Starting phenix.real_space_refine on Wed Sep 17 19:23:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hel_52080/09_2025/9hel_52080.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hel_52080/09_2025/9hel_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_52080/09_2025/9hel_52080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hel_52080/09_2025/9hel_52080.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hel_52080/09_2025/9hel_52080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hel_52080/09_2025/9hel_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-2.0-5805/lib/python3.9/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, 31 Unusual residues: {' CA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 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: 2.37, per 1000 atoms: 0.22 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: 1.16 Conformation dependent library (CDL) restraints added in 575.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.55 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: 2.58 Time building geometry restraints manager: 1.45 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 2.510 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: 13.150 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.660 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 aren 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 covalent geometry : bond 0.00330 (10848) covalent geometry : angle 0.65522 (14696) SS BOND : bond 0.00363 ( 50) SS BOND : angle 0.96845 ( 100) hydrogen bonds : bond 0.13625 ( 293) hydrogen bonds : angle 5.26925 ( 942) link_BETA1-4 : bond 0.00845 ( 5) link_BETA1-4 : angle 4.23734 ( 15) link_NAG-ASN : bond 0.00385 ( 6) link_NAG-ASN : angle 2.79940 ( 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 : 0.444 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: 0.1351 time to fit residues: 45.6459 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 : 0.402 ------------------------------------------------------------------------------- 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: 0.9980 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3921 r_free = 0.3921 target = 0.144982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.121751 restraints weight = 15678.030| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.01 r_work: 0.3458 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.0686 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= 0.215 Angle : 0.658 13.379 14829 Z= 0.338 Chirality : 0.047 0.279 1580 Planarity : 0.005 0.064 1915 Dihedral : 7.981 57.410 1694 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.46 % Allowed : 20.74 % 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 aren not related in a simple way. whole: -1.17 (0.21), residues: 1374 helix: 0.82 (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 0.007 0.001 ARG A 838 TYR 0.010 0.002 TYR B 465 PHE 0.008 0.001 PHE B 842 TRP 0.018 0.002 TRP A 847 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00484 (10848) covalent geometry : angle 0.62661 (14696) SS BOND : bond 0.00492 ( 50) SS BOND : angle 1.01786 ( 100) hydrogen bonds : bond 0.04278 ( 293) hydrogen bonds : angle 4.66000 ( 942) link_BETA1-4 : bond 0.00878 ( 5) link_BETA1-4 : angle 4.94169 ( 15) link_NAG-ASN : bond 0.00478 ( 6) link_NAG-ASN : angle 3.20178 ( 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 292 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 CYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7583 (m) REVERT: A 405 LYS cc_start: 0.8742 (ttpp) cc_final: 0.8480 (ttpp) REVERT: A 408 ASP cc_start: 0.7959 (t0) cc_final: 0.7730 (t0) REVERT: A 446 GLU cc_start: 0.8284 (mp0) cc_final: 0.7899 (mp0) REVERT: A 578 SER cc_start: 0.8260 (m) cc_final: 0.7956 (p) REVERT: A 620 LEU cc_start: 0.8245 (tp) cc_final: 0.7976 (tt) REVERT: A 968 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 290 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7601 (mt) REVERT: B 502 ILE cc_start: 0.7935 (mt) cc_final: 0.7354 (tt) REVERT: B 847 TRP cc_start: 0.8172 (m100) cc_final: 0.7962 (m100) REVERT: B 872 LYS cc_start: 0.7953 (mttt) cc_final: 0.7576 (mmtt) outliers start: 39 outliers final: 22 residues processed: 274 average time/residue: 0.1302 time to fit residues: 48.3011 Evaluate side-chains 262 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS 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: 2.9990 chunk 134 optimal weight: 0.0970 chunk 19 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 91 optimal weight: 0.0870 chunk 96 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.1980 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 425 GLN A 618 