Starting phenix.real_space_refine on Sat Jul 4 09:01:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nb5_49213/07_2026/9nb5_49213.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nb5_49213/07_2026/9nb5_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 { model { file = "/net/cci-nas-00/data/ceres_data/9nb5_49213/07_2026/9nb5_49213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nb5_49213/07_2026/9nb5_49213.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nb5_49213/07_2026/9nb5_49213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nb5_49213/07_2026/9nb5_49213.map" } 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-dev-6108/lib/python3.11/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, 42 Ad-hoc single atom residues: {' CA': 7} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 7 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, 42 Ad-hoc single atom residues: {' CA': 7} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 7 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, 42 Ad-hoc single atom residues: {' CA': 6} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.13, per 1000 atoms: 0.21 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: 1.41 Conformation dependent library (CDL) restraints added in 622.3 milliseconds 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: 0.75 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: 4.01 Time building geometry restraints manager: 1.90 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 3.250 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: 4.550 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.550 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 are 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/Z covalent geometry : bond 0.00336 / 0.16 (20036) covalent geometry : angle 0.52470 / 0.30 (27128) SS BOND : bond 0.00235 / 0.17 ( 95) SS BOND : angle 0.90493 / 0.56 ( 190) hydrogen bonds : bond 0.25542 / 17.21 ( 533) hydrogen bonds : angle 8.46109 / 6.03 ( 1728) link_NAG-ASN : bond 0.00294 / 0.20 ( 9) link_NAG-ASN : angle 3.10394 / 1.58 ( 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 : 0.544 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: 0.4709 time to fit residues: 116.5961 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 : 0.531 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.9980 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3727 r_free = 0.3727 target = 0.111252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082822 restraints weight = 39767.651| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.59 r_work: 0.3101 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20140 Z= 0.181 Angle : 0.555 6.938 27345 Z= 0.303 Chirality : 0.044 0.233 2850 Planarity : 0.004 0.067 3569 Dihedral : 6.437 59.932 2978 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.03 % Rotamer: Outliers : 4.93 % Allowed : 20.56 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.15), residues: 2561 helix: 0.88 (0.30), residues: 309 sheet: -0.07 (0.32), residues: 278 loop : -1.04 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 758 TYR 0.011 0.002 TYR A 465 PHE 0.032 0.002 PHE A 176 TRP 0.019 0.001 TRP A 910 HIS 0.008 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (20036) covalent geometry : angle 0.54556 / 0.30 (27128) SS BOND : bond 0.00316 / 0.22 ( 95) SS BOND : angle 1.09925 / 0.68 ( 190) hydrogen bonds : bond 0.04548 / 3.07 ( 533) hydrogen bonds : angle 5.40090 / 3.88 ( 1728) link_NAG-ASN : bond 0.00366 / 0.25 ( 9) link_NAG-ASN : angle 2.10892 / 1.18 ( 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 252 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 149 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASN cc_start: 0.7863 (m110) cc_final: 0.7194 (t0) REVERT: A 180 TRP cc_start: 0.6595 (m100) cc_final: 0.5968 (m100) REVERT: A 223 PHE cc_start: 0.5998 (OUTLIER) cc_final: 0.5493 (t80) REVERT: A 392 ARG cc_start: 0.8857 (mtp180) cc_final: 0.8300 (mtm110) REVERT: A 649 MET cc_start: 0.8911 (mtm) cc_final: 0.8684 (mtp) REVERT: A 722 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8840 (t) REVERT: A 889 TRP cc_start: 0.9392 (OUTLIER) cc_final: 0.9136 (m100) REVERT: A 970 LEU cc_start: 0.8274 (tp) cc_final: 0.7862 (tm) REVERT: B 160 ARG cc_start: 0.7606 (pmt-80) cc_final: 0.6885 (pmt-80) REVERT: B 163 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7661 (mtm-85) REVERT: B 208 PHE cc_start: 0.6852 (t80) cc_final: 0.6515 (OUTLIER) REVERT: B 460 LEU cc_start: 0.8536 (mt) cc_final: 0.8270 (tt) REVERT: B 611 HIS cc_start: 0.7428 (OUTLIER) cc_final: 0.6688 (m90) REVERT: B 889 TRP cc_start: 0.9153 (OUTLIER) cc_final: 0.7797 (m100) REVERT: B 977 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7547 (tptm) REVERT: B 981 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6970 (mm-30) REVERT: B 1023 ASP cc_start: 0.7656 (p0) cc_final: 0.7187 (m-30) REVERT: C 208 PHE cc_start: 0.8763 (p90) cc_final: 0.8551 (p90) REVERT: C 396 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7334 (mtpp) REVERT: C 507 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7269 (t80) REVERT: C 548 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8118 (tt0) REVERT: C 569 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.7332 (m-70) REVERT: C 572 ASP cc_start: 0.8135 (p0) cc_final: 0.7089 (m-30) REVERT: C 718 GLN cc_start: 0.6872 (mp10) cc_final: 0.6637 (mp10) REVERT: C 888 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8957 (ttp) outliers start: 103 outliers final: 55 residues processed: 237 average time/residue: 0.4520 time to fit residues: 123.5794 Evaluate side-chains 198 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 135 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 827 THR Chi-restraints excluded: chain A residue 889 TRP 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 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 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 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 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: 0.4980 chunk 143 optimal weight: 0.8980 chunk 133 optimal weight: 0.0870 chunk 144 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 159 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 HIS C 213 ASN C 391 GLN C 754 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.112984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.084606 restraints weight = 40199.013| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.62 r_work: 0.3130 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20140 Z= 0.104 Angle : 0.481 9.518 27345 Z= 0.262 Chirality : 0.042 0.215 2850 Planarity : 0.003 0.059 3569 Dihedral : 5.788 57.121 2948 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.50 % Favored : 97.46 % Rotamer: Outliers : 4.02 % Allowed : 21.71 % 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 are not related in a simple way. whole: -0.79 (0.15), residues: 2561 helix: 1.51 (0.30), residues: 307 sheet: -0.37 (0.31), residues: 291 loop : -0.94 (0.12), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 913 TYR 0.008 0.001 TYR C 735 PHE 0.018 0.001 PHE A 979 TRP 0.020 0.001 TRP A 222 HIS 0.005 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (20036) covalent geometry : angle 0.47089 / 0.26 (27128) SS BOND : bond 0.00223 / 0.16 ( 95) SS BOND : angle 0.86310 / 0.53 ( 190) hydrogen bonds : bond 0.03441 / 2.31 ( 533) hydrogen bonds : angle 4.63916 / 3.36 ( 1728) link_NAG-ASN : bond 0.00846 / 0.63 ( 9) link_NAG-ASN : angle 2.42199 / 1.25 ( 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 231 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 147 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASN cc_start: 0.7855 (m110) cc_final: 0.7229 (t0) REVERT: A 180 TRP cc_start: 0.6496 (m100) cc_final: 0.6004 (m100) REVERT: A 223 PHE cc_start: 0.6024 (OUTLIER) cc_final: 0.5470 (t80) REVERT: A 392 ARG cc_start: 0.8831 (mtp180) cc_final: 0.8291 (mtm110) REVERT: A 644 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7126 (tp40) REVERT: A 649 MET cc_start: 0.8825 (mtm) cc_final: 0.8601 (mtp) REVERT: A 722 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8878 (t) REVERT: A 970 LEU cc_start: 0.8290 (tp) cc_final: 0.7914 (tm) REVERT: B 460 LEU cc_start: 0.8528 (mt) cc_final: 0.8249 (tt) REVERT: B 476 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8029 (mmp80) REVERT: B 611 HIS cc_start: 0.7385 (OUTLIER) cc_final: 0.6622 (m90) REVERT: B 977 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7566 (tptm) REVERT: B 981 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6948 (mm-30) REVERT: B 1011 ARG cc_start: 0.7624 (mmm160) cc_final: 0.6881 (mtp85) REVERT: B 1023 ASP cc_start: 0.7459 (p0) cc_final: 0.7094 (m-30) REVERT: C 208 PHE cc_start: 0.8712 (p90) cc_final: 0.8497 (p90) REVERT: C 396 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7178 (mtpp) REVERT: C 507 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7290 (t80) REVERT: C 548 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8048 (tt0) REVERT: C 572 ASP cc_start: 0.8124 (p0) cc_final: 0.7161 (m-30) REVERT: C 718 GLN cc_start: 0.6855 (mp10) cc_final: 0.6587 (mp10) REVERT: C 888 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8879 (ttp) outliers start: 84 outliers final: 43 residues processed: 214 average time/residue: 0.4713 time to fit residues: 117.5082 Evaluate side-chains 194 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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 208 PHE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 333 VAL 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 466 GLU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 481 VAL 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 890 VAL 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 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 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: 0.5980 chunk 237 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 HIS C 284 GLN C 391 GLN C 754 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.112991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089287 restraints weight = 40059.432| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.91 r_work: 0.3120 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20140 Z= 0.118 Angle : 0.492 11.222 27345 Z= 0.266 Chirality : 0.042 0.327 2850 Planarity : 0.003 0.060 3569 Dihedral : 5.614 57.504 2938 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.34 % Rotamer: Outliers : 4.30 % Allowed : 22.00 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 2561 helix: 1.57 (0.30), residues: 307 sheet: -0.45 (0.30), residues: 296 loop : -0.94 (0.12), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 913 TYR 0.009 0.001 TYR A 465 PHE 0.016 0.001 PHE A 208 TRP 0.020 