A 426 " pdb=" C VAL A 426 " ideal model delta sigma weight residual 108.23 113.81 -5.58 1.53e+00 4.27e-01 1.33e+01 angle pdb=" CB ARG B 267 " pdb=" CG ARG B 267 " pdb=" CD ARG B 267 " ideal model delta sigma weight residual 111.30 119.14 -7.84 2.30e+00 1.89e-01 1.16e+01 angle pdb=" N TRP A1006 " pdb=" CA TRP A1006 " pdb=" C TRP A1006 " ideal model delta sigma weight residual 113.21 109.37 3.84 1.15e+00 7.56e-01 1.11e+01 angle pdb=" N LEU A 970 " pdb=" CA LEU A 970 " pdb=" C LEU A 970 " ideal model delta sigma weight residual 110.50 105.82 4.68 1.41e+00 5.03e-01 1.10e+01 ... (remaining 14691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5668 17.96 - 35.93: 689 35.93 - 53.89: 171 53.89 - 71.85: 45 71.85 - 89.82: 22 Dihedral angle restraints: 6595 sinusoidal: 2772 harmonic: 3823 Sorted by residual: dihedral pdb=" CB CYS A 608 " pdb=" SG CYS A 608 " pdb=" SG CYS A 672 " pdb=" CB CYS A 672 " ideal model delta sinusoidal sigma weight residual 93.00 174.68 -81.68 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CD ARG A1011 " pdb=" NE ARG A1011 " pdb=" CZ ARG A1011 " pdb=" NH1 ARG A1011 " ideal model delta sinusoidal sigma weight residual 0.00 -79.29 79.29 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS A 503 " pdb=" SG CYS A 503 " pdb=" SG CYS A 567 " pdb=" CB CYS A 567 " ideal model delta sinusoidal sigma weight residual -86.00 -155.79 69.79 1 1.00e+01 1.00e-02 6.28e+01 ... (remaining 6592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1400 0.071 - 0.142: 170 0.142 - 0.213: 8 0.213 - 0.284: 1 0.284 - 0.355: 1 Chirality restraints: 1580 Sorted by residual: chirality pdb=" CB ILE A 540 " pdb=" CA ILE A 540 " pdb=" CG1 ILE A 540 " pdb=" CG2 ILE A 540 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 767 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ASN A 454 " pdb=" N ASN A 454 " pdb=" C ASN A 454 " pdb=" CB ASN A 454 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 1577 not shown) Planarity restraints: 1921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1011 " 1.085 9.50e-02 1.11e+02 4.86e-01 1.42e+02 pdb=" NE ARG A1011 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A1011 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A1011 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A1011 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 838 " 0.935 9.50e-02 1.11e+02 4.19e-01 1.06e+02 pdb=" NE ARG A 838 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG A 838 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 838 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 838 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1012 " -0.604 9.50e-02 1.11e+02 2.71e-01 4.48e+01 pdb=" NE ARG A1012 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A1012 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A1012 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1012 " -0.019 2.00e-02 2.50e+03 ... (remaining 1918 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 228 2.67 - 3.23: 9720 3.23 - 3.79: 15444 3.79 - 4.34: 20885 4.34 - 4.90: 35070 Nonbonded interactions: 81347 Sorted by model distance: nonbonded pdb=" O GLY A 203 " pdb=" OG SER A 259 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR A 427 " pdb=" NH2 ARG A 476 " model vdw 2.182 3.120 nonbonded pdb=" OE1 GLU A1022 " pdb="CA CA A1204 " model vdw 2.248 3.250 nonbonded pdb=" O SER A 957 " pdb=" OG SER A 957 " model vdw 2.254 3.040 nonbonded pdb=" OG SER A 440 " pdb=" OD1 ASN A 454 " model vdw 2.268 3.040 ... (remaining 81342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 9.