HIS A 648 HIS B 357 HIS B 358 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.146295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123002 restraints weight = 15723.661| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.02 r_work: 0.3488 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10909 Z= 0.124 Angle : 0.594 12.071 14829 Z= 0.306 Chirality : 0.045 0.258 1580 Planarity : 0.004 0.055 1915 Dihedral : 6.362 59.233 1689 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.34 % Allowed : 19.24 % Favored : 76.42 % 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 aren not related in a simple way. whole: -1.05 (0.21), residues: 1374 helix: 0.87 (0.43), residues: 166 sheet: -0.27 (0.34), residues: 221 loop : -1.14 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 825 TYR 0.008 0.001 TYR B 465 PHE 0.008 0.001 PHE B 842 TRP 0.027 0.001 TRP A 847 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00281 (10848) covalent geometry : angle 0.56304 (14696) SS BOND : bond 0.00356 ( 50) SS BOND : angle 0.94748 ( 100) hydrogen bonds : bond 0.03505 ( 293) hydrogen bonds : angle 4.35623 ( 942) link_BETA1-4 : bond 0.00734 ( 5) link_BETA1-4 : angle 4.72176 ( 15) link_NAG-ASN : bond 0.00411 ( 6) link_NAG-ASN : angle 2.92701 ( 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: 49 poor density : 248 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5274 (mm-30) REVERT: A 365 CYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7391 (m) REVERT: A 405 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8479 (ttpp) REVERT: A 408 ASP cc_start: 0.7934 (t0) cc_final: 0.7616 (t0) REVERT: A 446 GLU cc_start: 0.8286 (mp0) cc_final: 0.7701 (mp0) REVERT: A 578 SER cc_start: 0.8212 (m) cc_final: 0.7864 (p) REVERT: A 620 LEU cc_start: 0.8233 (tp) cc_final: 0.8007 (tt) REVERT: A 968 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 1011 ARG cc_start: 0.8345 (ttm170) cc_final: 0.8017 (ttm170) REVERT: B 502 ILE cc_start: 0.7985 (mt) cc_final: 0.7369 (tp) REVERT: B 847 TRP cc_start: 0.8164 (m100) cc_final: 0.7946 (m100) REVERT: B 872 LYS cc_start: 0.7918 (mttt) cc_final: 0.7591 (mttt) outliers start: 49 outliers final: 28 residues processed: 275 average time/residue: 0.1290 time to fit residues: 48.0226 Evaluate side-chains 262 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 252 GLU 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 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 886 ILE 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 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 621 CYS Chi-restraints excluded: chain B residue 630 LEU 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: 1.9990 chunk 35 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 49 optimal weight: 0.0000 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 495 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 = 0.3922 r_free = 0.3922 target = 0.145313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.121737 restraints weight = 15768.918| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.14 r_work: 0.3458 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10909 Z= 0.174 Angle : 0.602 12.099 14829 Z= 0.312 Chirality : 0.045 0.267 1580 Planarity : 0.004 0.050 1915 Dihedral : 6.040 57.889 1689 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.70 % Allowed : 19.24 % Favored : 76.06 % 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 aren not related in a simple way. whole: -1.03 (0.21), residues: 1374 helix: 0.88 (0.42), residues: 166 sheet: -0.16 (0.34), residues: 217 loop : -1.15 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 825 TYR 0.008 0.001 TYR B 465 PHE 0.008 0.001 PHE B 842 TRP 0.043 0.001 TRP A 847 HIS 0.007 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00395 (10848) covalent geometry : angle 0.57007 (14696) SS BOND : bond 0.00523 ( 50) SS BOND : angle 1.05653 ( 100) hydrogen bonds : bond 0.03559 ( 293) hydrogen bonds : angle 4.35139 ( 942) link_BETA1-4 : bond 0.00808 ( 5) link_BETA1-4 : angle 4.66553 ( 15) link_NAG-ASN : bond 0.00421 ( 6) link_NAG-ASN : angle 2.97662 ( 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 296 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 HIS cc_start: 0.6205 (OUTLIER) cc_final: 0.4630 (m-70) REVERT: A 252 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.6033 (mm-30) REVERT: A 365 CYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7398 (m) REVERT: A 405 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8500 (ttpp) REVERT: A 446 GLU cc_start: 0.8268 (mp0) cc_final: 0.7653 (mp0) REVERT: A 578 SER cc_start: 0.8273 (m) cc_final: 0.8015 (p) REVERT: A 597 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7264 (mt-10) REVERT: A 968 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 1011 ARG cc_start: 0.8372 (ttm170) cc_final: 0.7988 (ttm170) REVERT: B 372 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7136 (mt-10) REVERT: B 435 THR cc_start: 0.7408 (OUTLIER) cc_final: 0.6368 (t) REVERT: B 502 ILE cc_start: 0.8073 (mt) cc_final: 0.7494 (tt) REVERT: B 661 ASP cc_start: 0.7734 (m-30) cc_final: 0.7471 (m-30) REVERT: B 746 ASP cc_start: 0.7529 (m-30) cc_final: 0.7250 (m-30) REVERT: B 847 TRP cc_start: 0.8181 (m100) cc_final: 0.7932 (m100) REVERT: B 872 LYS cc_start: 0.7941 (mttt) cc_final: 0.7596 (mttt) outliers start: 53 outliers final: 35 residues processed: 275 average time/residue: 0.1290 time to fit residues: 48.2312 Evaluate side-chains 281 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 252 GLU 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 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 264 LEU 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 430 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 CYS 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 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 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 886 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 26 optimal weight: 0.6980 chunk 125 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 495 HIS B 357 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.144373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120898 restraints weight = 15700.503| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.12 r_work: 0.3449 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10909 Z= 0.195 Angle : 0.622 12.342 14829 Z= 0.319 Chirality : 0.046 0.269 1580 Planarity : 0.004 0.050 1915 Dihedral : 5.960 56.841 1689 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.14 % Allowed : 19.33 % Favored : 75.53 % 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 aren not related in a simple way. whole: -1.04 (0.21), residues: 1374 helix: 0.89 (0.42), residues: 166 sheet: -0.28 (0.35), residues: 208 loop : -1.13 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 913 TYR 0.010 0.001 TYR B 465 PHE 0.009 0.001 PHE B 842 TRP 0.026 0.001 TRP A 847 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00441 (10848) covalent geometry : angle 0.59039 (14696) SS BOND : bond 0.00578 ( 50) SS BOND : angle 1.08670 ( 100) hydrogen bonds : bond 0.03614 ( 293) hydrogen bonds : angle 4.39101 ( 942) link_BETA1-4 : bond 0.00810 ( 5) link_BETA1-4 : angle 4.68654 ( 15) link_NAG-ASN : bond 0.00444 ( 6) link_NAG-ASN : angle 3.02573 ( 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 306 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 HIS cc_start: 0.6251 (OUTLIER) cc_final: 0.4623 (m-70) REVERT: A 252 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5761 (mm-30) REVERT: A 365 CYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7559 (m) REVERT: A 405 LYS cc_start: 0.8718 (ttpp) cc_final: 0.8495 (ttpp) REVERT: A 578 SER cc_start: 0.8271 (m) cc_final: 0.8020 (p) REVERT: A 582 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6842 (mt-10) REVERT: A 597 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7266 (mt-10) REVERT: A 823 SER cc_start: 0.8757 (t) cc_final: 0.8408 (p) REVERT: A 968 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7513 (tm-30) REVERT: A 1011 ARG cc_start: 0.8358 (ttm170) cc_final: 0.8039 (ttm170) REVERT: B 372 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7140 (mt-10) REVERT: B 405 LYS cc_start: 0.8414 (tttp) cc_final: 0.8056 (tptp) REVERT: B 435 THR cc_start: 0.7438 (OUTLIER) cc_final: 0.6431 (t) REVERT: B 661 ASP cc_start: 0.7741 (m-30) cc_final: 0.7478 (m-30) REVERT: B 746 ASP cc_start: 0.7552 (m-30) cc_final: 0.7197 (m-30) REVERT: B 847 TRP cc_start: 0.8166 (m100) cc_final: 0.7906 (m100) outliers start: 58 outliers final: 39 residues processed: 278 average time/residue: 0.1308 time to fit residues: 49.4598 Evaluate side-chains 288 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 252 GLU 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 386 VAL 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 495 HIS 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 453 LYS Chi-restraints excluded: chain B residue 466 GLU 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 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 886 ILE Chi-restraints excluded: chain B residue 888 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 74 optimal weight: 0.4980 chunk 130 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 86 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 104 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 