0.001 TRP A 222 HIS 0.005 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (20036) covalent geometry : angle 0.48069 / 0.26 (27128) SS BOND : bond 0.00253 / 0.18 ( 95) SS BOND : angle 0.93735 / 0.60 ( 190) hydrogen bonds : bond 0.03326 / 2.26 ( 533) hydrogen bonds : angle 4.51683 / 3.27 ( 1728) link_NAG-ASN : bond 0.00257 / 0.18 ( 9) link_NAG-ASN : angle 2.65841 / 1.35 ( 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 240 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 150 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7750 (p0) cc_final: 0.7284 (p0) REVERT: A 166 ASN cc_start: 0.7712 (m110) cc_final: 0.7192 (t0) REVERT: A 392 ARG cc_start: 0.8800 (mtp180) cc_final: 0.8396 (mtm110) REVERT: A 644 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7243 (tp40) REVERT: A 649 MET cc_start: 0.8826 (mtm) cc_final: 0.8607 (mtp) REVERT: A 722 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8880 (t) REVERT: A 812 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: A 889 TRP cc_start: 0.9370 (OUTLIER) cc_final: 0.9067 (m100) REVERT: A 970 LEU cc_start: 0.8445 (tp) cc_final: 0.8091 (tm) REVERT: B 159 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7455 (ptp) REVERT: B 160 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7481 (pmt-80) REVERT: B 199 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: B 476 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8236 (mmp80) REVERT: B 611 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6568 (m90) REVERT: B 977 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7695 (tptm) REVERT: B 981 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6951 (mm-30) REVERT: B 1011 ARG cc_start: 0.7728 (mmm160) cc_final: 0.7082 (mtp85) REVERT: B 1023 ASP cc_start: 0.7488 (p0) cc_final: 0.7228 (m-30) REVERT: C 208 PHE cc_start: 0.8654 (p90) cc_final: 0.8409 (p90) REVERT: C 226 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5885 (tm) REVERT: C 396 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7392 (mtpp) REVERT: C 507 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7457 (t80) REVERT: C 548 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8135 (tt0) REVERT: C 572 ASP cc_start: 0.8131 (p0) cc_final: 0.7260 (m-30) REVERT: C 718 GLN cc_start: 0.6768 (mp10) cc_final: 0.6507 (mp10) REVERT: C 888 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8901 (ttp) REVERT: C 1017 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8245 (mm-30) outliers start: 90 outliers final: 48 residues processed: 226 average time/residue: 0.4929 time to fit residues: 127.4488 Evaluate side-chains 201 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 140 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 355 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 HIS 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 889 TRP 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 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 161 LEU Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 333 VAL 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 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 812 GLU Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 822 MET 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 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 485 ILE Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 535 GLU 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 888 MET Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 196 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 234 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.110720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.087094 restraints weight = 40055.665| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.93 r_work: 0.3075 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20140 Z= 0.229 Angle : 0.607 13.146 27345 Z= 0.326 Chirality : 0.047 0.392 2850 Planarity : 0.004 0.069 3569 Dihedral : 6.043 58.863 2932 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 5.45 % Allowed : 21.47 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.15), residues: 2561 helix: 1.12 (0.29), residues: 309 sheet: -0.56 (0.31), residues: 272 loop : -1.15 (0.12), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 941 TYR 0.011 0.002 TYR A 424 PHE 0.017 0.002 PHE A 208 TRP 0.022 0.002 TRP A 910 HIS 0.009 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (20036) covalent geometry : angle 0.58567 / 0.32 (27128) SS BOND : bond 0.00384 / 0.27 ( 95) SS BOND : angle 1.59367 / 0.99 ( 190) hydrogen bonds : bond 0.04182 / 2.86 ( 533) hydrogen bonds : angle 4.91612 / 3.54 ( 1728) link_NAG-ASN : bond 0.00561 / 0.40 ( 9) link_NAG-ASN : angle 3.17663 / 1.60 ( 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 256 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 142 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7673 (p0) cc_final: 0.7189 (p0) REVERT: A 166 ASN cc_start: 0.7800 (m110) cc_final: 0.7172 (t0) REVERT: A 392 ARG cc_start: 0.8853 (mtp180) cc_final: 0.8398 (mtm110) REVERT: A 467 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: A 644 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7355 (tp40) REVERT: A 649 MET cc_start: 0.8886 (mtm) cc_final: 0.8682 (mtp) REVERT: A 686 GLN cc_start: 0.8365 (mp10) cc_final: 0.7995 (mp10) REVERT: A 812 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: A 970 LEU cc_start: 0.8371 (tp) cc_final: 0.8021 (tm) REVERT: B 159 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7639 (ptp) REVERT: B 160 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7481 (pmt-80) REVERT: B 171 ARG cc_start: 0.7106 (ttt180) cc_final: 0.6623 (tpt170) REVERT: B 199 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: B 476 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7784 (mmp80) REVERT: B 611 HIS cc_start: 0.7551 (OUTLIER) cc_final: 0.6936 (m-70) REVERT: B 889 TRP cc_start: 0.9191 (OUTLIER) cc_final: 0.7886 (m100) REVERT: B 981 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7047 (mm-30) REVERT: B 1011 ARG cc_start: 0.7653 (mmm160) cc_final: 0.7070 (mtp85) REVERT: B 1023 ASP cc_start: 0.7720 (p0) cc_final: 0.7351 (m-30) REVERT: C 226 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6190 (tm) REVERT: C 507 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7558 (t80) REVERT: C 548 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: C 572 ASP cc_start: 0.8356 (p0) cc_final: 0.7444 (m-30) REVERT: C 599 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8644 (ttmt) REVERT: C 718 GLN cc_start: 0.6914 (mp10) cc_final: 0.6680 (mp10) REVERT: C 750 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7622 (tp) REVERT: C 888 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.9026 (ttp) outliers start: 114 outliers final: 70 residues processed: 238 average time/residue: 0.4592 time to fit residues: 126.4588 Evaluate side-chains 222 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 137 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL 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 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 467 GLU Chi-restraints excluded: chain A residue 481 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 957 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 161 LEU 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 333 VAL 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 484 ASP 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 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 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 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 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 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 949 SER Chi-restraints excluded: chain C residue 960 LEU 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: 0.8980 chunk 97 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 211 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 187 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 91 optimal weight: 0.0570 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 HIS B 240 HIS ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 GLN C 284 GLN C 391 GLN C 754 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.112719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088840 restraints weight = 39777.549| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.82 r_work: 0.3127 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20140 Z= 0.106 Angle : 0.499 13.048 27345 Z= 0.269 Chirality : 0.043 0.430 2850 Planarity : 0.003 0.061 3569 Dihedral : 5.661 58.512 2932 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer: Outliers : 4.69 % Allowed : 22.72 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.15), residues: 2561 helix: 1.60 (0.30), residues: 305 sheet: -0.58 (0.30), residues: 285 loop : -1.05 (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 354 PHE 0.016 0.001 PHE A 208 TRP 0.025 0.001 TRP C 782 HIS 0.005 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (20036) covalent geometry : angle 0.48307 / 0.26 (27128) SS BOND : bond 0.00225 / 0.16 ( 95) SS BOND : angle 1.09845 / 0.67 ( 190) hydrogen bonds : bond 0.03109 / 2.10 ( 533) hydrogen bonds : angle 4.38107 / 3.17 ( 1728) link_NAG-ASN : bond 0.00454 / 0.33 ( 9) link_NAG-ASN : angle 3.04775 / 1.51 ( 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 244 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 146 time to evaluate : 0.846 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: 0.7722 (p0) cc_final: 0.7177 (p0) REVERT: A 166 ASN cc_start: 0.7713 (m110) cc_final: 0.7177 (t0) REVERT: A 223 PHE cc_start: 0.5697 (OUTLIER) cc_final: 0.5185 (t80) REVERT: A 392 ARG cc_start: 0.8775 (mtp180) cc_final: 0.8369 (mtm110) REVERT: A 476 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8491 (mmt90) REVERT: A 644 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7279 (tp40) REVERT: A 649 MET cc_start: 0.8807 (mtm) cc_final: 0.8581 (mtp) REVERT: A 812 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: A 970 LEU cc_start: 0.8454 (tp) cc_final: 0.8101 (tm) REVERT: B 159 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7437 (ptp) REVERT: B 160 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7427 (pmt-80) REVERT: B 171 ARG cc_start: 0.6955 (ttt180) cc_final: 0.6687 (tpt170) REVERT: B 199 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: B 367 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6974 (p0) REVERT: B 476 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8376 (mmp80) REVERT: B 611 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.6872 (m-70) REVERT: B 981 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6906 (mm-30) REVERT: B 1005 LEU cc_start: 0.8308 (tp) cc_final: 0.8049 (tp) REVERT: B 1011 