Starting phenix.real_space_refine on Mon Jul 28 22:00:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hel_52080/07_2025/9hel_52080.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hel_52080/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9hel_52080/07_2025/9hel_52080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hel_52080/07_2025/9hel_52080.map" model { file = "/net/cci-nas-00/data/ceres_data/9hel_52080/07_2025/9hel_52080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hel_52080/07_2025/9hel_52080.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.07, per 1000 atoms: 0.85 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: 3.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 4.11 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: 5.46 Time building geometry restraints manager: 4.25 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: 104.130 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 36.700 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.100 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.045 0.002 TRP A 847 HIS 0.007 0.001 HIS A 348 PHE 0.012 0.001 PHE A 507 TYR 0.009 0.001 TYR B 580 ARG 0.026 0.001 ARG B 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 6) link_NAG-ASN : angle 2.79940 ( 18) link_BETA1-4 : bond 0.00845 ( 5) link_BETA1-4 : angle 4.23734 ( 15) hydrogen bonds : bond 0.13625 ( 293) hydrogen bonds : angle 5.26925 ( 942) SS BOND : bond 0.00363 ( 50) SS BOND : angle 0.96845 ( 100) covalent geometry : bond 0.00330 (10848) covalent geometry : angle 0.65522 (14696) *********************** 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 : 1.068 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: 0.3518 time to fit residues: 118.1490 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 : 1.633 ------------------------------------------------------------------------------- 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 115 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.144687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121213 restraints weight = 15693.692| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.09 r_work: 0.3457 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.0749 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= 0.223 Angle : 0.666 13.614 14829 Z= 0.341 Chirality : 0.047 0.283 1580 Planarity : 0.005 0.064 1915 Dihedral : 7.793 57.160 1694 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.81 % Allowed : 20.57 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1374 helix: 0.79 (0.42), residues: 166 sheet: -0.38 (0.33), residues: 235 loop : -1.25 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 847 HIS 0.006 0.001 HIS A 348 PHE 0.009 0.001 PHE B 842 TYR 0.011 0.002 TYR B 465 ARG 0.005 0.001 ARG B 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 6) link_NAG-ASN : angle 3.26002 ( 18) link_BETA1-4 : bond 0.00934 ( 5) link_BETA1-4 : angle 5.03233 ( 15) hydrogen bonds : bond 0.04265 ( 293) hydrogen bonds : angle 4.66634 ( 942) SS BOND : bond 0.00534 ( 50) SS BOND : angle 1.03224 ( 100) covalent geometry : bond 0.00504 (10848) covalent geometry : angle 0.63308 (14696) *********************** 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 301 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 CYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7581 (m) REVERT: A 405 LYS cc_start: 0.8746 (ttpp) cc_final: 0.8480 (ttpp) REVERT: A 408 ASP cc_start: 0.7956 (t0) cc_final: 0.7710 (t0) REVERT: A 446 GLU cc_start: 0.8297 (mp0) cc_final: 0.7910 (mp0) REVERT: A 578 SER cc_start: 0.8289 (m) cc_final: 0.7976 (p) REVERT: A 620 LEU cc_start: 0.8228 (tp) cc_final: 0.7960 (tt) REVERT: A 968 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7391 (tm-30) REVERT: B 290 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7590 (mt) REVERT: B 502 ILE cc_start: 0.7947 (mt) cc_final: 0.7354 (tt) REVERT: B 686 GLN cc_start: 0.7485 (tm-30) cc_final: 0.7277 (tm-30) REVERT: B 847 TRP cc_start: 0.8185 (m100) cc_final: 0.7950 (m100) REVERT: B 872 LYS cc_start: 0.7932 (mttt) cc_final: 0.7551 (mmtt) outliers start: 43 outliers final: 24 residues processed: 281 average time/residue: 0.2679 time to fit residues: 102.1375 Evaluate side-chains 269 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 569 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 914 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 95 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 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 = 0.3902 r_free = 0.3902 target = 0.143792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120372 restraints weight = 15876.078| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.10 r_work: 0.3444 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10909 Z= 0.237 Angle : 0.659 13.780 14829 Z= 0.339 Chirality : 0.048 0.280 1580 Planarity : 0.005 0.056 1915 Dihedral : 6.624 57.937 1689 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.14 % Allowed : 19.