495 HIS B 357 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.145017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121492 restraints weight = 15879.396| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.13 r_work: 0.3450 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10909 Z= 0.158 Angle : 0.607 12.028 14829 Z= 0.312 Chirality : 0.045 0.262 1580 Planarity : 0.004 0.049 1915 Dihedral : 5.856 58.201 1689 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.23 % Allowed : 19.41 % Favored : 75.35 % 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 aren not related in a simple way. whole: -1.01 (0.21), residues: 1374 helix: 0.92 (0.42), residues: 166 sheet: -0.23 (0.35), residues: 217 loop : -1.12 (0.18), residues: 991 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 0.008 0.001 PHE B 842 TRP 0.016 0.001 TRP A 847 HIS 0.011 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00360 (10848) covalent geometry : angle 0.57656 (14696) SS BOND : bond 0.00433 ( 50) SS BOND : angle 1.03484 ( 100) hydrogen bonds : bond 0.03420 ( 293) hydrogen bonds : angle 4.29819 ( 942) link_BETA1-4 : bond 0.00778 ( 5) link_BETA1-4 : angle 4.58522 ( 15) link_NAG-ASN : bond 0.00398 ( 6) link_NAG-ASN : angle 2.91044 ( 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 311 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 252 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TRP cc_start: 0.6492 (m100) cc_final: 0.6067 (m100) REVERT: A 250 HIS cc_start: 0.6225 (OUTLIER) cc_final: 0.4541 (m-70) REVERT: A 252 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5539 (mm-30) REVERT: A 365 CYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7555 (m) REVERT: A 396 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8237 (mmtp) REVERT: A 408 ASP cc_start: 0.8051 (t70) cc_final: 0.7480 (t0) REVERT: A 454 ASN cc_start: 0.8134 (p0) cc_final: 0.7848 (p0) REVERT: A 517 ARG cc_start: 0.8581 (ttp-110) cc_final: 0.8327 (ttp-110) REVERT: A 578 SER cc_start: 0.8294 (m) cc_final: 0.8035 (p) REVERT: A 582 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6841 (mt-10) REVERT: A 823 SER cc_start: 0.8763 (t) cc_final: 0.8409 (p) REVERT: A 911 GLU cc_start: 0.7135 (pm20) cc_final: 0.6883 (pm20) REVERT: A 968 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 997 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7932 (mttt) REVERT: A 1011 ARG cc_start: 0.8344 (ttm170) cc_final: 0.7997 (ttm170) REVERT: B 372 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7138 (mt-10) REVERT: B 405 LYS cc_start: 0.8453 (tttp) cc_final: 0.8116 (tptp) REVERT: B 661 ASP cc_start: 0.7758 (m-30) cc_final: 0.7502 (m-30) REVERT: B 676 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: B 847 TRP cc_start: 0.8177 (m100) cc_final: 0.7930 (m100) outliers start: 59 outliers final: 41 residues processed: 285 average time/residue: 0.1254 time to fit residues: 48.7759 Evaluate side-chains 289 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 252 GLU 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 386 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 484 ASP 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 997 LYS 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 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 442 CYS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 471 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS B 357 HIS B 358 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.143402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120047 restraints weight = 15766.037| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.11 r_work: 0.3436 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10909 Z= 0.255 Angle : 0.660 12.922 14829 Z= 0.342 Chirality : 0.048 0.280 1580 Planarity : 0.004 0.052 1915 Dihedral : 6.033 55.742 1689 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.67 % Allowed : 18.97 % Favored : 75.35 % 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 aren not related in a simple way. whole: -1.16 (0.21), residues: 1374 helix: 0.87 (0.42), residues: 166 sheet: -0.40 (0.34), residues: 216 loop : -1.21 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 913 TYR 0.010 0.002 TYR B 465 PHE 0.016 0.001 PHE B 283 TRP 0.019 0.002 TRP A 847 HIS 0.016 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00573 (10848) covalent geometry : angle 0.62811 (14696) SS BOND : bond 0.00584 ( 50) SS BOND : angle 1.20496 ( 100) hydrogen bonds : bond 0.03854 ( 293) hydrogen bonds : angle 4.45736 ( 942) link_BETA1-4 : bond 0.00821 ( 5) link_BETA1-4 : angle 4.80319 ( 15) link_NAG-ASN : bond 0.00498 ( 6) link_NAG-ASN : angle 3.14961 ( 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 