Starting phenix.real_space_refine on Thu Sep 18 20:08:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nb5_49213/09_2025/9nb5_49213.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nb5_49213/09_2025/9nb5_49213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nb5_49213/09_2025/9nb5_49213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nb5_49213/09_2025/9nb5_49213.map" model { file = "/net/cci-nas-00/data/ceres_data/9nb5_49213/09_2025/9nb5_49213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nb5_49213/09_2025/9nb5_49213.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 sd= 0.087 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 20 9.91 5 S 217 5.16 5 C 12001 2.51 5 N 3545 2.21 5 O 3825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19608 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6492 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 24, 'TRANS': 833} Chain breaks: 1 Chain: "B" Number of atoms: 6549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6549 Classifications: {'peptide': 867} Link IDs: {'PTRANS': 25, 'TRANS': 841} Chain breaks: 1 Chain: "C" Number of atoms: 6421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6421 Classifications: {'peptide': 848} Link IDs: {'PTRANS': 24, 'TRANS': 823} Chain breaks: 1 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 49 Unusual residues: {' CA': 7, 'NAG': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 49 Unusual residues: {' CA': 7, 'NAG': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 48 Unusual residues: {' CA': 6, 'NAG': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.97, per 1000 atoms: 0.20 Number of scatterers: 19608 At special positions: 0 Unit cell: (128.76, 150.96, 207.57, 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 20 19.99 S 217 16.00 O 3825 8.00 N 3545 7.00 C 12001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=95, 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=2.04 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 258 " distance=2.03 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=2.03 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=2.03 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 693 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 808 " distance=2.03 Simple disulfide: pdb=" SG CYS A 757 " - pdb=" SG CYS A 818 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 798 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 998 " - pdb=" SG CYS A1008 " distance=2.03 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 258 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 238 " 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=2.03 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=2.04 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 693 " - pdb=" SG CYS B 713 " 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=2.03 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 Simple disulfide: pdb=" SG CYS B 938 " - pdb=" SG CYS B 972 " distance=2.03 Simple disulfide: pdb=" SG CYS B 954 " - pdb=" SG CYS B1018 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B1028 " distance=2.03 Simple disulfide: pdb=" SG CYS B 998 " - pdb=" SG CYS B1008 " distance=2.03 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 197 " - pdb=" SG CYS C 258 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 238 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 309 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 355 " distance=2.03 Simple disulfide: pdb=" SG CYS C 304 " - pdb=" SG CYS C 365 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 416 " distance=2.03 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 462 " distance=2.03 Simple disulfide: pdb=" SG CYS C 411 " - pdb=" SG CYS C 472 " distance=2.03 Simple disulfide: pdb=" SG CYS C 442 " - pdb=" SG CYS C 452 " distance=2.03 Simple disulfide: pdb=" SG CYS C 487 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 516 " - pdb=" SG CYS C 577 " distance=2.04 Simple disulfide: pdb=" SG CYS C 547 " - pdb=" SG CYS C 557 " distance=2.03 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 626 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 682 " distance=2.03 Simple disulfide: pdb=" SG CYS C 652 " - pdb=" SG CYS C 662 " distance=2.03 Simple disulfide: pdb=" SG CYS C 728 " - pdb=" SG CYS C 762 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 808 " distance=2.03 Simple disulfide: pdb=" SG CYS C 757 " - pdb=" SG CYS C 818 " distance=2.03 Simple disulfide: pdb=" SG CYS C 788 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 869 " distance=2.03 Simple disulfide: pdb=" SG CYS C 864 " - pdb=" SG CYS C 925 " distance=2.03 Simple disulfide: pdb=" SG CYS C 895 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C 938 " - pdb=" SG CYS C 972 " distance=2.03 Simple disulfide: pdb=" SG CYS C 954 " - pdb=" SG CYS C1018 " distance=2.02 Simple disulfide: pdb=" SG CYS C 967 " - pdb=" SG CYS C1028 " distance=2.03 Simple disulfide: pdb=" SG CYS C 998 " - pdb=" SG CYS C1008 " 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 NAG-ASN " NAG A1208 " - " ASN A 320 " " NAG A1209 " - " ASN A 445 " " NAG A1210 " - " ASN A 767 " " NAG B1208 " - " ASN B 320 " " NAG B1209 " - " ASN B 445 " " NAG B1210 " - " ASN B 767 " " NAG C1207 " - " ASN C 320 " " NAG C1208 " - " ASN C 445 " " NAG C1209 " - " ASN C 767 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 852.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4502 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 52 sheets defined 15.2% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 403 through 415 removed outlier: 4.236A pdb=" N VAL A 409 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.540A pdb=" N CYS A 452 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.543A pdb=" N ARG A 571 " --> pdb=" O SER A 568 " (cutoff:3.500A) removed outlier: 3.871A 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: 3.544A pdb=" N CYS A 662 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 removed outlier: 3.641A pdb=" N VAL A 755 " --> pdb=" O SER A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 868 Processing helix chain 'A' and resid 901 through 905 removed outlier: 3.755A pdb=" N GLN A 904 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS A 905 " --> pdb=" O LEU A 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 901 through 905' Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.511A pdb=" N VAL A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.635A pdb=" N ALA B 193 " --> pdb=" O ASN B 189 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 200 " --> pdb=" O ILE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 341 through 345 Processing helix chain 'B' and resid 403 through 415 removed outlier: 3.932A pdb=" N VAL B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 3.732A 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 568 through 572 removed outlier: 3.504A pdb=" N ASP B 572 " --> pdb=" O HIS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 624 Processing helix chain 'B' and resid 749 through 760 removed outlier: 3.954A pdb=" N VAL B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 756 " --> pdb=" O ASP B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 798 Processing helix chain 'B' and resid 856 through 868 Processing helix chain 'B' and resid 901 through 905 removed outlier: 3.624A pdb=" N GLN B 904 " --> pdb=" O THR B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 970 Processing helix chain 'B' and resid 1019 through 1023 Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 296 through 308 Processing helix chain 'C' and resid 403 through 415 removed outlier: 3.553A pdb=" N VAL C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 452 Processing helix chain 'C' and resid 474 through 476 No H-bonds generated for 'chain 'C' and resid 474 through 476' Processing helix chain 'C' and resid 508 through 519 Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.562A pdb=" N LEU C 556 " --> pdb=" O HIS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.649A pdb=" N ASP C 572 " --> pdb=" O HIS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 624 Processing helix chain 'C' and resid 658 through 662 Processing helix chain 'C' and resid 749 through 761 removed outlier: 