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7067 (mtp85) REVERT: C 226 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6202 (tm) REVERT: C 396 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7519 (mtpp) REVERT: C 507 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7455 (t80) REVERT: C 548 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: C 572 ASP cc_start: 0.8263 (p0) cc_final: 0.7367 (m-30) REVERT: C 718 GLN cc_start: 0.6901 (mp10) cc_final: 0.6633 (mp10) REVERT: C 888 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8935 (ttp) outliers start: 98 outliers final: 52 residues processed: 229 average time/residue: 0.4780 time to fit residues: 125.7621 Evaluate side-chains 207 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 140 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 311 THR Chi-restraints excluded: chain A residue 355 CYS 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 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 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 957 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 197 CYS Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 259 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 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 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 812 GLU 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 1028 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 365 CYS 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 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 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: 0.8980 chunk 172 optimal weight: 5.9990 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: 4.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 HIS A 685 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.110388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.086705 restraints weight = 39987.654| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.91 r_work: 0.3071 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20140 Z= 0.238 Angle : 0.607 12.998 27345 Z= 0.327 Chirality : 0.047 0.422 2850 Planarity : 0.004 0.069 3569 Dihedral : 5.865 54.976 2930 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 4.97 % Allowed : 22.86 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 2561 helix: 1.16 (0.30), residues: 307 sheet: -0.63 (0.30), residues: 286 loop : -1.21 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 941 TYR 0.011 0.002 TYR A 424 PHE 0.019 0.002 PHE A 208 TRP 0.025 0.002 TRP A 222 HIS 0.010 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 (20036) covalent geometry : angle 0.58981 / 0.32 (27128) SS BOND : bond 0.00385 / 0.27 ( 95) SS BOND : angle 1.41365 / 0.91 ( 190) hydrogen bonds : bond 0.04125 / 2.83 ( 533) hydrogen bonds : angle 4.84084 / 3.48 ( 1728) link_NAG-ASN : bond 0.00435 / 0.29 ( 9) link_NAG-ASN : angle 3.11424 / 1.59 ( 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 253 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 149 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7549 (p0) cc_final: 0.6959 (p0) REVERT: A 166 ASN cc_start: 0.7832 (m110) cc_final: 0.7506 (t160) REVERT: A 184 CYS cc_start: 0.6940 (m) cc_final: 0.6601 (m) REVERT: A 223 PHE cc_start: 0.5738 (OUTLIER) cc_final: 0.5242 (t80) REVERT: A 392 ARG cc_start: 0.8868 (mtp180) cc_final: 0.8476 (mtm110) REVERT: A 644 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7379 (tp40) REVERT: A 649 MET cc_start: 0.8889 (mtm) cc_final: 0.8670 (mtp) REVERT: A 970 LEU cc_start: 0.8384 (tp) cc_final: 0.8055 (tm) REVERT: B 159 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8079 (ptt) REVERT: B 160 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7293 (pmt-80) REVERT: B 163 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.7211 (mtm-85) REVERT: B 171 ARG cc_start: 0.7152 (ttt180) cc_final: 0.6869 (tpt170) REVERT: B 199 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: B 476 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7686 (mmp80) REVERT: B 611 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.6904 (m-70) REVERT: B 889 TRP cc_start: 0.9184 (OUTLIER) cc_final: 0.7890 (m100) REVERT: B 913 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7226 (ptt180) REVERT: B 981 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7016 (mm-30) REVERT: B 1005 LEU cc_start: 0.8552 (tp) cc_final: 0.8298 (tp) REVERT: B 1011 ARG cc_start: 0.7718 (mmm160) cc_final: 0.6981 (mtp85) REVERT: C 226 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6265 (tm) REVERT: C 252 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6383 (mm-30) REVERT: C 507 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7599 (t80) REVERT: C 548 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: C 572 ASP cc_start: 0.8342 (p0) cc_final: 0.7465 (m-30) REVERT: C 718 GLN cc_start: 0.6978 (mp10) cc_final: 0.6718 (mp10) REVERT: C 720 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7484 (mtp-110) outliers start: 104 outliers final: 71 residues processed: 235 average time/residue: 0.4681 time to fit residues: 127.5197 Evaluate side-chains 226 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 143 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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 447 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 610 SER Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 752 ASP 