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.290 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 0.003 0.065 10909 Z= 0.153 Angle : 0.678 12.190 14829 Z= 0.365 Chirality : 0.047 0.355 1580 Planarity : 0.017 0.486 1915 Dihedral : 17.018 89.816 4015 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.35 % Allowed : 23.94 % Favored : 75.71 % 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: -1.30 (0.20), residues: 1374 helix: 0.75 (0.41), residues: 161 sheet: -0.56 (0.34), residues: 207 loop : -1.28 (0.17), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 318 TYR 0.009 0.001 TYR B 580 PHE 0.012 0.001 PHE A 507 TRP 0.045 0.002 TRP A 847 HIS 0.007 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (10848) covalent geometry : angle 0.65522 / 0.36 (14696) SS BOND : bond 0.00363 / 0.21 ( 50) SS BOND : angle 0.96845 / 0.63 ( 100) hydrogen bonds : bond 0.13625 / 9.29 ( 293) hydrogen bonds : angle 5.26925 / 3.62 ( 942) link_BETA1-4 : bond 0.00845 / 0.43 ( 5) link_BETA1-4 : angle 4.23734 / 2.26 ( 15) link_NAG-ASN : bond 0.00385 / 0.21 ( 6) link_NAG-ASN : angle 2.79940 / 1.79 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 251 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 ASP cc_start: 0.7864 (t0) cc_final: 0.7629 (t0) REVERT: B 718 GLN cc_start: 0.6378 (tt0) cc_final: 0.6079 (tt0) outliers start: 4 outliers final: 3 residues processed: 252 average time/residue: 0.1066 time to fit residues: 36.3821 Evaluate side-chains 244 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 388 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0270 chunk 55 optimal weight: 0.4980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS A 546 GLN A 618 HIS ** B 736 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 = 0.3920 r_free = 0.3920 target = 0.144988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121552 restraints weight = 15721.589| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.11 r_work: 0.3460 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10909 Z= 0.212 Angle : 0.658 13.447 14829 Z= 0.338 Chirality : 0.047 0.278 1580 Planarity : 0.005 0.063 1915 Dihedral : 7.955 57.428 1694 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.81 % Allowed : 20.57 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.17 (0.21), residues: 1374 helix: 0.81 (0.42), residues: 166 sheet: -0.38 (0.33), residues: 235 loop : -1.23 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 913 TYR 0.011 0.002 TYR B 465 PHE 0.009 0.001 PHE A 979 TRP 0.021 0.002 TRP A 847 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (10848) covalent geometry : angle 0.62588 / 0.33 (14696) SS BOND : bond 0.00536 / 0.30 ( 50) SS BOND : angle 1.02516 / 0.72 ( 100) hydrogen bonds : bond 0.04276 / 2.93 ( 293) hydrogen bonds : angle 4.64915 / 3.23 ( 942) link_BETA1-4 : bond 0.00886 / 0.46 ( 5) link_BETA1-4 : angle 4.98010 / 2.64 ( 15) link_NAG-ASN : bond 0.00488 / 0.27 ( 6) link_NAG-ASN : angle 3.19441 / 2.00 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 CYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7600 (m) REVERT: A 405 LYS cc_start: 0.8738 (ttpp) cc_final: 0.8478 (ttpp) REVERT: A 408 ASP cc_start: 0.7958 (t0) cc_final: 0.7721 (t0) REVERT: A 446 GLU cc_start: 0.8302 (mp0) cc_final: 0.7919 (mp0) REVERT: A 578 SER cc_start: 0.8263 (m) cc_final: 0.7952 (p) REVERT: A 620 LEU cc_start: 0.8220 (tp) cc_final: 0.7959 (tt) REVERT: A 968 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7372 (tm-30) REVERT: B 290 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7571 (mt) REVERT: B 502 ILE cc_start: 0.7934 (mt) cc_final: 0.7262 (tp) REVERT: B 847 TRP cc_start: 0.8181 (m100) cc_final: 0.7955 (m100) REVERT: B 872 LYS cc_start: 0.7922 (mttt) cc_final: 0.7559 (mmtt) outliers start: 43 outliers final: 25 residues processed: 275 average time/residue: 0.1004 time to fit residues: 37.6519 Evaluate side-chains 268 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 4 optimal weight: 0.9980 chunk 134 optimal weight: 0.0870 chunk 19 optimal weight: 0.0060 chunk 126 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS A 648 HIS B 357 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.145850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122378 restraints weight = 15732.788| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.13 r_work: 0.3469 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10909 Z= 0.148 Angle : 0.609 12.407 14829 Z= 0.314 Chirality : 0.045 0.261 1580 Planarity : 0.004 0.054 1915 Dihedral : 6.450 59.980 1689 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.26 % Allowed : 19.15 % Favored : 76.60 % 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: -1.07 (0.21), residues: 1374 helix: 0.85 (0.42), residues: 166 sheet: -0.28 (0.33), residues: 228 loop : -1.17 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 825 TYR 0.009 0.001 TYR B 465 PHE 0.008 0.001 PHE B 842 TRP 0.034 0.001 TRP A 847 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (10848) covalent geometry : angle 0.57716 / 0.31 (14696) SS BOND : bond 0.00417 / 0.25 ( 50) SS BOND : angle 0.94482 / 0.68 ( 100) hydrogen bonds : bond 0.03646 / 2.50 ( 293) hydrogen bonds : angle 4.42606 / 3.07 ( 942) link_BETA1-4 : bond 0.00841 / 0.43 ( 5) link_BETA1-4 : angle 4.81812 / 2.60 ( 15) link_NAG-ASN : bond 0.00423 / 0.23 ( 6) link_NAG-ASN : angle 3.02670 / 1.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 249 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 CYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7418 (m) REVERT: A 405 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8507 (ttpp) REVERT: A 446 GLU cc_start: 0.8295 (mp0) cc_final: 0.7828 (mp0) REVERT: A 578 SER cc_start: 0.8221 (m) cc_final: 0.7858 (p) REVERT: A 597 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7212 (mt-10) REVERT: A 620 LEU cc_start: 0.8204 (tp) cc_final: 0.7983 (tt) REVERT: A 968 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 1011 ARG cc_start: 0.8359 (ttm170) cc_final: 0.8008 (ttm170) REVERT: B 433 THR cc_start: 0.8412 (p) cc_final: 0.8212 (p) REVERT: B 847 TRP cc_start: 0.8178 (m100) cc_final: 0.7925 (m100) REVERT: B 872 LYS cc_start: 0.7929 (mttt) cc_final: 0.7591 (mttt) outliers start: 48 outliers final: 28 residues processed: 276 average time/residue: 0.0996 time to fit residues: 38.0907 Evaluate side-chains 266 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS A 495 HIS ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120360 restraints weight = 15608.325| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.01 r_work: 0.3445 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10909 Z= 0.249 Angle : 0.648 13.220 14829 Z= 0.334 Chirality : 0.048 0.280 1580 Planarity : 0.004 0.050 1915 Dihedral : 6.264 56.441 1689 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.05 % Allowed : 18.71 % Favored : 76.24 % 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: -1.17 (0.21), residues: 1374 helix: 0.78 (0.42), residues: 166 sheet: -0.40 (0.33), residues: 224 loop : -1.22 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 913 TYR 0.011 0.002 TYR B 465 PHE 0.009 0.001 PHE B 842 TRP 0.019 0.002 TRP A 847 HIS 0.008 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 (10848) covalent geometry : angle 0.61283 / 0.33 (14696) SS BOND : bond 0.00577 / 0.33 ( 50) SS BOND : angle 1.18052 / 0.85 ( 100) hydrogen bonds : bond 0.03921 / 2.70 ( 293) hydrogen bonds : angle 4.53704 / 3.17 ( 942) link_BETA1-4 : bond 0.00843 / 0.43 ( 5) link_BETA1-4 : angle 4.98841 / 2.67 ( 15) link_NAG-ASN : bond 0.00503 / 0.29 ( 6) link_NAG-ASN : angle 3.25214 / 2.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 255 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 HIS cc_start: 0.6261 (OUTLIER) cc_final: 0.4635 (m-70) REVERT: A 365 CYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7556 (m) REVERT: A 396 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8292 (mmtp) REVERT: A 436 TRP cc_start: 0.8682 (m100) cc_final: 0.8449 (m100) REVERT: A 571 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8083 (mtm180) REVERT: A 578 SER cc_start: 0.8255 (m) cc_final: 0.8032 (p) REVERT: A 582 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6842 (mt-10) REVERT: A 597 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7301 (mt-10) REVERT: A 823 SER cc_start: 0.8773 (t) cc_final: 0.8455 (p) REVERT: A 968 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7550 (tm-30) REVERT: A 1011 ARG cc_start: 0.8400 (ttm170) cc_final: 0.8006 (ttm170) REVERT: B 372 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7157 (mt-10) REVERT: B 435 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.6493 (t) REVERT: B 847 TRP cc_start: 0.8165 (m100) cc_final: 0.7904 (m100) outliers start: 57 outliers final: 36 residues processed: 284 average time/residue: 0.0983 time to fit residues: 38.2703 Evaluate side-chains 289 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 250 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 914 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 26 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS A 495 HIS B 357 HIS B 358 ASN B 644 GLN ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.142292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.118954 restraints weight = 15690.360| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.11 r_work: 0.3415 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10909 Z= 0.267 Angle : 0.679 13.853 14829 Z= 0.348 Chirality : 0.048 0.284 1580 Planarity : 0.005 0.052 1915 Dihedral : 6.302 57.041 1689 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.14 % Allowed : 19.06 % Favored : 75.80 % 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: -1.28 (0.21), residues: 1374 helix: 0.74 (0.41), residues: 166 sheet: -0.44 (0.34), residues: 216 loop : -1.31 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 913 TYR 0.012 0.002 TYR B 465 PHE 0.010 0.001 PHE B 842 TRP 0.044 0.002 TRP A 847 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.27 (10848) covalent geometry : angle 0.64467 / 0.34 (14696) SS BOND : bond 0.00626 / 0.37 ( 50) SS BOND : angle 1.09121 / 0.77 ( 100) hydrogen bonds : bond 0.04023 / 2.79 ( 293) hydrogen bonds : angle 4.62351 / 3.23 ( 942) link_BETA1-4 : bond 0.00898 / 0.46 ( 5) link_BETA1-4 : angle 5.17654 / 2.78 ( 15) link_NAG-ASN : bond 0.00539 / 0.30 ( 6) link_NAG-ASN : angle 3.33648 / 2.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 265 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 HIS cc_start: 0.6376 (OUTLIER) cc_final: 0.4657 (m-70) REVERT: A 365 CYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7585 (m) REVERT: A 408 ASP cc_start: 0.8076 (t70) cc_final: 0.7461 (t0) REVERT: A 454 ASN cc_start: 0.8183 (p0) cc_final: 0.7974 (p0) REVERT: A 571 ARG cc_start: 0.8688 (mmm-85) cc_final: 0.8039 (mtm180) REVERT: A 578 SER cc_start: 0.8256 (m) cc_final: 0.8042 (p) REVERT: A 582 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6864 (mt-10) REVERT: A 823 SER cc_start: 0.8772 (t) cc_final: 0.8429 (p) REVERT: A 910 TRP cc_start: 0.8424 (m100) cc_final: 0.8061 (m100) REVERT: A 968 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 1011 ARG cc_start: 0.8396 (ttm170) cc_final: 0.8115 (ttm170) REVERT: B 372 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7198 (mt-10) REVERT: B 405 LYS cc_start: 0.8421 (tttp) cc_final: 0.8046 (tptp) REVERT: B 435 THR cc_start: 0.7463 (OUTLIER) cc_final: 0.6533 (t) outliers start: 58 outliers final: 37 residues processed: 295 average time/residue: 0.0952 time to fit residues: 38.8318 Evaluate side-chains 292 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 914 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 74 optimal weight: 0.6980 chunk 130 optimal weight: 0.1980 chunk 94 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 86 optimal weight: 0.4980 chunk 36 optimal weight: 0.3980 chunk 104 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.143938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120363 restraints weight = 15823.218| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.15 r_work: 0.3444 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10909 Z= 0.161 Angle : 0.629 13.105 14829 Z= 0.322 Chirality : 0.046 0.263 1580 Planarity : 0.004 0.050 1915 Dihedral : 6.092 59.894 1689 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.14 % Allowed : 19.68 % Favored : 75.18 % 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: -1.17 (0.21), residues: 1374 helix: 0.89 (0.42), residues: 166 sheet: -0.40 (0.34), residues: 216 loop : -1.23 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 913 TYR 0.009 0.001 TYR B 465 PHE 0.009 0.001 PHE A 638 TRP 0.020 0.001 TRP A 847 HIS 0.011 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (10848) covalent geometry : angle 0.59742 / 0.31 (14696) SS BOND : bond 0.00438 / 0.26 ( 50) SS BOND : angle 0.92715 / 0.65 ( 100) hydrogen bonds : bond 0.03529 / 2.42 ( 293) hydrogen bonds : angle 4.42759 / 3.09 ( 942) link_BETA1-4 : bond 0.00843 / 0.43 ( 5) link_BETA1-4 : angle 4.96979 / 2.69 ( 15) link_NAG-ASN : bond 0.00439 / 0.24 ( 6) link_NAG-ASN : angle 3.10985 / 1.