3.569A pdb=" N VAL C 755 " --> pdb=" O SER C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 868 Processing helix chain 'C' and resid 901 through 905 Processing helix chain 'C' and resid 916 through 920 removed outlier: 3.524A pdb=" N GLU C 920 " --> pdb=" O PRO C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 971 Processing helix chain 'C' and resid 1019 through 1023 removed outlier: 3.658A pdb=" N GLU C1022 " --> pdb=" O GLY C1019 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP C1023 " --> pdb=" O HIS C1020 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1019 through 1023' Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 269 removed outlier: 3.707A pdb=" N SER A 265 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 363 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY A 362 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N TRP A 457 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 316 " --> pdb=" O TRP A 457 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP A 436 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR A 435 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 397 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL A 386 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ALA A 383 " --> pdb=" O GLY A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 7.557A pdb=" N TRP A 329 " --> pdb=" O TRP A 287 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N THR A 289 " --> pdb=" O TRP A 329 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE A 290 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU A 279 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 363 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY A 362 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N TRP A 457 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 316 " --> pdb=" O TRP A 457 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP A 436 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR A 435 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 397 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL A 386 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR A 471 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 476 through 481 removed outlier: 6.493A pdb=" N GLY A 574 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE A 527 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 576 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 481 removed outlier: 4.664A pdb=" N GLN A 539 " --> pdb=" O TRP A 499 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA8, first strand: chain 'A' and resid 583 through 586 Processing sheet with id=AA9, first strand: chain 'A' and resid 583 through 586 removed outlier: 7.135A pdb=" N ILE A 681 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 649 through 650 Processing sheet with id=AB2, first strand: chain 'A' and resid 719 through 726 removed outlier: 3.725A pdb=" N GLY A 724 " --> pdb=" O ALA A 729 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA A 729 " --> pdb=" O GLY A 724 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY A 815 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA A 768 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 817 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 719 through 726 removed outlier: 3.725A pdb=" N GLY A 724 " --> pdb=" O ALA A 729 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA A 729 " --> pdb=" O GLY A 724 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 732 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 743 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TRP A 782 " --> pdb=" O TRP A 740 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR A 742 " --> pdb=" O TRP A 782 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 824 through 827 Processing sheet with id=AB5, first strand: chain 'A' and resid 824 through 827 removed outlier: 6.480A pdb=" N LEU A 839 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 850 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TRP A 889 " --> pdb=" O TRP A 847 " (cutoff:3.500A) removed outlier: 7.175A 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: 7.282A pdb=" N ASN A1027 " --> pdb=" O LEU A 976 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 929 through 932 removed outlier: 6.937A pdb=" N VAL A 942 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 953 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TRP A 992 " --> pdb=" O TRP A 950 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N THR A 952 " --> pdb=" O TRP A 992 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 994 " --> pdb=" O THR A 952 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A 994 " --> pdb=" O ARG A1011 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AB9, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AC1, first strand: chain 'B' and resid 266 through 269 Processing sheet with id=AC2, first strand: chain 'B' and resid 266 through 269 removed outlier: 6.715A pdb=" N LEU B 279 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE B 290 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N TRP B 329 " --> pdb=" O TRP B 287 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N THR B 289 " --> pdb=" O TRP B 329 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 371 through 380 removed outlier: 3.504A pdb=" N GLY B 378 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ALA B 383 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 471 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 371 through 380 removed outlier: 3.504A pdb=" N GLY B 378 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ALA B 383 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 386 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL B 397 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N LEU B 437 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS B 396 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 477 through 481 removed outlier: 3.912A pdb=" N GLU B 477 " --> pdb=" O LYS B 494 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 477 through 481 removed outlier: 3.912A pdb=" N GLU B 477 " --> pdb=" O LYS B 494 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 491 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE B 502 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 498 " --> pdb=" O HIS B 495 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N TRP B 541 " --> pdb=" O TRP B 499 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER B 501 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 543 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 583 through 586 removed outlier: 7.186A pdb=" N ILE B 681 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 583 through 586 removed outlier: 6.473A pdb=" N VAL B 596 " --> pdb=" O LEU B 607 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 607 " --> pdb=" O VAL B 596 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N TRP B 646 " --> pdb=" O TRP B 604 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER B 606 " --> pdb=" O TRP B 646 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 649 through 650 Processing sheet with id=AD2, first strand: chain 'B' and resid 719 through 726 removed outlier: 3.580A pdb=" N GLY B 724 " --> pdb=" O ALA B 729 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ALA B 729 " --> pdb=" O GLY B 724 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY B 815 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA B 768 " --> pdb=" O GLY B 815 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 817 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 719 through 726 removed outlier: 3.580A pdb=" N GLY B 724 " --> pdb=" O ALA B 729 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ALA B 729 " --> pdb=" O GLY B 724 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 732 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE B 743 " --> pdb=" O VAL B 732 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TRP B 782 " --> pdb=" O TRP B 740 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR B 742 " --> pdb=" O TRP B 782 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 823 through 827 Processing sheet with id=AD5, first strand: chain 'B' and resid 823 through 827 removed outlier: 6.617A pdb=" N LEU B 839 " --> pdb=" O VAL B 850 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 850 " --> pdb=" O LEU B 839 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP B 889 " --> pdb=" O TRP B 847 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR B 849 " --> pdb=" O TRP B 889 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 929 through 932 removed outlier: 6.470A pdb=" N ALA B1025 " --> pdb=" O ALA B 978 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA B 978 " --> pdb=" O ALA B1025 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN B1027 " --> pdb=" O LEU B 976 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 929 through 932 removed outlier: 6.748A pdb=" N VAL B 942 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL B 953 " --> pdb=" O VAL B 942 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TRP B 992 " --> pdb=" O TRP B 950 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR B 952 " --> pdb=" O TRP B 992 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 159 through 162 Processing sheet with id=AD9, first strand: chain 'C' and resid 159 through 162 Processing sheet with id=AE1, first strand: chain 'C' and resid 266 through 269 removed outlier: 3.507A pdb=" N VAL C 363 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 315 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 266 through 269 removed outlier: 6.760A pdb=" N LEU C 279 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE C 290 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TRP C 329 " --> pdb=" O TRP C 287 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR C 289 " --> pdb=" O TRP C 329 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 371 through 376 removed outlier: 6.868A pdb=" N THR C 471 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 371 through 376 removed outlier: 6.591A pdb=" N VAL C 386 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL C 397 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU C 437 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS C 396 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 477 through 481 Processing sheet with id=AE6, first strand: chain 'C' and resid 477 through 481 removed outlier: 6.557A pdb=" N VAL C 491 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE C 502 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN C 539 " --> pdb=" O TRP C 499 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 544 through 545 Processing sheet with id=AE8, first strand: chain 'C' and resid 583 through 586 Processing sheet with id=AE9, first strand: chain 'C' and resid 583 through 586 removed outlier: 6.783A pdb=" N VAL C 596 " --> pdb=" O LEU C 607 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 607 " --> pdb=" O VAL C 596 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TRP C 646 " --> pdb=" O TRP C 604 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER C 606 " --> pdb=" O TRP C 646 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 649 through 650 Processing sheet with id=AF2, first strand: chain 'C' and resid 719 through 726 removed outlier: 3.852A pdb=" N GLY C 724 " --> pdb=" O ALA C 729 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA C 729 " --> pdb=" O GLY C 724 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE C 817 " --> pdb=" O ILE C 766 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 719 through 726 removed outlier: 3.852A pdb=" N GLY C 724 " --> pdb=" O ALA C 729 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA C 729 " --> pdb=" O GLY C 724 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL C 732 " --> pdb=" O ILE C 743 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE C 743 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TRP C 782 " --> pdb=" O TRP C 740 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR C 742 " --> pdb=" O TRP C 782 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 824 through 827 Processing sheet with id=AF5, first strand: chain 'C' and resid 824 through 827 removed outlier: 6.699A pdb=" N LEU C 839 " --> pdb=" O VAL C 850 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 850 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP C 889 " --> pdb=" O TRP C 847 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR C 849 " --> pdb=" O TRP C 889 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 929 through 932 removed outlier: 6.538A pdb=" N ALA C1025 " --> pdb=" O ALA C 978 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA C 978 " --> pdb=" O ALA C1025 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN C1027 " --> pdb=" O LEU C 976 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 929 through 932 removed outlier: 6.602A pdb=" N VAL C 942 " --> pdb=" O VAL C 953 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL C 953 " --> pdb=" O VAL C 942 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N TRP C 992 " --> pdb=" O TRP C 950 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR C 952 " --> pdb=" O TRP C 992 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN C 994 " --> pdb=" O THR C 952 " (cutoff:3.500A) 646 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5332 1.33 - 1.46: 4614 1.46 - 1.58: 9846 1.58 - 1.70: 0 1.70 - 1.83: 244 Bond restraints: 20036 Sorted by residual: bond pdb=" CA GLN B 425 " pdb=" C GLN B 425 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.23e-02 6.61e+03 1.24e+01 bond pdb=" CA CYS B 365 " pdb=" C CYS B 365 " ideal model delta sigma weight residual 1.523 1.485 0.037 1.23e-02 6.61e+03 9.27e+00 bond pdb=" C GLN B 425 " pdb=" O GLN B 425 " ideal model delta sigma weight residual 1.236 1.206 0.030 1.22e-02 6.72e+03 6.16e+00 bond pdb=" CA GLN B 425 " pdb=" CB GLN B 425 " ideal model delta sigma weight residual 1.529 1.497 0.032 1.34e-02 5.57e+03 5.76e+00 bond pdb=" C LEU B 371 " pdb=" O LEU B 371 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.24e-02 6.50e+03 5.50e+00 ... (remaining 20031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 26866 2.11 - 4.22: 233 4.22 - 6.33: 25 6.33 - 8.44: 2 8.44 - 10.55: 2 Bond angle restraints: 27128 Sorted by residual: angle pdb=" N SER B 369 " pdb=" CA SER B 369 " pdb=" C SER B 369 " ideal model delta sigma weight residual 111.28 120.35 -9.07 1.09e+00 8.42e-01 6.92e+01 angle pdb=" N SER B 366 " pdb=" CA SER B 366 " pdb=" C SER B 366 " ideal model delta sigma weight residual 109.50 120.05 -10.55 1.58e+00 4.01e-01 4.46e+01 angle pdb=" N ASP B 370 " pdb=" CA ASP B 370 " pdb=" C ASP B 370 " ideal model delta sigma weight residual 113.16 119.42 -6.26 1.24e+00 6.50e-01 2.55e+01 angle pdb=" N VAL B 426 " pdb=" CA VAL B 426 " pdb=" C VAL B 426 " ideal model delta sigma weight residual 109.80 116.19 -6.39 1.33e+00 5.65e-01 2.31e+01 angle pdb=" N TYR B 427 " pdb=" CA TYR B 427 " pdb=" C TYR B 427 " ideal model delta sigma weight residual 114.56 108.70 5.86 1.27e+00 6.20e-01 2.13e+01 ... (remaining 27123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10325 17.96 - 35.92: 1267 35.92 - 53.88: 355 53.88 - 71.84: 48 71.84 - 89.80: 16 Dihedral angle restraints: 12011 sinusoidal: 4918 harmonic: 7093 Sorted by residual: dihedral pdb=" CB CYS C 835 " pdb=" SG CYS C 835 " pdb=" SG CYS C 869 " pdb=" CB CYS C 869 " ideal model delta sinusoidal sigma weight residual 93.00 176.78 -83.78 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 355 " pdb=" CB CYS C 355 " ideal model delta sinusoidal sigma weight residual 93.00 167.94 -74.94 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS A 398 " pdb=" SG CYS A 398 " pdb=" SG CYS A 462 " pdb=" CB CYS A 462 " ideal model delta sinusoidal sigma weight residual -86.00 -154.91 68.91 1 1.00e+01 1.00e-02 6.15e+01 ... (remaining 12008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2690 0.089 - 0.177: 157 0.177 - 0.266: 2 0.266 - 0.354: 0 0.354 - 0.443: 1 Chirality restraints: 2850 Sorted by residual: chirality pdb=" C1 NAG B1208 " pdb=" ND2 ASN B 320 " pdb=" C2 NAG B1208 " pdb=" O5 NAG B1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CA ASP B 370 " pdb=" N ASP B 370 " pdb=" C ASP B 370 " pdb=" CB ASP B 370 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA SER B 366 " pdb=" N SER B 366 " pdb=" C SER B 366 " pdb=" CB SER B 366 