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 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 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 333 VAL Chi-restraints excluded: chain B residue 365 CYS 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 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 665 THR Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 750 LEU 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 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 252 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 365 CYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 112 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 210 optimal weight: 0.6980 chunk 168 optimal weight: 0.3980 chunk 185 optimal weight: 0.6980 chunk 121 optimal weight: 0.2980 chunk 239 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 HIS A 932 GLN B 187 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 = 0.3742 r_free = 0.3742 target = 0.112304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.088644 restraints weight = 39894.613| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.83 r_work: 0.3118 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20140 Z= 0.118 Angle : 0.519 14.114 27345 Z= 0.280 Chirality : 0.043 0.488 2850 Planarity : 0.003 0.063 3569 Dihedral : 5.557 54.151 2929 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.50 % Favored : 97.46 % Rotamer: Outliers : 4.11 % Allowed : 23.82 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 2561 helix: 1.55 (0.30), residues: 305 sheet: -0.61 (0.29), residues: 305 loop : -1.11 (0.12), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 930 TYR 0.006 0.001 TYR B 843 PHE 0.020 0.001 PHE A 208 TRP 0.026 0.001 TRP A 222 HIS 0.004 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (20036) covalent geometry : angle 0.50394 / 0.28 (27128) SS BOND : bond 0.00227 / 0.16 ( 95) SS BOND : angle 0.99923 / 0.63 ( 190) hydrogen bonds : bond 0.03182 / 2.15 ( 533) hydrogen bonds : angle 4.41747 / 3.19 ( 1728) link_NAG-ASN : bond 0.00355 / 0.25 ( 9) link_NAG-ASN : angle 3.25842 / 1.61 ( 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 232 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 146 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7562 (p0) cc_final: 0.6974 (p0) REVERT: A 166 ASN cc_start: 0.7725 (m110) cc_final: 0.7503 (t160) REVERT: A 223 PHE cc_start: 0.5590 (OUTLIER) cc_final: 0.5118 (t80) REVERT: A 392 ARG cc_start: 0.8804 (mtp180) cc_final: 0.8417 (mtm110) REVERT: A 644 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7275 (tp40) REVERT: A 649 MET cc_start: 0.8789 (mtm) cc_final: 0.8571 (mtp) REVERT: A 970 LEU cc_start: 0.8458 (tp) cc_final: 0.8092 (tm) REVERT: B 159 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7976 (ptt) REVERT: B 160 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7453 (pmt-80) REVERT: B 163 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.7163 (mtm-85) REVERT: B 199 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: B 343 TRP cc_start: 0.9102 (OUTLIER) cc_final: 0.8575 (p90) REVERT: B 476 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8247 (mmp80) REVERT: B 611 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7035 (m-70) REVERT: B 884 MET cc_start: 0.7417 (mtm) cc_final: 0.6913 (mtt) REVERT: B 913 ARG cc_start: 0.7994 (mtp-110) cc_final: 0.7774 (ptt180) REVERT: B 1005 LEU cc_start: 0.8391 (tp) cc_final: 0.8142 (tp) REVERT: B 1011 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7154 (mtp85) REVERT: C 226 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6351 (tm) REVERT: C 391 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.5562 (mp-120) REVERT: C 507 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7521 (t80) REVERT: C 548 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: C 572 ASP cc_start: 0.8331 (p0) cc_final: 0.7505 (m-30) REVERT: C 718 GLN cc_start: 0.6933 (mp10) cc_final: 0.6670 (mp10) REVERT: C 720 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7606 (mtm110) REVERT: C 750 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7505 (tp) outliers start: 86 outliers final: 60 residues processed: 218 average time/residue: 0.4598 time to fit residues: 115.9200 Evaluate side-chains 211 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 138 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 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 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 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 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 197 CYS Chi-restraints excluded: chain B residue 199 GLN 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 333 VAL 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 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 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 679 SER Chi-restraints excluded: chain B residue 750 LEU 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 890 VAL Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 1028 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 391 GLN 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 732 VAL Chi-restraints excluded: chain C residue 750 LEU 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 949 SER Chi-restraints excluded: chain C residue 960 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 59 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 