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1374 helix: 0.74 (0.42), residues: 166 sheet: -0.30 (0.33), residues: 223 loop : -1.26 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 847 HIS 0.006 0.001 HIS A 348 PHE 0.010 0.001 PHE B 842 TYR 0.012 0.002 TYR B 465 ARG 0.006 0.000 ARG B 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 6) link_NAG-ASN : angle 3.35044 ( 18) link_BETA1-4 : bond 0.00926 ( 5) link_BETA1-4 : angle 5.19612 ( 15) hydrogen bonds : bond 0.04112 ( 293) hydrogen bonds : angle 4.61112 ( 942) SS BOND : bond 0.00594 ( 50) SS BOND : angle 1.05721 ( 100) covalent geometry : bond 0.00534 (10848) covalent geometry : angle 0.62444 (14696) *********************** 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 317 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 259 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.5672 (mm-30) REVERT: A 365 CYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7514 (m) REVERT: A 446 GLU cc_start: 0.8270 (mp0) cc_final: 0.7856 (mp0) REVERT: A 578 SER cc_start: 0.8267 (m) cc_final: 0.7979 (p) REVERT: A 968 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7551 (tm-30) REVERT: A 1011 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8080 (ttm170) REVERT: B 290 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7601 (mt) REVERT: B 435 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.6488 (t) REVERT: B 686 GLN cc_start: 0.7634 (tm-30) cc_final: 0.7340 (tm-30) REVERT: B 847 TRP cc_start: 0.8182 (m100) cc_final: 0.7892 (m100) outliers start: 58 outliers final: 34 residues processed: 293 average time/residue: 0.2641 time to fit residues: 105.0092 Evaluate side-chains 286 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 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 539 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 290 ILE 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 485 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 914 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 47 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 74 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 618 HIS B 358 ASN B 736 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.143732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120312 restraints weight = 15632.872| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.09 r_work: 0.3446 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10909 Z= 0.219 Angle : 0.644 13.611 14829 Z= 0.331 Chirality : 0.047 0.278 1580 Planarity : 0.004 0.050 1915 Dihedral : 6.313 58.761 1689 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.50 % Allowed : 19.50 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1374 helix: 0.79 (0.42), residues: 166 sheet: -0.40 (0.34), residues: 214 loop : -1.26 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 847 HIS 0.008 0.001 HIS B 357 PHE 0.009 0.001 PHE B 842 TYR 0.011 0.001 TYR B 465 ARG 0.004 0.000 ARG B 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 6) link_NAG-ASN : angle 3.27862 ( 18) link_BETA1-4 : bond 0.00860 ( 5) link_BETA1-4 : angle 5.14574 ( 15) hydrogen bonds : bond 0.03887 ( 293) hydrogen bonds : angle 4.56152 ( 942) SS BOND : bond 0.00522 ( 50) SS BOND : angle 1.05251 ( 100) covalent geometry : bond 0.00494 (10848) covalent geometry : angle 0.60845 (14696) *********************** 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 314 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 252 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 HIS cc_start: 0.6334 (OUTLIER) cc_final: 0.4770 (m-70) REVERT: A 252 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.5659 (mm-30) REVERT: A 365 CYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7560 (m) REVERT: A 446 GLU cc_start: 0.8260 (mp0) cc_final: 0.7699 (mp0) REVERT: A 454 ASN cc_start: 0.8224 (p0) cc_final: 0.8020 (p0) REVERT: A 571 ARG cc_start: 0.8707 (mmm-85) cc_final: 0.8071 (mtm180) REVERT: A 578 SER cc_start: 0.8261 (m) cc_final: 0.7997 (p) REVERT: A 582 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6831 (mt-10) REVERT: A 597 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7299 (mt-10) REVERT: A 823 SER cc_start: 0.8758 (t) cc_final: 0.8431 (p) REVERT: A 968 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 1007 ASP cc_start: 0.7625 (m-30) cc_final: 0.7416 (m-30) REVERT: A 1011 ARG cc_start: 0.8404 (ttm170) cc_final: 0.8170 (ttm170) REVERT: B 290 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7602 (mt) REVERT: B 372 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7168 (mt-10) REVERT: B 686 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 746 ASP cc_start: 0.7595 (m-30) cc_final: 0.7302 (m-30) REVERT: B 791 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8223 (mtpm) REVERT: B 847 TRP