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.00e-01 ... (remaining 2847 not shown) Planarity restraints: 3578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 222 " 0.024 2.00e-02 2.50e+03 1.77e-02 7.87e+00 pdb=" CG TRP A 222 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 222 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 222 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 222 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 222 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 222 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 222 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 222 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 222 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 898 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO A 899 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 422 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C THR C 422 " -0.033 2.00e-02 2.50e+03 pdb=" O THR C 422 " 0.012 2.00e-02 2.50e+03 pdb=" N SER C 423 " 0.011 2.00e-02 2.50e+03 ... (remaining 3575 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2310 2.75 - 3.29: 18005 3.29 - 3.82: 31675 3.82 - 4.36: 38349 4.36 - 4.90: 66820 Nonbonded interactions: 157159 Sorted by model distance: nonbonded pdb=" O LYS B 352 " pdb=" ND1 HIS B 353 " model vdw 2.210 3.120 nonbonded pdb=" OG SER A 683 " pdb=" OD1 ASN A 685 " model vdw 2.232 3.040 nonbonded pdb=" O GLY C 215 " pdb=" OG SER C 218 " model vdw 2.232 3.040 nonbonded pdb=" O GLY B 294 " pdb="CA CA B1202 " model vdw 2.237 2.510 nonbonded pdb=" NH2 ARG C 758 " pdb=" O GLY C 790 " model vdw 2.244 3.120 ... (remaining 157154 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 'A' and (resid 154 through 687 or resid 717 through 1206 or resid 1208 th \ rough 1209)) selection = (chain 'B' and (resid 154 through 687 or resid 717 through 1206 or resid 1208 th \ rough 1209)) selection = (chain 'C' and (resid 154 through 1206 or resid 1208 through 1209)) } 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: 6.100 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.040 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 0.043 20140 Z= 0.158 Angle : 0.537 12.699 27345 Z= 0.306 Chirality : 0.043 0.443 2850 Planarity : 0.003 0.062 3569 Dihedral : 16.227 89.795 7224 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.85 % Favored : 97.11 % Rotamer: Outliers : 3.25 % Allowed : 20.56 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.15), residues: 2561 helix: 0.22 (0.29), residues: 306 sheet: 0.02 (0.30), residues: 308 loop : -0.93 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 913 TYR 0.013 0.001 TYR B 427 PHE 0.010 0.001 PHE B 842 TRP 0.046 0.001 TRP A 222 HIS 0.008 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00336 (20036) covalent geometry : angle 0.52470 (27128) SS BOND : bond 0.00235 ( 95) SS BOND : angle 0.90493 ( 190) hydrogen bonds : bond 0.25542 ( 533) hydrogen bonds : angle 8.46109 ( 1728) link_NAG-ASN : bond 0.00294 ( 9) link_NAG-ASN : angle 3.10394 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 155 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7742 (p0) cc_final: 0.7079 (p0) REVERT: A 392 ARG cc_start: 0.8587 (mtp180) cc_final: 0.8278 (mtm110) REVERT: A 543 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7895 (pt0) REVERT: A 649 MET cc_start: 0.8725 (mtm) cc_final: 0.8425 (mtp) REVERT: B 208 PHE cc_start: 0.6981 (t80) cc_final: 0.6583 (OUTLIER) REVERT: B 343 TRP cc_start: 0.8981 (OUTLIER) cc_final: 0.8209 (p90) REVERT: B 611 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6454 (m90) REVERT: B 889 TRP cc_start: 0.9195 (OUTLIER) cc_final: 0.7922 (m100) REVERT: B 977 LYS cc_start: 0.7922 (mtmt) cc_final: 0.7521 (tptm) REVERT: B 988 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8472 (p) REVERT: C 396 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7003 (mtpp) REVERT: C 548 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7844 (tt0) REVERT: C 718 GLN cc_start: 0.6791 (mp10) cc_final: 0.6583 (mp10) REVERT: C 754 HIS cc_start: 0.7918 (m90) cc_final: 0.7686 (m90) REVERT: C 888 MET cc_start: 0.9087 (ttm) cc_final: 0.8827 (ttp) REVERT: C 1017 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8073 (mm-30) outliers start: 68 outliers final: 44 residues processed: 215 average time/residue: 0.5543 time to fit residues: 136.3066 Evaluate side-chains 183 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1018 CYS Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 343 TRP Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 611 HIS Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 889 TRP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 901 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 1.9990 overall best weight: 1.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS A 623 GLN A1027 ASN B 464 HIS C 391 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.110762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.082281 restraints weight = 39793.286| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.61 r_work: 0.3092 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20140 Z= 0.208 Angle : 0.578 6.965 27345 Z= 0.315 Chirality : 0.045 0.232 2850 Planarity : 0.004 0.070 3569 Dihedral : 6.570 58.810 2978 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 5.02 % Allowed : 20.71 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.15), residues: 2561 helix: 0.77 (0.30), residues: 309 sheet: -0.04 (0.32), residues: 267 loop : -1.09 (0.12), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 758 TYR 0.011 0.002 TYR C 298 PHE 0.030 0.002 PHE A 176 TRP 0.021 0.002 TRP A 910 HIS 0.009 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00496 (20036) covalent geometry : angle 0.56818 (27128) SS BOND : bond 0.00356 ( 95) SS BOND : angle 1.17464 ( 190) hydrogen bonds : bond 0.04658 ( 533) hydrogen bonds : angle 5.46228 ( 1728) link_NAG-ASN : bond 0.00408 ( 9) link_NAG-ASN : angle 2.15966 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 149 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASN cc_start: 0.7873 (m110) cc_final: 0.7196 (t0) REVERT: A 180 TRP cc_start: 0.6616 (m100) cc_final: 0.6066 (m100) REVERT: A 223 PHE cc_start: 0.6049 (OUTLIER) cc_final: 0.5524 (t80) REVERT: A 392 ARG cc_start: 0.8854 (mtp180) cc_final: 0.8280 (mtm110) REVERT: A 649 MET cc_start: 0.8927 (mtm) cc_final: 0.8700 (mtp) REVERT: A 722 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8855 (t) REVERT: A 970 LEU cc_start: 0.8299 (tp) cc_final: 0.7891 (tm) REVERT: B 160 ARG cc_start: 0.7582 (pmt-80) cc_final: 0.6856 (pmt-80) REVERT: B 163 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7747 (mtm-85) REVERT: B 208 PHE cc_start: 0.6882 (t80) cc_final: 0.6529 (OUTLIER) REVERT: B 460 LEU cc_start: 0.8550 (mt) cc_final: 0.8276 (tt) REVERT: B 611 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.6864 (m90) REVERT: B 764 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: B 889 TRP cc_start: 0.9152 (OUTLIER) cc_final: 0.7803 (m100) REVERT: B 977 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7527 (tptm) REVERT: B 981 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6975 (mm-30) REVERT: B 1023 ASP cc_start: 0.7684 (p0) cc_final: 0.7180 (m-30) REVERT: C 208 PHE cc_start: 0.8778 (p90) cc_final: 0.8561 (p90) REVERT: C 226 LEU cc_start: 0.5899 (OUTLIER) cc_final: 0.5540 (tm) REVERT: C 396 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7307 (mtpp) REVERT: C 507 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7393 (t80) REVERT: C 540 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8639 (pp) REVERT: C 548 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8070 (tt0) REVERT: C 569 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7274 (m-70) REVERT: C 572 ASP cc_start: 0.8146 (p0) cc_final: 0.7085 (m-30) REVERT: C 718 GLN cc_start: 0.6889 (mp10) cc_final: 0.6654 (mp10) REVERT: C 888 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8970 (ttp) outliers start: 105 outliers final: 57 residues processed: 238 average time/residue: 0.5640 time to fit residues: 154.3184 Evaluate side-chains 199 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 132 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 786 