192 optimal weight: 0.0170 chunk 180 optimal weight: 0.0770 chunk 63 optimal weight: 0.2980 chunk 121 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 HIS A 932 GLN A1027 ASN B 189 ASN ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.113287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089523 restraints weight = 39709.028| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.81 r_work: 0.3136 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20140 Z= 0.097 Angle : 0.501 11.797 27345 Z= 0.271 Chirality : 0.042 0.441 2850 Planarity : 0.003 0.058 3569 Dihedral : 5.154 55.444 2927 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.34 % Rotamer: Outliers : 3.40 % Allowed : 24.58 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.15), residues: 2561 helix: 1.85 (0.30), residues: 305 sheet: -0.72 (0.30), residues: 291 loop : -1.01 (0.12), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 171 TYR 0.007 0.001 TYR C 354 PHE 0.021 0.001 PHE A 208 TRP 0.026 0.001 TRP A 222 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (20036) covalent geometry : angle 0.48974 / 0.27 (27128) SS BOND : bond 0.00201 / 0.14 ( 95) SS BOND : angle 0.87101 / 0.55 ( 190) hydrogen bonds : bond 0.02885 / 1.95 ( 533) hydrogen bonds : angle 4.23682 / 3.07 ( 1728) link_NAG-ASN : bond 0.00278 / 0.20 ( 9) link_NAG-ASN : angle 2.79287 / 1.38 ( 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 217 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 146 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7600 (p0) cc_final: 0.6867 (p0) REVERT: A 166 ASN cc_start: 0.7815 (m110) cc_final: 0.7573 (t160) REVERT: A 182 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7625 (t) REVERT: A 223 PHE cc_start: 0.5604 (OUTLIER) cc_final: 0.5049 (t80) REVERT: A 392 ARG cc_start: 0.8805 (mtp180) cc_final: 0.8444 (mtm110) REVERT: A 649 MET cc_start: 0.8780 (mtm) cc_final: 0.8548 (mtp) REVERT: A 970 LEU cc_start: 0.8445 (tp) cc_final: 0.8104 (tm) REVERT: B 159 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7926 (ptt) REVERT: B 160 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7392 (pmt-80) REVERT: B 199 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: B 343 TRP cc_start: 0.9076 (OUTLIER) cc_final: 0.8618 (p90) REVERT: B 476 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8208 (mmp80) REVERT: B 611 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7133 (m-70) REVERT: B 822 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8638 (mtm) REVERT: B 884 MET cc_start: 0.7398 (mtm) cc_final: 0.6841 (mtt) REVERT: B 981 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6861 (mm-30) REVERT: B 1005 LEU cc_start: 0.8293 (tp) cc_final: 0.8034 (tp) REVERT: B 1011 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7014 (mtp85) REVERT: C 226 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6324 (tm) REVERT: C 507 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7540 (t80) REVERT: C 548 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: C 572 ASP cc_start: 0.8247 (p0) cc_final: 0.7403 (m-30) REVERT: C 637 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.5692 (mtp180) REVERT: C 718 GLN cc_start: 0.6827 (mp10) cc_final: 0.6568 (mp10) REVERT: C 720 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7626 (mtm110) REVERT: C 750 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7556 (tp) REVERT: C 983 GLU cc_start: 0.6166 (mm-30) cc_final: 0.5846 (mm-30) outliers start: 71 outliers final: 49 residues processed: 207 average time/residue: 0.4956 time to fit residues: 118.0920 Evaluate side-chains 208 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 145 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 404 LEU 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 575 VAL 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 957 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 197 CYS Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 343 TRP Chi-restraints excluded: chain B residue 365 CYS 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 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 679 SER Chi-restraints excluded: chain B residue 750 LEU 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 890 VAL Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 1028 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 365 CYS 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 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 637 ARG Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 750 LEU 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 949 SER Chi-restraints excluded: chain C residue 960 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 169 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 217 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 36 optimal weight: 0.0070 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 HIS A 932 GLN B 189 ASN ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 GLN ** 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 = 0.3746 r_free = 0.3746 target = 0.112545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.088696 restraints weight = 39970.962| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.83 r_work: 0.3119 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1839 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= 0.126 Angle : 0.518 11.483 27345 Z= 0.280 Chirality : 0.043 0.405 