cc_start: 0.8170 (m100) cc_final: 0.7905 (m100) outliers start: 62 outliers final: 39 residues processed: 290 average time/residue: 0.2755 time to fit residues: 109.6566 Evaluate side-chains 294 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 263 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 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 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 264 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 290 ILE 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 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 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 616 ASP 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 791 LYS Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 914 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 128 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.142367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118981 restraints weight = 15637.925| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.10 r_work: 0.3425 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10909 Z= 0.282 Angle : 0.693 14.467 14829 Z= 0.354 Chirality : 0.049 0.289 1580 Planarity : 0.005 0.054 1915 Dihedral : 6.390 57.478 1689 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.76 % Allowed : 19.50 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.21), residues: 1374 helix: 0.69 (0.41), residues: 166 sheet: -0.48 (0.34), residues: 216 loop : -1.36 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 847 HIS 0.006 0.001 HIS A 348 PHE 0.010 0.001 PHE B 842 TYR 0.012 0.002 TYR B 465 ARG 0.009 0.001 ARG B 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 6) link_NAG-ASN : angle 3.44008 ( 18) link_BETA1-4 : bond 0.00984 ( 5) link_BETA1-4 : angle 5.34333 ( 15) hydrogen bonds : bond 0.04166 ( 293) hydrogen bonds : angle 4.66874 ( 942) SS BOND : bond 0.00634 ( 50) SS BOND : angle 1.18500 ( 100) covalent geometry : bond 0.00630 (10848) covalent geometry : angle 0.65726 (14696) *********************** 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 327 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 262 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 HIS cc_start: 0.6456 (OUTLIER) cc_final: 0.4818 (m-70) REVERT: A 252 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5710 (mm-30) REVERT: A 408 ASP cc_start: 0.8069 (t70) cc_final: 0.7451 (t0) REVERT: A 446 GLU cc_start: 0.8182 (mp0) cc_final: 0.7668 (mp0) REVERT: A 494 LYS cc_start: 0.8426 (ttpp) cc_final: 0.8195 (ttpp) REVERT: A 524 VAL cc_start: 0.7826 (p) cc_final: 0.7561 (t) REVERT: A 578 SER cc_start: 0.8276 (m) cc_final: 0.8042 (p) REVERT: A 582 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6864 (mt-10) REVERT: A 597 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7342 (mt-10) REVERT: A 823 SER cc_start: 0.8762 (t) cc_final: 0.8431 (p) REVERT: A 849 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8423 (m) REVERT: A 968 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7592 (tm-30) REVERT: A 1011 ARG cc_start: 0.8403 (ttm170) cc_final: 0.8116 (ttm170) REVERT: B 290 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7654 (mt) REVERT: B 372 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7163 (mt-10) REVERT: B 435 THR cc_start: 0.7493 (OUTLIER) cc_final: 0.6538 (t) REVERT: B 502 ILE cc_start: 0.8119 (mt) cc_final: 0.7558 (tt) REVERT: B 686 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7516 (tm-30) REVERT: B 720 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7656 (ptt180) REVERT: B 746 ASP cc_start: 0.7656 (m-30) cc_final: 0.7297 (m-30) REVERT: B 791 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8257 (mtpm) REVERT: B 858 THR cc_start: 0.7106 (OUTLIER) cc_final: 0.6525 (p) outliers start: 65 outliers final: 44 residues processed: 299 average time/residue: 0.2795 time to fit residues: 114.6449 Evaluate side-chains 305 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 263 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 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 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 653 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 290 ILE 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 470 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 720 ARG Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 791 LYS Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 914 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 38 optimal weight: 0.0980 chunk 65 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 108 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 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 = 0.3895 r_free = 0.3895 target = 0.143163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119928 restraints weight = 15664.099| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.09 r_work: 0.3433 