MET Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 239 LYS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 611 HIS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 889 TRP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 953 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 159 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS C 391 GLN C 754 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.111807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.083401 restraints weight = 40088.929| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.61 r_work: 0.3112 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20140 Z= 0.129 Angle : 0.505 9.184 27345 Z= 0.276 Chirality : 0.043 0.297 2850 Planarity : 0.004 0.062 3569 Dihedral : 6.068 56.428 2951 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.23 % Rotamer: Outliers : 4.64 % Allowed : 21.76 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.15), residues: 2561 helix: 1.24 (0.30), residues: 309 sheet: -0.35 (0.31), residues: 281 loop : -1.04 (0.12), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 913 TYR 0.006 0.001 TYR C 735 PHE 0.019 0.001 PHE A 176 TRP 0.021 0.001 TRP A 222 HIS 0.006 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00303 (20036) covalent geometry : angle 0.49444 (27128) SS BOND : bond 0.00254 ( 95) SS BOND : angle 0.96892 ( 190) hydrogen bonds : bond 0.03749 ( 533) hydrogen bonds : angle 4.81237 ( 1728) link_NAG-ASN : bond 0.00552 ( 9) link_NAG-ASN : angle 2.46312 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 141 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASN cc_start: 0.7918 (m110) cc_final: 0.7279 (t0) REVERT: A 223 PHE cc_start: 0.5946 (OUTLIER) cc_final: 0.5436 (t80) REVERT: A 392 ARG cc_start: 0.8829 (mtp180) cc_final: 0.8283 (mtm110) REVERT: A 644 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7363 (tp40) REVERT: A 649 MET cc_start: 0.8843 (mtm) cc_final: 0.8627 (mtp) REVERT: A 722 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8858 (t) REVERT: A 970 LEU cc_start: 0.8309 (tp) cc_final: 0.7915 (tm) REVERT: B 160 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7026 (pmt-80) REVERT: B 208 PHE cc_start: 0.6891 (t80) cc_final: 0.6622 (t80) REVERT: B 476 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8135 (mmp80) REVERT: B 611 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.6733 (m90) REVERT: B 888 MET cc_start: 0.8676 (ttm) cc_final: 0.8396 (ttm) REVERT: B 977 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7558 (tptm) REVERT: B 981 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6995 (mm-30) REVERT: B 1011 ARG cc_start: 0.7649 (mmm160) cc_final: 0.6921 (mtp85) REVERT: B 1023 ASP cc_start: 0.7491 (p0) cc_final: 0.7110 (m-30) REVERT: C 208 PHE cc_start: 0.8730 (p90) cc_final: 0.8512 (p90) REVERT: C 226 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5642 (tm) REVERT: C 396 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7302 (mtpp) REVERT: C 507 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7340 (t80) REVERT: C 548 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8042 (tt0) REVERT: C 572 ASP cc_start: 0.8167 (p0) cc_final: 0.7181 (m-30) REVERT: C 718 GLN cc_start: 0.6879 (mp10) cc_final: 0.6615 (mp10) REVERT: C 888 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8921 (ttp) outliers start: 97 outliers final: 50 residues processed: 220 average time/residue: 0.5784 time to fit residues: 145.7666 Evaluate side-chains 193 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 133 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 786 MET Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 239 LYS Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 611 HIS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 237 optimal weight: 0.2980 chunk 175 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.0030 chunk 71 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS C 391 GLN C 754 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.112137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.088920 restraints weight = 39893.037| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.71 r_work: 0.3142 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20140 Z= 0.117 Angle : 0.491 8.543 27345 Z= 0.267 Chirality : 0.042 0.321 2850 Planarity : 0.003 0.061 3569 Dihedral : 5.794 57.045 2943 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.69 % Favored : 97.27 % Rotamer: Outliers : 4.73 % Allowed : 22.05 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.15), residues: 2561 helix: 1.49 (0.30), residues: 307 sheet: -0.42 (0.30), residues: 304 loop : -0.98 (0.12), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 913 TYR 0.009 0.001 TYR A 465 PHE 0.017 0.001 PHE A 208 TRP 0.021 0.001 TRP A 222 HIS 0.005 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00274 (20036) covalent geometry : angle 0.48122 (27128) SS BOND : bond 0.00238 ( 95) SS BOND : angle 0.96389 ( 190) hydrogen bonds : bond 0.03369 ( 533) hydrogen bonds : angle 4.57991 ( 1728) link_NAG-ASN : bond 0.00310 ( 9) link_NAG-ASN : angle 2.29517 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 145 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7652 (p0) cc_final: 0.7207 (p0) REVERT: A 166 ASN cc_start: 0.7695 (m110) cc_final: 0.7196 (t0) REVERT: A 223 PHE cc_start: 0.5924 (OUTLIER) cc_final: 0.5485 (t80) REVERT: A 392 ARG cc_start: 0.8761 (mtp180) cc_final: 0.8352 (mtm110) REVERT: A 644 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7245 (tp40) REVERT: A 649 MET cc_start: 0.8799 (mtm) cc_final: 0.8574 (mtp) REVERT: A 722 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8858 (t) REVERT: A 970 LEU cc_start: 0.8458 (tp) cc_final: 0.8104 (tm) REVERT: B 159 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7540 (ptp) REVERT: B 160 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7646 (pmt-80) REVERT: B 171 ARG cc_start: 0.6916 (ttt180) cc_final: 0.6391 (tpt170) REVERT: B 199 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: B 476 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8217 (mmp80) REVERT: B 611 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6485 (m90) REVERT: B 888 MET cc_start: 0.8714 (ttm) cc_final: 0.8436 (ttm) REVERT: B 977 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7722 (tptm) REVERT: B 981 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6928 (mm-30) REVERT: B 1005 LEU cc_start: 0.8227 (tp) cc_final: 0.8020 (tp) REVERT: B 1011 ARG cc_start: 0.7712 (mmm160) cc_final: 0.7118 (mtp85) REVERT: B 1023 ASP cc_start: 0.7427 (p0) cc_final: 0.7166 (m-30) REVERT: C 208 PHE cc_start: 0.8651 (p90) cc_final: 0.8416 (p90) REVERT: C 226 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.6080 (tm) REVERT: C 396 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7466 (mtpp) REVERT: C 507 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7470 (t80) REVERT: C 548 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: C 572 ASP cc_start: 0.8110 (p0) cc_final: 0.7274 (m-30) REVERT: C 599 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8626 (ttmt) REVERT: C 718 GLN cc_start: 0.6916 (mp10) cc_final: 0.6670 (mp10) REVERT: C 888 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8910 (ttp) outliers start: 99 outliers final: 57 residues processed: 226 average time/residue: 0.5995 time to fit residues: 154.8624 Evaluate side-chains 208 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 137 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 786 MET Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 611 HIS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 548 GLU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 764 GLU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 949 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 196 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 618 HIS A 685 ASN B 240 HIS ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 HIS B 622 GLN C 391 GLN C 651 HIS C 754 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.108631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.085302 restraints weight = 40091.244| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.80 r_work: 0.3058 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 20140 Z= 0.353 Angle : 0.707 13.529 