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 HIS cc_start: 0.6370 (OUTLIER) cc_final: 0.4644 (m-70) REVERT: A 365 CYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7568 (m) REVERT: A 408 ASP cc_start: 0.8025 (t70) cc_final: 0.7406 (t0) REVERT: A 524 VAL cc_start: 0.7790 (p) cc_final: 0.7493 (t) REVERT: A 578 SER cc_start: 0.8261 (m) cc_final: 0.8026 (p) REVERT: A 582 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6835 (mt-10) REVERT: A 823 SER cc_start: 0.8752 (t) cc_final: 0.8412 (p) REVERT: A 911 GLU cc_start: 0.7146 (pm20) cc_final: 0.6897 (pm20) REVERT: A 968 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 1011 ARG cc_start: 0.8367 (ttm170) cc_final: 0.8038 (ttm170) REVERT: B 372 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7176 (mt-10) REVERT: B 405 LYS cc_start: 0.8459 (tttp) cc_final: 0.8062 (tptp) REVERT: B 435 THR cc_start: 0.7444 (OUTLIER) cc_final: 0.6477 (t) REVERT: B 720 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7525 (ptt180) REVERT: B 847 TRP cc_start: 0.8164 (m100) cc_final: 0.7917 (m100) outliers start: 58 outliers final: 39 residues processed: 291 average time/residue: 0.0966 time to fit residues: 38.6378 Evaluate side-chains 294 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 720 ARG Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 914 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 100 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS B 357 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.143320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119989 restraints weight = 15666.211| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.10 r_work: 0.3423 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10909 Z= 0.228 Angle : 0.658 13.466 14829 Z= 0.336 Chirality : 0.047 0.276 1580 Planarity : 0.004 0.051 1915 Dihedral : 6.131 58.055 1689 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.23 % Allowed : 20.21 % Favored : 74.56 % 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: -1.24 (0.21), residues: 1374 helix: 0.87 (0.42), residues: 166 sheet: -0.49 (0.34), residues: 216 loop : -1.28 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 913 TYR 0.009 0.001 TYR B 465 PHE 0.009 0.001 PHE B 842 TRP 0.019 0.002 TRP A 847 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.23 (10848) covalent geometry : angle 0.62549 / 0.33 (14696) SS BOND : bond 0.00530 / 0.31 ( 50) SS BOND : angle 1.02458 / 0.72 ( 100) hydrogen bonds : bond 0.03745 / 2.57 ( 293) hydrogen bonds : angle 4.48878 / 3.14 ( 942) link_BETA1-4 : bond 0.00867 / 0.44 ( 5) link_BETA1-4 : angle 4.98932 / 2.68 ( 15) link_NAG-ASN : bond 0.00481 / 0.27 ( 6) link_NAG-ASN : angle 3.20904 / 1.97 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 259 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TRP cc_start: 0.6595 (m100) cc_final: 0.6131 (m100) REVERT: A 250 HIS cc_start: 0.6444 (OUTLIER) cc_final: 0.4660 (m-70) REVERT: A 365 CYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7555 (m) REVERT: A 408 ASP cc_start: 0.8028 (t70) cc_final: 0.7394 (t0) REVERT: A 454 ASN cc_start: 0.8133 (p0) cc_final: 0.7925 (p0) REVERT: A 524 VAL cc_start: 0.7815 (p) cc_final: 0.7521 (t) REVERT: A 528 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8354 (mt) REVERT: A 578 SER cc_start: 0.8257 (m) cc_final: 0.8033 (p) REVERT: A 582 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6851 (mt-10) REVERT: A 659 MET cc_start: 0.8293 (mmm) cc_final: 0.7818 (mmm) REVERT: A 823 SER cc_start: 0.8763 (t) cc_final: 0.8439 (p) REVERT: A 911 GLU cc_start: 0.7247 (pm20) cc_final: 0.6923 (pm20) REVERT: A 968 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 1011 ARG cc_start: 0.8381 (ttm170) cc_final: 0.8027 (ttm170) REVERT: B 