323 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 259 time to evaluate : 0.414 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: 0.6406 (OUTLIER) cc_final: 0.4690 (m-70) REVERT: A 365 CYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7577 (m) REVERT: A 408 ASP cc_start: 0.8072 (t70) cc_final: 0.7468 (t0) REVERT: A 436 TRP cc_start: 0.8696 (m100) cc_final: 0.8468 (m100) REVERT: A 454 ASN cc_start: 0.8103 (p0) cc_final: 0.7824 (p0) REVERT: A 460 LEU cc_start: 0.8358 (mp) cc_final: 0.8151 (mp) REVERT: A 517 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8320 (ttp-110) REVERT: A 578 SER cc_start: 0.8277 (m) cc_final: 0.8035 (p) REVERT: A 582 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: A 823 SER cc_start: 0.8773 (t) cc_final: 0.8434 (p) REVERT: A 911 GLU cc_start: 0.7216 (pm20) cc_final: 0.6894 (pm20) REVERT: A 918 SER cc_start: 0.8688 (m) cc_final: 0.8298 (t) REVERT: A 968 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7564 (tm-30) REVERT: A 1011 ARG cc_start: 0.8374 (ttm170) cc_final: 0.8151 (ttm170) REVERT: B 372 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7175 (mt-10) REVERT: B 435 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.6531 (t) REVERT: B 676 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7044 (mp10) outliers start: 64 outliers final: 47 residues processed: 294 average time/residue: 0.1243 time to fit residues: 49.8717 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 : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 MET 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 365 CYS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 452 CYS 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 527 ILE 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 647 ARG 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 19 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 7 optimal weight: 0.0570 chunk 23 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS B 357 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 736 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.144126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120829 restraints weight = 15599.840| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.08 r_work: 0.3453 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10909 Z= 0.190 Angle : 0.643 12.626 14829 Z= 0.329 Chirality : 0.046 0.265 1580 Planarity : 0.004 0.050 1915 Dihedral : 5.983 57.919 1689 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.88 % Allowed : 19.86 % Favored : 75.27 % 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 aren not related in a simple way. whole: -1.13 (0.21), residues: 1374 helix: 0.91 (0.42), residues: 166 sheet: -0.43 (0.34), residues: 216 loop : -1.18 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 913 TYR 0.009 0.001 TYR A 843 PHE 0.016 0.001 PHE B 283 TRP 0.067 0.002 TRP A 847 HIS 0.010 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00428 (10848) covalent geometry : angle 0.61131 (14696) SS BOND : bond 0.00511 ( 50) SS BOND : angle 1.17005 ( 100) hydrogen bonds : bond 0.03616 ( 293) hydrogen bonds : angle 4.39547 ( 942) link_BETA1-4 : bond 0.00789 ( 5) link_BETA1-4 : angle 4.74701 ( 15) link_NAG-ASN : bond 0.00449 ( 6) link_NAG-ASN : angle 3.07315 ( 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 312 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 257 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TRP cc_start: 0.6540 (m100) cc_final: 0.6151 (m100) REVERT: A 365 CYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7534 (m) REVERT: A 408 ASP cc_start: 0.7997 (t70) cc_final: 0.7415 (t0) REVERT: A 436 TRP cc_start: 0.8683 (m100) cc_final: 0.8441 (m100) REVERT: A 454 ASN cc_start: 0.8078 (p0) cc_final: 0.7805 (p0) REVERT: A 517 ARG cc_start: 0.8576 (ttp-110) cc_final: 0.8320 (ttp-110) REVERT: A 528 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8332 (mt) REVERT: A 578 SER cc_start: 0.8278 (m) cc_final: 0.8031 (p) REVERT: A 582 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6823 (mt-10) REVERT: A 823 SER cc_start: 0.8759 (t) cc_final: 0.8410 (p) REVERT: A 911 GLU cc_start: 0.7240 (pm20) cc_final: 0.6932 (pm20) REVERT: A 918 SER cc_start: 0.8671 (m) cc_final: 0.8275 (t) REVERT: A 968 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 1011 ARG cc_start: 0.8369 (ttm170) cc_final: 0.8012 (ttm170) REVERT: B 372 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7153 (mt-10) REVERT: B 435 THR cc_start: 0.7469 (OUTLIER) cc_final: 0.6545 (t) REVERT: B 676 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.7039 (mp10) outliers start: 55 outliers final: 44 residues processed: 285 average time/residue: 