27345 Z= 0.380 Chirality : 0.051 0.353 2850 Planarity : 0.005 0.078 3569 Dihedral : 6.758 59.966 2941 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.18 % Favored : 95.78 % Rotamer: Outliers : 6.60 % Allowed : 21.04 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.14), residues: 2561 helix: 0.67 (0.29), residues: 309 sheet: -0.65 (0.29), residues: 310 loop : -1.39 (0.12), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 941 TYR 0.014 0.003 TYR C 298 PHE 0.022 0.002 PHE B 842 TRP 0.026 0.002 TRP A 910 HIS 0.012 0.002 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00853 (20036) covalent geometry : angle 0.68463 (27128) SS BOND : bond 0.00532 ( 95) SS BOND : angle 1.94105 ( 190) hydrogen bonds : bond 0.04978 ( 533) hydrogen bonds : angle 5.29018 ( 1728) link_NAG-ASN : bond 0.00556 ( 9) link_NAG-ASN : angle 2.98256 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 144 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7604 (p0) cc_final: 0.7069 (p0) REVERT: A 166 ASN cc_start: 0.7966 (m110) cc_final: 0.7612 (t160) REVERT: A 182 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7821 (t) REVERT: A 184 CYS cc_start: 0.6923 (m) cc_final: 0.6606 (m) REVERT: A 223 PHE cc_start: 0.5807 (OUTLIER) cc_final: 0.5423 (t80) REVERT: A 392 ARG cc_start: 0.8838 (mtp180) cc_final: 0.8445 (mtm110) REVERT: A 609 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7617 (m-40) REVERT: A 644 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7442 (tp40) REVERT: A 649 MET cc_start: 0.8909 (mtm) cc_final: 0.8703 (mtp) REVERT: A 686 GLN cc_start: 0.8327 (mp10) cc_final: 0.7968 (mp10) REVERT: A 970 LEU cc_start: 0.8404 (tp) cc_final: 0.8025 (tm) REVERT: B 159 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8006 (ptt) REVERT: B 160 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7327 (pmt-80) REVERT: B 171 ARG cc_start: 0.7202 (ttt180) cc_final: 0.6581 (tpt170) REVERT: B 199 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8059 (mt0) REVERT: B 208 PHE cc_start: 0.7284 (t80) cc_final: 0.6881 (OUTLIER) REVERT: B 460 LEU cc_start: 0.8634 (mt) cc_final: 0.8404 (mt) REVERT: B 611 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.6956 (m-70) REVERT: B 889 TRP cc_start: 0.9191 (OUTLIER) cc_final: 0.7800 (m100) REVERT: B 981 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7134 (mm-30) REVERT: B 1011 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7071 (mtp85) REVERT: B 1023 ASP cc_start: 0.7768 (p0) cc_final: 0.7344 (m-30) REVERT: C 208 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8484 (p90) REVERT: C 226 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6438 (tm) REVERT: C 280 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8103 (mm-30) REVERT: C 507 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7632 (t80) REVERT: C 548 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: C 572 ASP cc_start: 0.8339 (p0) cc_final: 0.7473 (m-30) REVERT: C 599 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8634 (ttmt) REVERT: C 750 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7676 (tp) REVERT: C 888 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.9026 (ttp) REVERT: C 968 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7906 (tm-30) outliers start: 138 outliers final: 84 residues processed: 258 average time/residue: 0.5577 time to fit residues: 166.7376 Evaluate side-chains 240 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 139 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 786 MET Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 611 HIS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 889 TRP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 953 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 548 GLU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 764 GLU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 GLN Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 26 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 211 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 GLN C 754 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.111664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.088097 restraints weight = 39724.575| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.85 r_work: 0.3103 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20140 Z= 0.122 Angle : 0.521 11.709 27345 Z= 0.282 Chirality : 0.043 0.339 2850 Planarity : 0.004 0.065 3569 Dihedral : 6.211 59.754 2941 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.42 % Favored : 97.54 % Rotamer: Outliers : 4.59 % Allowed : 23.10 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.15), residues: 2561 helix: 1.36 (0.30), residues: 302 sheet: -0.65 (0.30), residues: 283 loop : -1.20 (0.12), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 913 TYR 0.006 0.001 TYR B 735 PHE 0.016 0.001 PHE A 208 TRP 0.023 0.001 TRP A 222 HIS 0.005 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00289 (20036) covalent geometry : angle 0.50530 (27128) SS BOND : bond 0.00251 ( 95) SS BOND : angle 1.20349 ( 190) hydrogen bonds : bond 0.03367 ( 533) hydrogen bonds : angle 4.57194 ( 1728) link_NAG-ASN : bond 0.00344 ( 9) link_NAG-ASN : angle 2.89807 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 141 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7605 (p0) cc_final: 0.7145 (p0) REVERT: A 166 ASN cc_start: 0.7751 (m110) cc_final: 0.7488 (t160) REVERT: A 392 ARG cc_start: 0.8847 (mtp180) cc_final: 0.8469 (mtm110) REVERT: A 644 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7328 (tp40) REVERT: A 649 MET cc_start: 0.8885 (mtm) cc_final: 0.8659 (mtp) REVERT: A 970 LEU cc_start: 0.8364 (tp) cc_final: 0.8027 (tm) REVERT: B 159 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7627 (ptp) REVERT: B 160 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7072 (pmt-80) REVERT: B 163 ARG cc_start: 0.7501 (mtm-85) cc_final: 0.7151 (mtm180) REVERT: B 171 ARG cc_start: 0.7077 (ttt180) cc_final: 0.6828 (tpt170) REVERT: B 199 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8156 (mt0) REVERT: B 343 TRP cc_start: 0.9157 (OUTLIER) cc_final: 0.8533 (p90) REVERT: B 476 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8278 (mmp80) REVERT: B 611 HIS cc_start: 0.7421 (OUTLIER) cc_final: 0.6836 (m-70) REVERT: B 1005 LEU cc_start: 0.8435 (tp) cc_final: 0.8209 (tp) REVERT: B 1011 ARG cc_start: 0.7832 (mmm160) cc_final: 0.7091 (mtp85) REVERT: B 1023 ASP cc_start: 0.7557 (p0) cc_final: 0.7254 (m-30) REVERT: C 208 PHE cc_start: 0.8649 (p90) cc_final: 0.8392 (p90) REVERT: C 226 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6336 (tm) REVERT: C 507 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7568 (t80) REVERT: C 548 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: C 572 ASP cc_start: 0.8359 (p0) cc_final: 0.7489 (m-30) REVERT: C 599 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8632 (ttmt) REVERT: C 718 GLN cc_start: 0.7164 (mp10) cc_final: 0.6901 (pm20) REVERT: C 720 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7543 (mtm110) REVERT: C 888 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8982 (ttp) outliers start: 96 outliers final: 59 residues processed: 219 average time/residue: 0.5623 time to fit residues: 141.2897 Evaluate side-chains 208 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 137 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 786 MET Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 239 LYS Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 343 TRP Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 611 HIS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 548 GLU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 24 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 164 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 GLN ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 HIS C 391 GLN C 413 GLN C 754 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.108651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.084113 restraints weight = 40159.707| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.66 r_work: 0.3055 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 20140 Z= 0.355 Angle : 0.710 11.937 27345 Z= 0.381 Chirality : 0.051 0.423 2850 Planarity : 0.005 0.078 