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10909 Z= 0.216 Angle : 0.660 14.102 14829 Z= 0.335 Chirality : 0.047 0.275 1580 Planarity : 0.004 0.051 1915 Dihedral : 6.269 59.660 1689 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.41 % Allowed : 20.48 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.21), residues: 1374 helix: 0.76 (0.42), residues: 166 sheet: -0.47 (0.34), residues: 216 loop : -1.34 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 847 HIS 0.010 0.001 HIS B 357 PHE 0.009 0.001 PHE A 638 TYR 0.009 0.001 TYR B 465 ARG 0.004 0.000 ARG B 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 6) link_NAG-ASN : angle 3.31628 ( 18) link_BETA1-4 : bond 0.00996 ( 5) link_BETA1-4 : angle 5.24066 ( 15) hydrogen bonds : bond 0.03826 ( 293) hydrogen bonds : angle 4.54852 ( 942) SS BOND : bond 0.00530 ( 50) SS BOND : angle 1.01946 ( 100) covalent geometry : bond 0.00485 (10848) covalent geometry : angle 0.62558 (14696) *********************** 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 315 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 254 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TRP cc_start: 0.6545 (m100) cc_final: 0.6116 (m100) REVERT: A 250 HIS cc_start: 0.6546 (OUTLIER) cc_final: 0.4863 (m-70) REVERT: A 408 ASP cc_start: 0.8025 (t70) cc_final: 0.7382 (t0) REVERT: A 524 VAL cc_start: 0.7833 (p) cc_final: 0.7554 (t) REVERT: A 528 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8336 (mt) REVERT: A 578 SER cc_start: 0.8284 (m) cc_final: 0.8048 (p) REVERT: A 579 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7668 (mtp180) REVERT: A 582 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6850 (mt-10) REVERT: A 823 SER cc_start: 0.8761 (t) cc_final: 0.8411 (p) REVERT: A 968 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 1011 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8061 (ttm170) REVERT: B 290 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7636 (mt) REVERT: B 372 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7154 (mt-10) REVERT: B 435 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.6562 (t) REVERT: B 502 ILE cc_start: 0.8168 (mt) cc_final: 0.7629 (tt) REVERT: B 686 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7517 (tm-30) REVERT: B 718 GLN cc_start: 0.6499 (OUTLIER) cc_final: 0.5050 (tt0) REVERT: B 720 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7618 (ptt180) REVERT: B 791 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8267 (mtpm) REVERT: B 858 THR cc_start: 0.7109 (OUTLIER) cc_final: 0.6535 (p) outliers start: 61 outliers final: 44 residues processed: 287 average time/residue: 0.2713 time to fit residues: 105.7464 Evaluate side-chains 306 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 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 509 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 290 ILE 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 470 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 720 ARG Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 791 LYS Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 914 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 125 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 104 optimal weight: 0.0670 chunk 34 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 0.0170 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 648 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS B 736 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122078 restraints weight = 15784.297| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.03 r_work: 0.3458 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10909 Z= 0.119 Angle : 0.606 12.861 14829 Z= 0.307 Chirality : 0.044 0.254 1580 Planarity : 0.004 0.049 1915 Dihedral : 5.909 58.339 1689 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1374 helix: 0.97 (0.42), residues: 166 sheet: -0.45 (0.34), residues: 220 loop : -1.21 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 847 HIS 0.012 0.001 HIS B 357 PHE 0.009 0.001 PHE A 979 TYR 0.006 0.001 TYR B 465 ARG 0.008 0.000 ARG B 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 6) link_NAG-ASN : angle 3.04149 ( 18) link_BETA1-4 : bond 0.00869 ( 5) link_BETA1-4 : angle 4.85140 ( 15) hydrogen bonds : bond 0.03273 ( 293) hydrogen bonds : angle 4.28538 ( 942) SS BOND : bond 0.00387 ( 50) SS BOND : angle 0.81509 ( 100) covalent geometry : bond 0.00269 (10848) covalent geometry : angle 0.57493 (14696) *********************** 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 312 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 CYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7446 (m) REVERT: A 408 ASP cc_start: 0.7966 (t70) cc_final: 0.7375 (t0) REVERT: A 443 ASN cc_start: 0.8339 (m110) cc_final: 0.7894 (m-40) REVERT: A 524 VAL cc_start: 0.7854 (p) cc_final: 0.7540 (t) REVERT: A 578 SER cc_start: 