Starting phenix.real_space_refine on Sat Sep 12 06:15:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6m22_30058/09_2026/6m22_30058.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m22_30058/09_2026/6m22_30058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m22_30058/09_2026/6m22_30058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m22_30058/09_2026/6m22_30058.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6m22_30058/09_2026/6m22_30058.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6m22_30058/09_2026/6m22_30058.cif" model { file = "/net/cci-nas-00/data/ceres_data/6m22_30058/09_2026/6m22_30058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m22_30058/09_2026/6m22_30058.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 96 5.16 5 Cl 8 4.86 5 C 9090 2.51 5 N 2290 2.21 5 O 2542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14028 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 6853 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 2 Chain: "B" Number of atoms: 6853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 6853 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {' K': 1, ' CL': 2, 'EZC': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {' K': 1, ' CL': 2, 'EZC': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 3.09, per 1000 atoms: 0.22 Number of scatterers: 14028 At special positions: 0 Unit cell: (92.395, 114.135, 155.441, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 8 17.00 S 96 16.00 O 2542 8.00 N 2290 7.00 C 9090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.04 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1110 " - " ASN A 347 " " NAG A1111 " - " ASN A 360 " " NAG B1110 " - " ASN B 347 " " NAG B1111 " - " ASN B 360 " " NAG C 1 " - " ASN A 328 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 377 " " NAG F 1 " - " ASN B 328 " " NAG G 1 " - " ASN B 366 " " NAG H 1 " - " ASN B 377 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 663.7 milliseconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 57.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.567A pdb=" N ASN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 removed outlier: 4.283A pdb=" N PHE A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 164 through 191 removed outlier: 3.701A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 180 " --> pdb=" O CYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.507A pdb=" N ALA A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 242 removed outlier: 3.572A pdb=" N ALA A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 Processing helix chain 'A' and resid 286 through 292 Processing helix chain 'A' and resid 292 through 314 removed outlier: 3.616A pdb=" N VAL A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 303 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.609A pdb=" N GLY A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 358' Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.533A pdb=" N THR A 393 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.557A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.528A pdb=" N ALA A 450 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 451 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 453 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.779A pdb=" N LEU A 458 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 491 Proline residue: A 466 - end of helix removed outlier: 3.768A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 498 through 502 removed outlier: 4.090A pdb=" N GLY A 501 " --> pdb=" O ASP A 498 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP A 502 " --> pdb=" O LYS A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 502' Processing helix chain 'A' and resid 508 through 514 removed outlier: 3.743A pdb=" N LEU A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 549 Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 553 through 560 removed outlier: 3.517A pdb=" N ARG A 557 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 removed outlier: 3.502A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 582 " --> pdb=" O ILE A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 616 removed outlier: 3.598A pdb=" N VAL A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 3.632A pdb=" N PHE A 598 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 614 " --> pdb=" O CYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 646 removed outlier: 3.587A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 673 removed outlier: 3.693A pdb=" N VAL A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 695 removed outlier: 3.867A pdb=" N SER A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 734 removed outlier: 3.655A pdb=" N THR A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 