3569 Dihedral : 6.602 59.298 2936 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 5.79 % Allowed : 22.72 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.14), residues: 2561 helix: 0.64 (0.29), residues: 309 sheet: -0.74 (0.29), residues: 296 loop : -1.48 (0.12), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 941 TYR 0.014 0.003 TYR C 298 PHE 0.022 0.002 PHE B 842 TRP 0.026 0.002 TRP A 222 HIS 0.012 0.002 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00856 (20036) covalent geometry : angle 0.69108 (27128) SS BOND : bond 0.00538 ( 95) SS BOND : angle 1.70459 ( 190) hydrogen bonds : bond 0.04915 ( 533) hydrogen bonds : angle 5.22514 ( 1728) link_NAG-ASN : bond 0.00620 ( 9) link_NAG-ASN : angle 3.24309 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 149 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7496 (p0) cc_final: 0.6864 (p0) REVERT: A 166 ASN cc_start: 0.7853 (m110) cc_final: 0.7541 (t160) REVERT: A 182 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7660 (t) REVERT: A 184 CYS cc_start: 0.6963 (m) cc_final: 0.6644 (m) REVERT: A 223 PHE cc_start: 0.5827 (OUTLIER) cc_final: 0.5312 (t80) REVERT: A 392 ARG cc_start: 0.8827 (mtp180) cc_final: 0.8427 (mtm110) REVERT: A 609 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7693 (m-40) REVERT: A 644 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7645 (tp40) REVERT: A 649 MET cc_start: 0.8907 (mtm) cc_final: 0.8687 (mtp) REVERT: A 686 GLN cc_start: 0.8411 (mp10) cc_final: 0.8040 (mp10) REVERT: A 970 LEU cc_start: 0.8429 (tp) cc_final: 0.8073 (tm) REVERT: B 159 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8050 (ptt) REVERT: B 160 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7083 (pmt-80) REVERT: B 163 ARG cc_start: 0.7451 (mtm-85) cc_final: 0.7128 (mtm-85) REVERT: B 171 ARG cc_start: 0.7332 (ttt180) cc_final: 0.7021 (tpt170) REVERT: B 199 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: B 460 LEU cc_start: 0.8624 (mt) cc_final: 0.8413 (mt) REVERT: B 889 TRP cc_start: 0.9194 (OUTLIER) cc_final: 0.7816 (m100) REVERT: B 981 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7122 (mm-30) REVERT: B 1005 LEU cc_start: 0.8643 (tp) cc_final: 0.8418 (tp) REVERT: B 1011 ARG cc_start: 0.7854 (mmm160) cc_final: 0.7091 (mtp85) REVERT: B 1023 ASP cc_start: 0.7740 (p0) cc_final: 0.7298 (m-30) REVERT: C 208 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8502 (p90) REVERT: C 226 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6363 (tm) REVERT: C 252 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5867 (mp0) REVERT: C 548 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: C 572 ASP cc_start: 0.8234 (p0) cc_final: 0.7388 (m-30) REVERT: C 599 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8652 (ttmt) REVERT: C 718 GLN cc_start: 0.7294 (mp10) cc_final: 0.7009 (pm20) REVERT: C 720 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7442 (ptp-110) REVERT: C 794 ARG cc_start: 0.6816 (mmt90) cc_final: 0.6138 (tpp-160) REVERT: C 888 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.9030 (ttp) outliers start: 121 outliers final: 81 residues processed: 250 average time/residue: 0.5433 time to fit residues: 155.6839 Evaluate side-chains 237 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 142 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 786 MET Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 932 GLN Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 889 TRP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 953 VAL Chi-restraints excluded: chain B residue 1015 HIS Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 548 GLU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 764 GLU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 112 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 GLN B 189 ASN ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN C 391 GLN C 413 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.110761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.087337 restraints weight = 39895.916| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.87 r_work: 0.3084 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20140 Z= 0.160 Angle : 0.560 13.972 27345 Z= 0.302 Chirality : 0.045 0.462 2850 Planarity : 0.004 0.070 3569 Dihedral : 5.997 59.831 2932 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 5.02 % Allowed : 23.48 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.15), residues: 2561 helix: 1.13 (0.30), residues: 304 sheet: -0.69 (0.29), residues: 296 loop : -1.36 (0.12), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 913 TYR 0.009 0.002 TYR B 354 PHE 0.018 0.001 PHE A 208 TRP 0.030 0.001 TRP A 222 HIS 0.006 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00383 (20036) covalent geometry : angle 0.54271 (27128) SS BOND : bond 0.00280 ( 95) SS BOND : angle 1.17127 ( 190) hydrogen bonds : bond 0.03661 ( 533) hydrogen bonds : angle 4.70182 ( 1728) link_NAG-ASN : bond 0.00433 ( 9) link_NAG-ASN : angle 3.40521 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 140 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7562 (p0) cc_final: 0.6948 (p0) REVERT: A 166 ASN cc_start: 0.7783 (m110) cc_final: 0.7565 (t160) REVERT: A 184 CYS cc_start: 0.6839 (m) cc_final: 0.6559 (m) REVERT: A 223 PHE cc_start: 0.5683 (OUTLIER) cc_final: 0.5235 (t80) REVERT: A 392 ARG cc_start: 0.8868 (mtp180) cc_final: 0.8469 (mtm110) REVERT: A 644 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7308 (tp40) REVERT: A 649 MET cc_start: 0.8900 (mtm) cc_final: 0.8689 (mtp) REVERT: A 970 LEU cc_start: 0.8387 (tp) cc_final: 0.8037 (tm) REVERT: B 159 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8060 (ptt) REVERT: B 160 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7117 (pmt-80) REVERT: B 163 ARG cc_start: 0.7488 (mtm-85) cc_final: 0.7181 (mtm-85) REVERT: B 171 ARG cc_start: 0.7164 (ttt180) cc_final: 0.6942 (tpt170) REVERT: B 199 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: B 208 PHE cc_start: 0.7133 (t80) cc_final: 0.6877 (t80) REVERT: B 476 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8263 (mmp80) REVERT: B 611 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.7061 (m-70) REVERT: B 981 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7002 (mm-30) REVERT: B 1011 ARG cc_start: 0.7859 (mmm160) cc_final: 0.7122 (mtp85) REVERT: B 1023 ASP cc_start: 0.7697 (p0) cc_final: 0.7395 (m-30) REVERT: C 208 PHE cc_start: 0.8642 (p90) cc_final: 0.8404 (p90) REVERT: C 226 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6420 (tm) REVERT: C 485 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7692 (mm) REVERT: C 548 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: C 572 ASP cc_start: 0.8376 (p0) cc_final: 0.7528 (m-30) REVERT: C 599 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8618 (ttmt) REVERT: C 720 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7583 (ptp-110) outliers start: 105 outliers final: 77 residues processed: 228 average time/residue: 0.5214 time to fit residues: 136.3403 Evaluate side-chains 225 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 137 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 786 MET Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 611 HIS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 953 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1028 CYS Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 548 GLU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 59 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 180 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 219 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS A 932 GLN B 189 ASN ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.111750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.088121 restraints weight = 39634.910| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.84 r_work: 0.3098 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20140 Z= 0.122 Angle : 0.523 12.144 27345 Z= 0.282 Chirality : 0.044 0.529 2850 Planarity : 0.004 0.064 3569 Dihedral : 5.681 59.040 2932 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 4.16 % Allowed : 24.44 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.15), residues: 2561 helix: 1.52 (0.30), residues: 302 sheet: -0.77 (0.30), residues: 277 loop : -1.24 (0.12), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 913 TYR 0.008 0.001 TYR C 354 PHE 0.019 0.001 PHE A 208 TRP 0.029 0.001 TRP A 222 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00290 (20036) covalent geometry : angle 0.50955 (27128) SS BOND : bond 0.00237 ( 95) SS BOND : angle 0.99672 ( 190) hydrogen bonds : bond 0.03216 ( 533) hydrogen bonds : angle 4.40502 ( 1728) link_NAG-ASN : bond 0.00275 ( 9) link_NAG-ASN : angle 3.06119 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 148 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7556 (p0) cc_final: 0.6967 (p0) REVERT: A 166 ASN cc_start: 0.7851 (m110) cc_final: 0.7606 (t160) REVERT: A 184 CYS cc_start: 0.6837 (m) cc_final: 0.6528 (m) REVERT: A 223 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.5077 (t80) REVERT: A 392 ARG cc_start: 0.8846 (mtp180) cc_final: 0.8450 (mtm110) REVERT: A 609 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7580 (m-40) REVERT: A 644 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7355 (tp40) REVERT: A 649 MET cc_start: 0.8813 (mtm) cc_final: 0.8598 (mtp) REVERT: A 970 LEU cc_start: 0.8378 (tp) cc_final: 0.8108 (tm) REVERT: B 159 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7597 (ptp) REVERT: B 160 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7083 (pmt-80) REVERT: B 163 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.7178 (mtm-85) REVERT: B 199 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8017 (mt0) REVERT: B 283 PHE cc_start: 0.8753 (t80) cc_final: 0.8525 (t80) REVERT: B 343 TRP cc_start: 0.9165 (OUTLIER) cc_final: 0.8623 (p90) REVERT: B 476 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8239 (mmp80) REVERT: B 611 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.7009 (m-70) REVERT: B 1005 LEU cc_start: 0.8330 (tp) cc_final: 0.8066 (tp) REVERT: B 1011 ARG cc_start: 0.7863 (mmm160) cc_final: 0.7120 (mtp85) REVERT: C 208 PHE cc_start: 0.8608 (p90) cc_final: 0.8384 (p90) REVERT: C 226 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6424 (tm) REVERT: C 548 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: C 572 ASP cc_start: 0.8356 (p0) cc_final: 0.7514 (m-30) REVERT: C 599 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8634 (ttmt) REVERT: C 720 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7590 (mtm110) outliers start: 87 outliers final: 66 residues processed: 223 average time/residue: 0.5480 time to fit residues: 140.4350 Evaluate side-chains 216 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 138 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 786 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 343 TRP Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 611 HIS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 953 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1028 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 548 GLU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 169 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 217 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS A 932 GLN ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.112005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088514 restraints weight = 40023.474| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.91 r_work: 0.3107 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20140 Z= 0.121 Angle : 0.531 13.236 27345 Z= 0.287 Chirality : 0.043 0.505 2850 Planarity : 0.004 0.063 3569 Dihedral : 5.486 58.701 2929 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.07 % Rotamer: Outliers : 3.78 % Allowed : 24.96 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.15), residues: 2561 helix: 1.67 (0.30), residues: 302 sheet: -0.73 (0.30), residues: 262 loop : -1.17 (0.12), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 913 TYR 0.015 0.001 TYR C 735 PHE 0.021 0.001 PHE A 208 TRP 0.030 0.001 TRP A 222 HIS 0.006 0.001 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00287 (20036) covalent geometry : angle 0.51813 (27128) SS BOND : bond 0.00231 ( 95) SS BOND : angle 0.97143 ( 190) hydrogen bonds : bond 0.03167 ( 533) hydrogen bonds : angle 4.37811 ( 1728) link_NAG-ASN : bond 0.00313 ( 9) link_NAG-ASN : angle 3.08794 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 140 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7589 (p0) cc_final: 0.6973 (p0) REVERT: A 166 ASN cc_start: 0.7895 (m110) cc_final: 0.7594 (t160) REVERT: A 182 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7554 (t) REVERT: A 223 PHE cc_start: 0.5938 (OUTLIER) cc_final: 0.5292 (t80) REVERT: A 392 ARG cc_start: 0.8823 (mtp180) cc_final: 0.8398 (mtm110) REVERT: A 609 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7542 (m-40) REVERT: A 644 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7374 (tp40) REVERT: A 649 MET cc_start: 0.8826 (mtm) cc_final: 0.8602 (mtp) REVERT: A 970 LEU cc_start: 0.8321 (tp) cc_final: 0.7999 (tm) REVERT: B 159 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7557 (ptp) REVERT: B 160 ARG cc_start: 0.7829 (pmt-80) cc_final: 0.7062 (pmt-80) REVERT: B 163 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7170 (mtm180) REVERT: B 199 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: B 343 TRP cc_start: 0.9143 (OUTLIER) cc_final: 0.8570 (p90) REVERT: B 476 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8237 (mmp80) REVERT: B 611 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.7058 (m-70) REVERT: B 1005 LEU cc_start: 0.8219 (tp) cc_final: 0.7947 (tp) REVERT: B 1011 ARG cc_start: 0.7913 (mmm160) cc_final: 0.7159 (mtp85) REVERT: C 208 PHE cc_start: 0.8680 (p90) cc_final: 0.8462 (p90) REVERT: C 226 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6280 (tm) REVERT: C 548 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: C 572 ASP cc_start: 0.8366 (p0) cc_final: 0.7473 (m-30) REVERT: C 599 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8657 (ttmt) REVERT: C 720 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7443 (mtm110) REVERT: C 983 GLU cc_start: 0.6277 (mm-30) cc_final: 0.5988 (mm-30) outliers start: 79 outliers final: 63 residues processed: 210 average time/residue: 0.5351 time to fit residues: 129.7232 Evaluate side-chains 210 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 135 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 786 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 932 GLN Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 343 TRP Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 611 HIS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1028 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 548 GLU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 735 TYR Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 33 optimal weight: 0.6980 chunk 209 optimal weight: 0.4980 chunk 139 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS A 932 GLN B 189 ASN ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 GLN C 754 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.111827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.088232 restraints weight = 39943.524| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.92 r_work: 0.3108 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20140 Z= 0.133 Angle : 0.530 12.376 27345 Z= 0.286 Chirality : 0.044 0.471 2850 Planarity : 0.004 0.064 3569 Dihedral : 5.478 59.207 2928 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.12 % Favored : 96.84 % Rotamer: Outliers : 4.07 % Allowed : 24.49 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.15), residues: 2561 helix: 1.66 (0.30), residues: 305 sheet: -0.61 (0.30), residues: 266 loop : -1.18 (0.12), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 171 TYR 0.017 0.001 TYR C 735 PHE 0.024 0.001 PHE B 208 TRP 0.035 0.001 TRP A 222 HIS 0.005 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00317 (20036) covalent geometry : angle 0.51658 (27128) SS BOND : bond 0.00243 ( 95) SS BOND : angle 1.00712 ( 190) hydrogen bonds : bond 0.03260 ( 533) hydrogen bonds : angle 4.41778 ( 1728) link_NAG-ASN : bond 0.00307 ( 9) link_NAG-ASN : angle 2.94977 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7637.17 seconds wall clock time: 130 minutes 29.69 seconds (7829.69 seconds total)