0.8269 (m) cc_final: 0.8032 (p) REVERT: A 579 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7678 (mtp180) REVERT: A 582 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: A 823 SER cc_start: 0.8738 (t) cc_final: 0.8402 (p) REVERT: A 968 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 1011 ARG cc_start: 0.8330 (ttm170) cc_final: 0.8015 (ttm170) REVERT: B 372 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7107 (mt-10) REVERT: B 435 THR cc_start: 0.7454 (OUTLIER) cc_final: 0.6461 (t) REVERT: B 686 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7484 (tm-30) REVERT: B 718 GLN cc_start: 0.6440 (OUTLIER) cc_final: 0.4997 (tt0) REVERT: B 791 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8238 (mtpm) REVERT: B 858 THR cc_start: 0.7127 (OUTLIER) cc_final: 0.6560 (p) outliers start: 52 outliers final: 33 residues processed: 285 average time/residue: 0.4042 time to fit residues: 155.1919 Evaluate side-chains 288 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 248 time to evaluate : 2.157 ------------------------------------------------------------------------------- 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 484 ASP Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 718 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 791 LYS Chi-restraints excluded: chain B residue 858 THR 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 58 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 129 optimal weight: 0.0980 chunk 123 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 736 HIS B 797 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.143438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.120728 restraints weight = 15686.289| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.05 r_work: 0.3433 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10909 Z= 0.175 Angle : 0.622 12.943 14829 Z= 0.317 Chirality : 0.046 0.269 1580 Planarity : 0.004 0.049 1915 Dihedral : 5.925 58.668 1689 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.32 % Allowed : 21.01 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1374 helix: 0.92 (0.42), residues: 166 sheet: -0.43 (0.34), residues: 216 loop : -1.22 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP A 847 HIS 0.004 0.001 HIS A 348 PHE 0.009 0.001 PHE A 842 TYR 0.008 0.001 TYR A 843 ARG 0.008 0.000 ARG B 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 6) link_NAG-ASN : angle 3.07099 ( 18) link_BETA1-4 : bond 0.00899 ( 5) link_BETA1-4 : angle 4.75808 ( 15) hydrogen bonds : bond 0.03511 ( 293) hydrogen bonds : angle 4.35233 ( 942) SS BOND : bond 0.00452 ( 50) SS BOND : angle 0.91434 ( 100) covalent geometry : bond 0.00396 (10848) covalent geometry : angle 0.59165 (14696) *********************** 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 314 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 254 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 HIS cc_start: 0.6429 (OUTLIER) cc_final: 0.4691 (m-70) REVERT: A 365 CYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7500 (m) REVERT: A 408 ASP cc_start: 0.8039 (t70) cc_final: 0.7391 (t0) REVERT: A 443 ASN cc_start: 0.8357 (m110) cc_final: 0.7887 (m-40) REVERT: A 494 LYS cc_start: 0.8436 (ttpp) cc_final: 0.8167 (ttpp) REVERT: A 517 ARG cc_start: 0.8692 (ttm110) cc_final: 0.8479 (ttp-110) REVERT: A 524 VAL cc_start: 0.7867 (p) cc_final: 0.7563 (t) REVERT: A 528 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8356 (mt) REVERT: A 578 SER cc_start: 0.8299 (m) cc_final: 0.8065 (p) REVERT: A 579 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7685 (mtp180) REVERT: A 582 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6858 (mt-10) REVERT: A 620 LEU cc_start: 0.8213 (tp) cc_final: 0.7968 (tt) REVERT: A 823 SER cc_start: 0.8778 (t) cc_final: 0.8430 (p) REVERT: A 918 SER cc_start: 0.8645 (m) cc_final: 0.8259 (t) REVERT: A 968 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7589 (tm-30) REVERT: A 1011 ARG cc_start: 0.8358 (ttm170) cc_final: 0.8033 (ttm170) REVERT: B 290 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7726 (mt) REVERT: B 372 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7187 (mt-10) REVERT: B 435 THR cc_start: 0.7431 (OUTLIER) cc_final: 0.6494 (t) REVERT: B 569 HIS cc_start: 0.7735 (OUTLIER) cc_final: 0.7208 (t-90) REVERT: B 661 ASP cc_start: 0.7765 (m-30) cc_final: 0.7519 (m-30) REVERT: B 676 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7088 (mp10) REVERT: B 686 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B 718 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.4947 (tt0) REVERT: B 791 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8242 (mtpm) REVERT: B 858 THR cc_start: 0.7152 (OUTLIER) cc_final: 0.6554 (p) outliers start: 60 outliers final: 42 residues processed: 287 average time/residue: 0.2624 time to fit residues: 101.7144 Evaluate side-chains 307 