770 removed outlier: 3.605A pdb=" N GLN A 761 " --> pdb=" O LEU A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 820 through 835 removed outlier: 3.840A pdb=" N PHE A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 826 " --> pdb=" O TRP A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 880 Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 902 through 915 removed outlier: 3.657A pdb=" N HIS A 915 " --> pdb=" O THR A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1048 removed outlier: 3.554A pdb=" N VAL A1042 " --> pdb=" O LYS A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1078 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.567A pdb=" N ASN B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 156 removed outlier: 4.283A pdb=" N PHE B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 164 through 191 removed outlier: 3.701A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 180 " --> pdb=" O CYS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.507A pdb=" N ALA B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 242 removed outlier: 3.572A pdb=" N ALA B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 285 Processing helix chain 'B' and resid 286 through 292 Processing helix chain 'B' and resid 292 through 314 removed outlier: 3.616A pdb=" N VAL B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 303 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 314 " --> pdb=" O GLY B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 358 removed outlier: 3.609A pdb=" N GLY B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 358' Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.533A pdb=" N THR B 393 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.557A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.528A pdb=" N ALA B 450 " --> pdb=" O GLY B 447 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 451 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 453 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 removed outlier: 3.779A pdb=" N LEU B 458 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 491 Proline residue: B 466 - end of helix removed outlier: 3.768A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 497 Processing helix chain 'B' and resid 498 through 502 removed outlier: 4.090A pdb=" N GLY B 501 " --> pdb=" O ASP B 498 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP B 502 " --> pdb=" O LYS B 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 498 through 502' Processing helix chain 'B' and resid 508 through 514 removed outlier: 3.743A pdb=" N LEU B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 514 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 549 Proline residue: B 541 - end of helix Processing helix chain 'B' and resid 553 through 560 removed outlier: 3.517A pdb=" N ARG B 557 " --> pdb=" O PRO B 554 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 585 removed outlier: 3.502A pdb=" N LEU B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 582 " --> pdb=" O ILE B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 616 removed outlier: 3.598A pdb=" N VAL B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Proline residue: B 593 - end of helix removed outlier: 3.632A pdb=" N PHE B 598 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 614 " --> pdb=" O CYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 646 removed outlier: 3.587A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 673 removed outlier: 3.693A pdb=" N VAL B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 695 removed outlier: 3.867A pdb=" N SER B 683 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 734 removed outlier: 3.655A pdb=" N THR B 727 " --> pdb=" O PRO B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 770 removed outlier: 3.605A pdb=" N GLN B 761 " --> pdb=" O LEU B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 Processing helix chain 'B' and resid 820 through 835 removed outlier: 3.840A pdb=" N PHE B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 826 " --> pdb=" O TRP B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 880 Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 902 through 915 removed outlier: 3.657A pdb=" N HIS B 915 " --> pdb=" O THR B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1048 removed outlier: 3.554A pdb=" N VAL B1042 " --> pdb=" O LYS B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1078 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'A' and resid 775 through 781 removed outlier: 4.976A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A1084 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A1056 " --> pdb=" O TRP A 863 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE A 860 " --> pdb=" O ARG A 891 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE A 893 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 862 " --> pdb=" O PHE A 893 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL A 895 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N TRP A 864 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE A 890 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLU A 923 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 892 " --> pdb=" O GLU A 923 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL A 925 " --> pdb=" O ILE A 892 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR A 894 " --> pdb=" O VAL A 925 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA4, first strand: chain 'B' and resid 775 through 781 removed outlier: 4.976A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN B1056 " --> pdb=" O TRP B 863 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE B 860 " --> pdb=" O ARG B 891 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE B 893 " --> pdb=" O ILE B 860 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 862 " --> pdb=" O PHE B 893 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL B 895 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N TRP B 864 " --> pdb=" O VAL B 895 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE B 890 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLU B 923 " --> pdb=" O ILE B 890 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 892 " --> pdb=" O GLU B 923 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL B 925 " --> pdb=" O ILE B 892 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR B 894 " --> pdb=" O VAL B 925 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2178 1.30 - 1.43: 3856 1.43 - 1.56: 8094 1.56 - 1.69: 16 1.69 - 1.82: 158 Bond restraints: 14302 Sorted by residual: bond pdb=" C07 EZC A1112 " pdb=" C11 EZC A1112 " ideal model delta sigma weight residual 1.543 1.330 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C07 EZC B1112 " pdb=" C11 EZC B1112 " ideal model delta sigma weight residual 1.543 1.330 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C08 EZC A1112 " pdb=" C10 EZC A1112 " ideal model delta sigma weight residual 1.537 1.345 0.192 2.00e-02 2.50e+03 9.19e+01 bond pdb=" C08 EZC B1112 " pdb=" C10 EZC B1112 " ideal model delta sigma weight residual 1.537 1.349 0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" C13 EZC B1112 " pdb=" C14 EZC B1112 " ideal model delta sigma weight residual 1.540 1.369 0.171 2.00e-02 2.50e+03 7.32e+01 ... (remaining 14297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 18874 2.64 - 5.28: 432 5.28 - 7.92: 88 7.92 - 10.57: 22 10.57 - 13.21: 6 Bond angle restraints: 19422 Sorted by residual: angle pdb=" N LEU B 708 " pdb=" CA LEU B 708 " pdb=" C LEU B 708 " ideal model delta sigma weight residual 110.48 123.69 -13.21 1.48e+00 4.57e-01 7.96e+01 angle pdb=" N LEU A 708 " pdb=" CA LEU A 708 " pdb=" C LEU A 708 " ideal model delta sigma weight residual 110.48 123.69 -13.21 1.48e+00 4.57e-01 7.96e+01 angle pdb=" N VAL B 374 " pdb=" CA VAL B 374 " pdb=" C VAL B 374 " ideal model delta sigma weight residual 110.62 105.12 5.50 1.02e+00 9.61e-01 2.90e+01 angle pdb=" N VAL A 374 " pdb=" CA VAL A 374 " pdb=" C VAL A 374 " ideal model delta sigma weight residual 110.62 105.12 5.50 1.02e+00 9.61e-01 2.90e+01 angle pdb=" N LEU A 709 " pdb=" CA LEU A 709 " pdb=" C LEU A 709 " ideal model delta sigma weight residual 108.02 98.89 9.13 1.78e+00 3.16e-01 2.63e+01 ... (remaining 19417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 7357 17.06 - 34.11: 724 34.11 - 51.17: 131 51.17 - 68.22: 32 68.22 - 85.28: 6 Dihedral angle restraints: 8250 sinusoidal: 3180 harmonic: 5070 Sorted by residual: dihedral pdb=" CA ALA B 216 " pdb=" C ALA B 216 " pdb=" N VAL B 217 " pdb=" CA VAL B 217 " ideal model delta harmonic sigma weight residual 180.00 153.73 26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ALA A 216 " pdb=" C ALA A 216 " pdb=" N VAL A 217 " pdb=" CA VAL A 217 " ideal model delta harmonic sigma weight residual 180.00 153.73 26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA GLU B 716 " pdb=" C GLU B 716 " pdb=" N ASP B 717 " pdb=" CA ASP B 717 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 8247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1820 0.066 - 0.132: 403 0.132 - 0.198: 53 0.198 - 0.264: 12 0.264 - 0.330: 8 Chirality restraints: 2296 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.71 0.31 2.00e-02 2.50e+03 2.40e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.71 0.31 2.00e-02 2.50e+03 2.40e+02 chirality pdb=" CA LEU A 708 " pdb=" N LEU A 708 " pdb=" C LEU A 708 " pdb=" CB LEU A 708 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 2293 