2850 Planarity : 0.004 0.060 3569 Dihedral : 5.216 57.788 2926 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.81 % Favored : 97.15 % Rotamer: Outliers : 3.49 % Allowed : 24.73 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.15), residues: 2561 helix: 1.79 (0.30), residues: 305 sheet: -0.42 (0.30), residues: 295 loop : -1.02 (0.12), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 171 TYR 0.008 0.001 TYR B 354 PHE 0.023 0.001 PHE A 208 TRP 0.027 0.001 TRP A 222 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (20036) covalent geometry : angle 0.50630 / 0.28 (27128) SS BOND : bond 0.00236 / 0.17 ( 95) SS BOND : angle 0.98874 / 0.63 ( 190) hydrogen bonds : bond 0.03150 / 2.14 ( 533) hydrogen bonds : angle 4.33326 / 3.13 ( 1728) link_NAG-ASN : bond 0.00299 / 0.21 ( 9) link_NAG-ASN : angle 2.71826 / 1.36 ( 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 216 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 143 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7591 (p0) cc_final: 0.6846 (p0) REVERT: A 166 ASN cc_start: 0.7837 (m110) cc_final: 0.7559 (t160) REVERT: A 182 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7686 (t) REVERT: A 223 PHE cc_start: 0.5598 (OUTLIER) cc_final: 0.5032 (t80) REVERT: A 392 ARG cc_start: 0.8813 (mtp180) cc_final: 0.8428 (mtm110) REVERT: A 649 MET cc_start: 0.8791 (mtm) cc_final: 0.8567 (mtp) REVERT: A 970 LEU cc_start: 0.8354 (tp) cc_final: 0.8047 (tm) REVERT: B 159 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7963 (ptt) REVERT: B 160 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7490 (pmt-80) REVERT: B 199 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: B 343 TRP cc_start: 0.9102 (OUTLIER) cc_final: 0.8545 (p90) REVERT: B 476 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8231 (mmp80) REVERT: B 611 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.7198 (m-70) REVERT: B 884 MET cc_start: 0.7427 (mtm) cc_final: 0.6847 (mtt) REVERT: B 1011 ARG cc_start: 0.7822 (mmm160) cc_final: 0.7143 (mtp85) REVERT: C 226 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6358 (tm) REVERT: C 396 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7576 (mtpp) REVERT: C 507 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7537 (t80) REVERT: C 548 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: C 572 ASP cc_start: 0.8336 (p0) cc_final: 0.7513 (m-30) REVERT: C 637 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.5880 (mtp180) REVERT: C 718 GLN cc_start: 0.6831 (mp10) cc_final: 0.6429 (pm20) REVERT: C 720 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7593 (mtp-110) outliers start: 73 outliers final: 51 residues processed: 203 average time/residue: 0.4835 time to fit residues: 113.7255 Evaluate side-chains 204 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 140 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 404 LEU 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 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 957 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 197 CYS Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 259 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 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 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 679 SER Chi-restraints excluded: chain B residue 750 LEU 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 1028 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 365 CYS 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 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 637 ARG 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 949 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 33 optimal weight: 0.7980 chunk 209 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 158 optimal weight: 0.0040 chunk 167 optimal weight: 0.1980 chunk 228 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 214 optimal weight: 0.0770 chunk 126 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 overall best weight: 0.2550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 HIS B 189 ASN ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.114343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090592 restraints weight = 40102.259| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.88 r_work: 0.3154 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20140 Z= 0.088 Angle : 0.480 9.246 27345 Z= 0.260 Chirality : 0.042 0.342 2850 Planarity : 0.003 0.057 3569 Dihedral : 4.897 59.078 2926 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.34 % Favored : 97.62 % Rotamer: Outliers : 2.77 % Allowed : 25.59 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.15), residues: 2561 helix: 2.08 (0.30), residues: 305 sheet: -0.52 (0.30), residues: 290 loop : -0.92 (0.12), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 171 TYR 0.007 0.001 TYR C 465 PHE 0.023 0.001 PHE A 208 TRP 0.023 0.001 TRP C 782 HIS 0.006 0.000 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (20036) covalent geometry : angle 0.47178 / 0.26 (27128) SS BOND : bond 0.00184 / 0.13 ( 95) SS BOND : angle 0.78099 / 0.49 ( 190) hydrogen bonds : bond 0.02662 / 1.79 ( 533) hydrogen bonds : angle 4.04210 / 2.94 ( 1728) link_NAG-ASN : bond 0.00278 / 0.20 ( 9) link_NAG-ASN : angle 2.27627 / 1.15 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6489.19 seconds wall clock time: 110 minutes 59.24 seconds (6659.24 seconds total)