372 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7183 (mt-10) REVERT: B 435 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.6535 (t) REVERT: B 569 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7268 (t-90) REVERT: B 676 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7051 (mp10) REVERT: B 720 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7610 (ptt180) REVERT: B 852 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8506 (ttpp) outliers start: 59 outliers final: 42 residues processed: 291 average time/residue: 0.0978 time to fit residues: 39.2023 Evaluate side-chains 305 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 254 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 720 ARG Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 852 LYS Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 914 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 19 optimal weight: 0.0970 chunk 74 optimal weight: 0.0270 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS B 357 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.144508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.121169 restraints weight = 15533.336| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.11 r_work: 0.3448 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10909 Z= 0.147 Angle : 0.616 12.715 14829 Z= 0.316 Chirality : 0.045 0.257 1580 Planarity : 0.004 0.049 1915 Dihedral : 5.950 59.824 1689 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.96 % Allowed : 20.57 % Favored : 74.47 % 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: -1.14 (0.21), residues: 1374 helix: 1.00 (0.42), residues: 166 sheet: -0.47 (0.34), residues: 216 loop : -1.20 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 913 TYR 0.007 0.001 TYR B 465 PHE 0.014 0.001 PHE A 842 TRP 0.058 0.001 TRP A 847 HIS 0.012 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (10848) covalent geometry : angle 0.58575 / 0.31 (14696) SS BOND : bond 0.00412 / 0.25 ( 50) SS BOND : angle 0.87646 / 0.61 ( 100) hydrogen bonds : bond 0.03391 / 2.32 ( 293) hydrogen bonds : angle 4.33796 / 3.02 ( 942) link_BETA1-4 : bond 0.00849 / 0.44 ( 5) link_BETA1-4 : angle 4.78090 / 2.59 ( 15) link_NAG-ASN : bond 0.00423 / 0.23 ( 6) link_NAG-ASN : angle 3.03482 / 1.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 254 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 CYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7526 (m) REVERT: A 408 ASP cc_start: 0.8005 (t70) cc_final: 0.7390 (t0) REVERT: A 454 ASN cc_start: 0.8128 (p0) cc_final: 0.7922 (p0) REVERT: A 524 VAL cc_start: 0.7823 (p) cc_final: 0.7511 (t) REVERT: A 528 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8334 (mt) REVERT: A 578 SER cc_start: 0.8279 (m) cc_final: 0.8036 (p) REVERT: A 582 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6821 (mt-10) REVERT: A 823 SER cc_start: 0.8741 (t) cc_final: 0.8401 (p) REVERT: A 911 GLU cc_start: 0.7289 (pm20) cc_final: 0.6966 (pm20) REVERT: A 920 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7067 (mt-10) REVERT: A 968 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 1011 ARG cc_start: 0.8352 (ttm170) cc_final: 0.8002 (ttm170) REVERT: B 372 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7167 (mt-10) REVERT: B 435 THR cc_start: 0.7448 (OUTLIER) cc_final: 0.6461 (t) REVERT: B 569 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.7269 (t-90) REVERT: B 676 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7035 (mp10) REVERT: B 718 GLN cc_start: 0.6421 (OUTLIER) cc_final: 0.4973 (tt0) REVERT: B 720 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7502 (ptt180) outliers start: 56 outliers final: 38 residues processed: 284 average time/residue: 0.0976 time to fit residues: 37.8985 Evaluate side-chains 295 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 720 ARG Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 914 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 85 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 61 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS B 357 