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 377 " 0.058 2.00e-02 2.50e+03 1.10e-01 1.50e+02 pdb=" CG ASN A 377 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 377 " 0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A 377 " -0.195 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 377 " -0.058 2.00e-02 2.50e+03 1.10e-01 1.50e+02 pdb=" CG ASN B 377 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN B 377 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN B 377 " 0.195 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 328 " -0.022 2.00e-02 2.50e+03 6.25e-02 4.89e+01 pdb=" CG ASN A 328 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 328 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A 328 " 0.111 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.064 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.60: 102 2.60 - 3.23: 12617 3.23 - 3.87: 26367 3.87 - 4.50: 36202 4.50 - 5.14: 56758 Nonbonded interactions: 132046 Sorted by model distance: nonbonded pdb=" OE1 GLU B1065 " pdb=" N GLY B1066 " model vdw 1.962 3.120 nonbonded pdb=" OE1 GLU A1065 " pdb=" N GLY A1066 " model vdw 1.962 3.120 nonbonded pdb=" N ASN A1063 " pdb=" OD1 ASN A1063 " model vdw 2.297 3.120 nonbonded pdb=" N ASN B1063 " pdb=" OD1 ASN B1063 " model vdw 2.297 3.120 nonbonded pdb=" OH TYR B 372 " pdb=" OG SER B 414 " model vdw 2.297 3.040 ... (remaining 132041 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.700 Find NCS groups from input model: 0.290 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:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 : 0.010 0.297 14320 Z= 0.478 Angle : 1.263 45.608 19474 Z= 0.619 Chirality : 0.059 0.330 2296 Planarity : 0.007 0.096 2390 Dihedral : 14.054 85.276 4988 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.51 % Favored : 91.70 % Rotamer: Outliers : 1.22 % Allowed : 4.06 % Favored : 94.72 % 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: -5.21 (0.14), residues: 1758 helix: -4.11 (0.07), residues: 914 sheet: 0.08 (0.37), residues: 168 loop : -3.20 (0.19), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 622 TYR 0.020 0.002 TYR B 372 PHE 0.015 0.002 PHE B 555 TRP 0.013 0.002 TRP A 649 HIS 0.008 0.001 HIS B 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00891 / 0.44 (14302) covalent geometry : angle 1.04549 / 0.57 (19422) SS BOND : bond 0.00532 / 0.27 ( 2) SS BOND : angle 1.90009 / 1.14 ( 4) hydrogen bonds : bond 0.30187 / 19.58 ( 686) hydrogen bonds : angle 9.16658 / 6.29 ( 1992) link_BETA1-4 : bond 0.00883 / 0.50 ( 6) link_BETA1-4 : angle 12.29874 / 7.38 ( 18) link_NAG-ASN : bond 0.13700 / 6.79 ( 10) link_NAG-ASN : angle 15.37932 / 9.28 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 256 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 703 ASN cc_start: 0.7459 (m-40) cc_final: 0.7173 (t0) REVERT: B 703 ASN cc_start: 0.7467 (m-40) cc_final: 0.7180 (t0) outliers start: 18 outliers final: 6 residues processed: 270 average time/residue: 0.6563 time to fit residues: 192.8302 Evaluate side-chains 152 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 1063 ASN Chi-restraints excluded: chain A residue 1065 GLU Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 1063 ASN Chi-restraints excluded: chain B residue 1065 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN A 507 ASN A 607 ASN A 613 GLN A 629 HIS A 707 GLN A 882 HIS ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 ASN B 110 GLN B 507 ASN B 607 ASN B 613 GLN B 629 HIS B 707 GLN B 882 HIS ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.093009 restraints weight = 19404.816| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.30 r_work: 0.2904 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14320 Z= 0.157 Angle : 0.738 15.652 19474 Z= 0.376 Chirality : 0.045 0.251 2296 Planarity : 0.006 0.072 2390 Dihedral : 6.961 107.717 1910 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.53 % Favored : 91.24 % Rotamer: Outliers : 2.57 % Allowed : 11.10 % Favored : 86.33 % 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: -2.19 (0.18), residues: 1758 helix: -0.76 (0.16), residues: 904 sheet: 0.38 (0.39), residues: 170 loop : -2.87 (0.20), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 622 TYR 0.012 0.002 TYR B 650 PHE 0.012 0.001 PHE B 441 TRP 0.009 0.001 TRP A 519 HIS 0.010 0.001 HIS A 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (14302) covalent geometry : angle 0.69296 / 0.37 (19422) SS BOND : bond 0.00838 / 0.42 ( 2) SS BOND : angle 2.04206 / 1.24 ( 4) hydrogen bonds : bond 0.05769 / 3.77 ( 686) hydrogen bonds : angle 4.25743 / 3.00 ( 1992) link_BETA1-4 : bond 0.00410 / 0.22 ( 6) link_BETA1-4 : angle 2.37859 / 1.35 ( 18) link_NAG-ASN : bond 0.00682 / 0.33 ( 10) link_NAG-ASN : angle 6.21747 / 3.76 