0.1293 time to fit residues: 50.2175 Evaluate side-chains 299 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 250 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 365 CYS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 452 CYS 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 647 ARG 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 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 85 optimal weight: 0.0170 chunk 41 optimal weight: 0.0470 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 105 optimal weight: 0.5980 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS B 736 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.145793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122588 restraints weight = 15708.629| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.09 r_work: 0.3465 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1651 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= 0.118 Angle : 0.610 11.538 14829 Z= 0.312 Chirality : 0.044 0.248 1580 Planarity : 0.004 0.048 1915 Dihedral : 5.755 59.830 1689 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.88 % Allowed : 20.30 % Favored : 74.82 % 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 aren not related in a simple way. whole: -0.96 (0.21), residues: 1374 helix: 1.05 (0.43), residues: 165 sheet: -0.38 (0.35), residues: 216 loop : -1.05 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 825 TYR 0.008 0.001 TYR A 843 PHE 0.025 0.001 PHE A 842 TRP 0.076 0.001 TRP A 847 HIS 0.011 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00267 (10848) covalent geometry : angle 0.58175 (14696) SS BOND : bond 0.00340 ( 50) SS BOND : angle 1.02088 ( 100) hydrogen bonds : bond 0.03234 ( 293) hydrogen bonds : angle 4.21934 ( 942) link_BETA1-4 : bond 0.00802 ( 5) link_BETA1-4 : angle 4.41067 ( 15) link_NAG-ASN : bond 0.00389 ( 6) link_NAG-ASN : angle 2.80548 ( 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 306 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 251 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TRP cc_start: 0.6588 (m100) cc_final: 0.6165 (m100) REVERT: A 365 CYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7515 (m) REVERT: A 408 ASP cc_start: 0.7968 (t70) cc_final: 0.7407 (t0) REVERT: A 436 TRP cc_start: 0.8670 (m100) cc_final: 0.8383 (m100) REVERT: A 454 ASN cc_start: 0.8085 (p0) cc_final: 0.7817 (p0) REVERT: A 517 ARG cc_start: 0.8598 (ttp-110) cc_final: 0.8315 (ttp-110) REVERT: A 528 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8330 (mt) REVERT: A 578 SER cc_start: 0.8265 (m) cc_final: 0.8005 (p) REVERT: A 582 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: A 620 LEU cc_start: 0.8217 (tp) cc_final: 0.7990 (tt) REVERT: A 911 GLU cc_start: 0.7325 (pm20) cc_final: 0.6988 (pm20) REVERT: A 918 SER cc_start: 0.8649 (m) cc_final: 0.8264 (t) REVERT: A 968 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 992 TRP cc_start: 0.7811 (m100) cc_final: 0.7459 (m100) REVERT: A 1011 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7923 (ttm170) REVERT: B 372 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7140 (mt-10) REVERT: B 435 THR cc_start: 0.7418 (OUTLIER) cc_final: 0.6430 (t) REVERT: B 569 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.7289 (t-90) REVERT: B 661 ASP cc_start: 0.7744 (m-30) cc_final: 0.7495 (m-30) REVERT: B 676 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.7023 (mp10) REVERT: B 847 TRP cc_start: 0.8172 (m100) cc_final: 0.7951 (m100) outliers start: 55 outliers final: 39 residues processed: 279 average time/residue: 0.1272 time to fit residues: 48.5039 Evaluate side-chains 291 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 365 CYS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 452 CYS 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 647 ARG 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 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 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 671 LEU Chi-restraints excluded: chain B residue 676 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 120 optimal weight: 0.8980 chunk 121 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 51 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 546 GLN ** 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 = 0.3903 r_free = 0.3903 target = 0.143966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.121205 restraints weight = 15716.652| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.08 r_work: 0.3445 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10909 Z= 0.170 Angle : 0.636 11.648 14829 Z= 0.324 Chirality : 0.045 0.269 1580 Planarity : 0.004 0.073 1915 Dihedral : 5.782 56.901 