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 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 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 579 ARG Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 601 LEU 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 290 ILE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 718 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 791 LYS Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 886 ILE 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 94 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 0.0060 chunk 121 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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 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 = 0.144762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122466 restraints weight = 15931.982| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.96 r_work: 0.3482 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10909 Z= 0.132 Angle : 0.603 12.050 14829 Z= 0.307 Chirality : 0.045 0.259 1580 Planarity : 0.004 0.049 1915 Dihedral : 5.778 59.714 1689 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.41 % Allowed : 21.28 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1374 helix: 1.01 (0.43), residues: 165 sheet: -0.39 (0.35), residues: 216 loop : -1.14 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 847 HIS 0.004 0.001 HIS A 348 PHE 0.014 0.001 PHE A 842 TYR 0.006 0.001 TYR B 465 ARG 0.010 0.000 ARG B 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 6) link_NAG-ASN : angle 2.91748 ( 18) link_BETA1-4 : bond 0.00798 ( 5) link_BETA1-4 : angle 4.52319 ( 15) hydrogen bonds : bond 0.03220 ( 293) hydrogen bonds : angle 4.24356 ( 942) SS BOND : bond 0.00367 ( 50) SS BOND : angle 0.85341 ( 100) covalent geometry : bond 0.00301 (10848) covalent geometry : angle 0.57461 (14696) *********************** 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 317 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 256 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 HIS cc_start: 0.6422 (OUTLIER) cc_final: 0.4653 (m-70) REVERT: A 365 CYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7563 (m) REVERT: A 408 ASP cc_start: 0.7975 (t70) cc_final: 0.7413 (t0) REVERT: A 443 ASN cc_start: 0.8282 (m110) cc_final: 0.7847 (m-40) REVERT: A 494 LYS cc_start: 0.8458 (ttpp) cc_final: 0.8196 (ttpp) REVERT: A 517 ARG cc_start: 0.8731 (ttm110) cc_final: 0.8529 (ttp-110) REVERT: A 524 VAL cc_start: 0.7859 (p) cc_final: 0.7610 (t) REVERT: A 528 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8414 (mt) REVERT: A 544 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7386 (mt-10) REVERT: A 578 SER cc_start: 0.8262 (m) cc_final: 0.8036 (p) REVERT: A 579 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7703 (mtp180) REVERT: A 620 LEU cc_start: 0.8275 (tp) cc_final: 0.8013 (tt) REVERT: A 823 SER cc_start: 0.8782 (t) cc_final: 0.8433 (p) REVERT: A 918 SER cc_start: 0.8614 (m) cc_final: 0.8255 (t) REVERT: A 968 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7550 (tm-30) REVERT: A 992 TRP cc_start: 0.7814 (m100) cc_final: 0.7480 (m100) REVERT: A 1011 ARG cc_start: 0.8307 (ttm170) cc_final: 0.7932 (ttm170) REVERT: B 290 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7658 (mt) REVERT: B 372 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7088 (mt-10) REVERT: B 435 THR cc_start: 0.7419 (OUTLIER) cc_final: 0.6436 (t) REVERT: B 569 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7269 (t-90) REVERT: B 661 ASP cc_start: 0.7780 (m-30) cc_final: 0.7555 (m-30) REVERT: B 676 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7077 (mp10) REVERT: B 686 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7556 (tm-30) REVERT: B 718 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.4984 (tt0) REVERT: B 791 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8157 (mtpm) REVERT: B 847 TRP cc_start: 0.8151 (m100) cc_final: 0.7941 (m100) outliers start: 61 outliers final: 37 residues processed: 287 average time/residue: 0.2942 time to fit residues: 115.5055 Evaluate side-chains 296 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 249 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 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 469 LYS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 579 ARG 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 290 ILE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 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 569 HIS Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 791 LYS 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 134 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 95 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 618 HIS B 357 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 = 0.3903 r_free = 0.3903 target = 