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.144291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121116 restraints weight = 15677.939| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.11 r_work: 0.3441 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10909 Z= 0.162 Angle : 0.624 12.557 14829 Z= 0.318 Chirality : 0.045 0.261 1580 Planarity : 0.004 0.049 1915 Dihedral : 5.895 59.211 1689 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.32 % Allowed : 20.30 % Favored : 74.38 % 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: -1.10 (0.21), residues: 1374 helix: 0.98 (0.42), residues: 166 sheet: -0.48 (0.34), residues: 216 loop : -1.16 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 913 TYR 0.007 0.001 TYR B 465 PHE 0.009 0.001 PHE B 283 TRP 0.043 0.001 TRP A 847 HIS 0.005 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (10848) covalent geometry : angle 0.59461 / 0.31 (14696) SS BOND : bond 0.00407 / 0.24 ( 50) SS BOND : angle 0.89526 / 0.62 ( 100) hydrogen bonds : bond 0.03404 / 2.32 ( 293) hydrogen bonds : angle 4.32931 / 3.02 ( 942) link_BETA1-4 : bond 0.00804 / 0.41 ( 5) link_BETA1-4 : angle 4.68243 / 2.53 ( 15) link_NAG-ASN : bond 0.00423 / 0.23 ( 6) link_NAG-ASN : angle 3.00745 / 1.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 253 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 CYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7537 (m) REVERT: A 408 ASP cc_start: 0.8003 (t70) cc_final: 0.7386 (t0) REVERT: A 454 ASN cc_start: 0.8128 (p0) cc_final: 0.7908 (p0) REVERT: A 524 VAL cc_start: 0.7845 (p) cc_final: 0.7541 (t) REVERT: A 528 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8342 (mt) REVERT: A 578 SER cc_start: 0.8282 (m) cc_final: 0.8038 (p) REVERT: A 582 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6828 (mt-10) REVERT: A 620 LEU cc_start: 0.8208 (tp) cc_final: 0.7985 (tt) REVERT: A 823 SER cc_start: 0.8730 (t) cc_final: 0.8401 (p) REVERT: A 911 GLU cc_start: 0.7326 (pm20) cc_final: 0.6987 (pm20) REVERT: A 968 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 1011 ARG cc_start: 0.8365 (ttm170) cc_final: 0.8011 (ttm170) REVERT: B 372 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7169 (mt-10) REVERT: B 435 THR cc_start: 0.7454 (OUTLIER) cc_final: 0.6515 (t) REVERT: B 569 HIS cc_start: 0.7745 (OUTLIER) cc_final: 0.7273 (t-90) REVERT: B 676 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: B 718 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.4905 (tt0) REVERT: B 720 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7512 (ptt180) outliers start: 60 outliers final: 42 residues processed: 283 average time/residue: 0.0980 time to fit residues: 37.9814 Evaluate side-chains 304 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 720 ARG Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 888 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 120 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 117 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 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 = 0.3897 r_free = 0.3897 target = 0.143460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.120319 restraints weight = 15624.358| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.03 r_work: 0.3441 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10909 Z= 0.209 Angle : 0.651 12.879 14829 Z= 0.334 Chirality : 0.047 0.270 1580 Planarity : 0.004 0.050 1915 Dihedral : 5.957 57.566 1689 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.39 % Favored : 94.54 % Rotamer: Outliers : 5.05 % Allowed : 20.74 % Favored : 74.20 % 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: -1.17 (0.21), residues: 1374 helix: 0.92 (0.42), residues: 166 sheet: -0.53 (0.34), residues: 216 loop : -1.20 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 913 TYR 0.009 0.001 TYR A 843 PHE 0.011 0.001 PHE B 283 TRP 0.053 0.002 TRP A 847 HIS 0.008 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (10848) covalent geometry : angle 0.62201 / 0.33 (14696) SS BOND : bond 0.00481 / 0.28 ( 50) SS BOND : angle 0.97709 / 0.68 ( 100) hydrogen bonds : bond 0.03603 / 2.46 ( 293) hydrogen bonds : angle 4.40402 / 3.08 ( 942) link_BETA1-4 : bond 0.00845 / 0.43 ( 5) link_BETA1-4 : angle 4.75134 / 2.56 ( 15) link_NAG-ASN : bond 0.00472 / 0.26 ( 6) link_NAG-ASN : angle 3.08560 / 1.90 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 254 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 HIS cc_start: 0.6582 (OUTLIER) cc_final: 0.4833 (m90) REVERT: A 365 CYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7505 (m) REVERT: A 408 ASP cc_start: 0.8038 (t70) cc_final: 0.7432 (t0) REVERT: A 454 ASN cc_start: 0.8099 (p0) cc_final: 0.7873 (p0) REVERT: A 517 ARG cc_start: 0.8705 (ttm110) cc_final: 0.8498 (ttp-110) REVERT: A 524 VAL cc_start: 0.7858 (p) cc_final: 0.7558 (t) REVERT: A 528 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 544 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7275 (mt-10) REVERT: A 578 SER cc_start: 0.8261 (m) cc_final: 0.8035 (p) REVERT: A 582 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6823 (mt-10) REVERT: A 620 LEU cc_start: 0.8245 (tp) cc_final: 0.8017 (tt) REVERT: A 659 MET cc_start: 0.8235 (mmm) cc_final: 0.7747 (mmm) REVERT: A 823 SER cc_start: 0.8746 (t) cc_final: 0.8414 (p) REVERT: A 911 GLU cc_start: 0.7358 (pm20) cc_final: 0.7012 (pm20) REVERT: A 920 GLU cc_start: 0.7308 (mt-10) cc_final: 0.7084 (mt-10) REVERT: A 968 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 1011 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8037 (ttm170) REVERT: B 372 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7162 (mt-10) REVERT: B 435 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.6551 (t) REVERT: B 569 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7271 (t-90) REVERT: B 661 ASP cc_start: 0.7742 (m-30) cc_final: 0.7505 (m-30) REVERT: B 676 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7057 (mp10) REVERT: B 718 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.4994 (tt0) REVERT: B 720 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6541 (ptm160) outliers start: 57 outliers final: 43 residues processed: 282 average time/residue: 0.0971 time to fit residues: 37.4470 Evaluate side-chains 305 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 253 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 720 ARG Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 888 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 118 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 123 optimal weight: 0.0060 chunk 71 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 89 optimal weight: 0.0970 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS B 357 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS B 736 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.144628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121512 restraints weight = 15749.438| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.04 r_work: 0.3459 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10909 Z= 0.145 Angle : 0.618 12.080 14829 Z= 0.316 Chirality : 0.045 0.258 1580 Planarity : 0.004 0.049 1915 Dihedral : 5.796 59.310 1689 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.61 % Allowed : 21.37 % 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: -1.05 (0.21), residues: 1374 helix: 1.02 (0.43), residues: 165 sheet: -0.48 (0.34), residues: 216 loop : -1.11 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 913 TYR 0.007 0.001 TYR A 843 PHE 0.010 0.001 PHE B 283 TRP 0.047 0.001 TRP A 847 HIS 0.005 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (10848) covalent geometry : angle 0.59045 / 0.31 (14696) SS BOND : bond 0.00377 / 0.22 ( 50) SS BOND : angle 0.87753 / 0.61 ( 100) hydrogen bonds : bond 0.03295 / 2.24 ( 293) hydrogen bonds : angle 4.29053 / 2.99 ( 942) link_BETA1-4 : bond 0.00807 / 0.41 ( 5) link_BETA1-4 : angle 4.52379 / 2.46 ( 15) link_NAG-ASN : bond 0.00416 / 0.23 ( 6) link_NAG-ASN : angle 2.91406 / 1.79 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2326.92 seconds wall clock time: 40 minutes 32.39 seconds (2432.39 seconds total)