1689 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 4.52 % Allowed : 21.10 % 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 aren not related in a simple way. whole: -0.99 (0.21), residues: 1374 helix: 1.00 (0.42), residues: 166 sheet: -0.40 (0.35), residues: 216 loop : -1.07 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 825 TYR 0.010 0.001 TYR A 843 PHE 0.018 0.001 PHE A 842 TRP 0.076 0.002 TRP A 847 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00386 (10848) covalent geometry : angle 0.60763 (14696) SS BOND : bond 0.00432 ( 50) SS BOND : angle 1.12725 ( 100) hydrogen bonds : bond 0.03443 ( 293) hydrogen bonds : angle 4.29648 ( 942) link_BETA1-4 : bond 0.00796 ( 5) link_BETA1-4 : angle 4.37817 ( 15) link_NAG-ASN : bond 0.00396 ( 6) link_NAG-ASN : angle 2.89522 ( 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 299 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 0.436 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 365 CYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7522 (m) REVERT: A 408 ASP cc_start: 0.8011 (t70) cc_final: 0.7440 (t0) REVERT: A 436 TRP cc_start: 0.8698 (m100) cc_final: 0.8453 (m100) REVERT: A 454 ASN cc_start: 0.8041 (p0) cc_final: 0.7774 (p0) REVERT: A 517 ARG cc_start: 0.8593 (ttp-110) cc_final: 0.8315 (ttp-110) REVERT: A 528 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8339 (mt) REVERT: A 578 SER cc_start: 0.8282 (m) cc_final: 0.8026 (p) REVERT: A 582 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: A 620 LEU cc_start: 0.8232 (tp) cc_final: 0.8006 (tt) REVERT: A 823 SER cc_start: 0.8743 (t) cc_final: 0.8386 (p) REVERT: A 911 GLU cc_start: 0.7406 (pm20) cc_final: 0.7039 (pm20) REVERT: A 918 SER cc_start: 0.8642 (m) cc_final: 0.8256 (t) REVERT: A 968 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7435 (tm-30) REVERT: A 1011 ARG cc_start: 0.8323 (ttm170) cc_final: 0.7951 (ttm170) REVERT: B 344 GLN cc_start: 0.8320 (mm110) cc_final: 0.8064 (mm-40) REVERT: B 372 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7158 (mt-10) REVERT: B 435 THR cc_start: 0.7425 (OUTLIER) cc_final: 0.6446 (t) REVERT: B 569 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7277 (t-90) REVERT: B 610 SER cc_start: 0.8687 (t) cc_final: 0.8468 (p) REVERT: B 661 ASP cc_start: 0.7786 (m-30) cc_final: 0.7551 (m-30) REVERT: B 676 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: B 876 ASN cc_start: 0.6865 (t0) cc_final: 0.6281 (t0) outliers start: 51 outliers final: 40 residues processed: 273 average time/residue: 0.1314 time to fit residues: 48.4645 Evaluate side-chains 294 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 365 CYS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 452 CYS 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 647 ARG 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 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 435 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 453 LYS 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 671 LEU Chi-restraints excluded: chain B residue 676 GLN 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 118 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 8 optimal weight: 0.0170 chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 0.0070 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 546 GLN B 327 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.143208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.120784 restraints weight = 15961.452| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.99 r_work: 0.3461 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10909 Z= 0.193 Angle : 0.649 11.978 14829 Z= 0.332 Chirality : 0.046 0.268 1580 Planarity : 0.004 0.068 1915 Dihedral : 5.850 56.236 1689 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 4.61 % Allowed : 21.10 % Favored : 74.29 % 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 aren not related in a simple way. whole: -1.04 (0.21), residues: 1374 helix: 1.00 (0.42), residues: 166 sheet: -0.47 (0.35), residues: 216 loop : -1.10 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 825 TYR 0.008 0.001 TYR B 465 PHE 0.021 0.001 PHE B 283 TRP 0.069 0.002 TRP A 847 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00437 (10848) covalent geometry : angle 0.61983 (14696) SS BOND : bond 0.00474 ( 50) SS BOND : angle 1.17145 ( 100) hydrogen bonds : bond 0.03560 ( 293) hydrogen bonds : angle 4.37952 ( 942) link_BETA1-4 : bond 0.00785 ( 5) link_BETA1-4 : angle 4.51163 ( 15) link_NAG-ASN : bond 0.00475 ( 6) link_NAG-ASN : angle 3.00958 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3012.09 seconds wall clock time: 52 minutes 30.74 seconds (3150.74 seconds total)