0.143260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120978 restraints weight = 15877.330| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.96 r_work: 0.3431 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10909 Z= 0.216 Angle : 0.657 12.736 14829 Z= 0.336 Chirality : 0.047 0.277 1580 Planarity : 0.004 0.050 1915 Dihedral : 5.927 56.407 1689 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.69 % Rotamer: Outliers : 4.61 % Allowed : 22.07 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1374 helix: 0.96 (0.42), residues: 166 sheet: -0.44 (0.34), residues: 216 loop : -1.19 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 847 HIS 0.005 0.001 HIS A 348 PHE 0.022 0.001 PHE B 283 TYR 0.008 0.001 TYR B 580 ARG 0.010 0.000 ARG B 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 6) link_NAG-ASN : angle 3.10494 ( 18) link_BETA1-4 : bond 0.00850 ( 5) link_BETA1-4 : angle 4.64134 ( 15) hydrogen bonds : bond 0.03624 ( 293) hydrogen bonds : angle 4.37221 ( 942) SS BOND : bond 0.00515 ( 50) SS BOND : angle 1.53398 ( 100) covalent geometry : bond 0.00488 (10848) covalent geometry : angle 0.62151 (14696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 HIS cc_start: 0.6610 (OUTLIER) cc_final: 0.4791 (m-70) REVERT: A 408 ASP cc_start: 0.8033 (t70) cc_final: 0.7438 (t0) REVERT: A 443 ASN cc_start: 0.8390 (m110) cc_final: 0.7929 (m-40) REVERT: A 494 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8197 (ttpp) REVERT: A 517 ARG cc_start: 0.8702 (ttm110) cc_final: 0.8491 (ttp-110) REVERT: A 524 VAL cc_start: 0.7856 (p) cc_final: 0.7553 (t) REVERT: A 528 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 544 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7394 (mt-10) REVERT: A 578 SER cc_start: 0.8278 (m) cc_final: 0.8052 (p) REVERT: A 579 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7708 (mtp180) REVERT: A 620 LEU cc_start: 0.8259 (tp) cc_final: 0.8003 (tt) REVERT: A 647 ARG cc_start: 0.8661 (mtm180) cc_final: 0.8282 (mtm180) REVERT: A 823 SER cc_start: 0.8799 (t) cc_final: 0.8464 (p) REVERT: A 918 SER cc_start: 0.8649 (m) cc_final: 0.8293 (t) REVERT: A 968 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 1011 ARG cc_start: 0.8341 (ttm170) cc_final: 0.8008 (ttm170) REVERT: B 290 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7810 (mt) REVERT: B 372 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7139 (mt-10) REVERT: B 435 THR cc_start: 0.7453 (OUTLIER) cc_final: 0.6502 (t) REVERT: B 569 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7298 (t-90) REVERT: B 661 ASP cc_start: 0.7779 (m-30) cc_final: 0.7560 (m-30) REVERT: B 676 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7117 (mp10) REVERT: B 686 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7623 (tm-30) REVERT: B 718 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.5071 (tt0) REVERT: B 791 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8200 (mtpm) outliers start: 52 outliers final: 40 residues processed: 285 average time/residue: 0.3464 time to fit residues: 135.3209 Evaluate side-chains 306 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 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 469 LYS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 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 718 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 791 LYS 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 87 optimal weight: 0.5980 chunk 93 optimal weight: 0.0870 chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.3980 chunk 92 optimal weight: 0.4980 chunk 74 optimal weight: 0.2980 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.144204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.121991 restraints weight = 15768.344| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.95 r_work: 0.3450 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10909 Z= 0.151 Angle : 0.629 12.201 14829 Z= 0.321 Chirality : 0.045 0.264 1580 Planarity : 0.004 0.050 1915 Dihedral : 5.836 58.455 1689 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.61 % Allowed : 22.43 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.21), residues: 1374 helix: 1.02 (0.42), residues: 166 sheet: -0.44 (0.34), residues: 216 loop : -1.11 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 847 HIS 0.004 0.001 HIS A 348 PHE 0.019 0.001 PHE B 283 TYR 0.007 0.001 TYR B 354 ARG 0.011 0.000 ARG B 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 6) link_NAG-ASN : angle 2.98933 ( 18) link_BETA1-4 : bond 0.00810 ( 5) link_BETA1-4 : angle 4.55120 ( 15) hydrogen bonds : bond 0.03331 ( 293) hydrogen bonds : angle 4.27846 ( 942) SS BOND : bond 0.00418 ( 50) SS BOND : angle 1.39034 ( 100) covalent geometry : bond 0.00344 (10848) covalent geometry : angle 0.59481 (14696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6361.09 seconds wall clock time: 114 minutes 24.03 seconds (6864.03 seconds total)