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 567 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6130 (tp30) REVERT: A 873 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8488 (mtt) REVERT: A 905 MET cc_start: 0.7372 (ptp) cc_final: 0.6917 (ptm) REVERT: B 567 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6127 (tp30) REVERT: B 873 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8505 (mtt) REVERT: B 905 MET cc_start: 0.7376 (ptp) cc_final: 0.6924 (ptm) outliers start: 38 outliers final: 16 residues processed: 184 average time/residue: 0.6494 time to fit residues: 130.2704 Evaluate side-chains 158 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 1029 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 97 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1029 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.093017 restraints weight = 19321.450| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.19 r_work: 0.2900 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14320 Z= 0.134 Angle : 0.627 9.683 19474 Z= 0.323 Chirality : 0.044 0.288 2296 Planarity : 0.005 0.070 2390 Dihedral : 5.395 36.917 1900 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.62 % Favored : 92.15 % Rotamer: Outliers : 1.89 % Allowed : 12.92 % Favored : 85.18 % 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: -0.71 (0.20), residues: 1758 helix: 0.91 (0.18), residues: 898 sheet: 0.55 (0.39), residues: 170 loop : -2.74 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 622 TYR 0.011 0.001 TYR A 650 PHE 0.012 0.001 PHE B 555 TRP 0.010 0.001 TRP A 649 HIS 0.004 0.001 HIS A 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (14302) covalent geometry : angle 0.60725 / 0.32 (19422) SS BOND : bond 0.00596 / 0.30 ( 2) SS BOND : angle 1.39109 / 0.83 ( 4) hydrogen bonds : bond 0.04932 / 3.21 ( 686) hydrogen bonds : angle 3.84945 / 2.75 ( 1992) link_BETA1-4 : bond 0.00482 / 0.26 ( 6) link_BETA1-4 : angle 1.81956 / 1.04 ( 18) link_NAG-ASN : bond 0.00576 / 0.28 ( 10) link_NAG-ASN : angle 3.80960 / 2.28 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.9035 (mmm) REVERT: A 422 ASN cc_start: 0.8429 (t0) cc_final: 0.7838 (t0) REVERT: A 873 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8876 (mpp) REVERT: A 905 MET cc_start: 0.7529 (ptp) cc_final: 0.7177 (ptm) REVERT: A 927 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.4986 (ttt) REVERT: A 1062 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7481 (tpp80) REVERT: B 138 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.9037 (mmm) REVERT: B 422 ASN cc_start: 0.8423 (t0) cc_final: 0.7826 (t0) REVERT: B 873 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8874 (mpp) REVERT: B 905 MET cc_start: 0.7530 (ptp) cc_final: 0.7184 (ptm) REVERT: B 927 MET cc_start: 0.5229 (OUTLIER) cc_final: 0.5001 (ttt) REVERT: B 1062 ARG cc_start: 0.7784 (tpp80) cc_final: 0.7478 (tpp80) outliers start: 28 outliers final: 8 residues processed: 160 average time/residue: 0.6235 time to fit residues: 109.2411 Evaluate side-chains 138 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 927 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.092802 restraints weight = 19246.289| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.20 r_work: 0.2922 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14320 Z= 0.128 Angle : 0.605 7.854 19474 Z= 0.312 Chirality : 0.044 0.293 2296 Planarity : 0.004 0.066 2390 Dihedral : 5.214 35.395 1900 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.91 % Favored : 91.87 % Rotamer: Outliers : 2.37 % Allowed : 13.06 % Favored : 84.57 % 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: -0.13 (0.21), residues: 1758 helix: 1.52 (0.18), residues: 914 sheet: 0.60 (0.40), residues: 170 loop : -2.70 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 622 TYR 0.013 0.001 TYR B 288 PHE 0.011 0.001 PHE B 555 TRP 0.013 0.001 TRP A 649 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (14302) covalent geometry : angle 0.59051 / 0.31 (19422) SS BOND : bond 0.00076 / 0.04 ( 2) SS BOND : angle 0.69657 / 0.41 ( 4) hydrogen bonds : bond 0.04498 / 2.94 ( 686) hydrogen bonds : angle 3.74551 / 2.68 ( 1992) link_BETA1-4 : bond 0.00537 / 0.28 ( 6) link_BETA1-4 : angle 1.45777 / 0.83 ( 18) link_NAG-ASN : bond 0.00447 / 0.22 ( 10) link_NAG-ASN : angle 3.22817 / 1.92 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ASN cc_start: 0.8381 (t0) cc_final: 0.7896 (t0) REVERT: A 429 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: A 567 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6219 (tp30) REVERT: A 672 GLU cc_start: 0.8913 (tt0) cc_final: 0.8585 (tm-30) REVERT: A 916 LEU cc_start: 0.7978 (mm) cc_final: 0.7320 (mm) REVERT: A 1062 ARG cc_start: 0.7761 (tpp80) cc_final: 0.7458 (tpp80) REVERT: B 422 ASN cc_start: 0.8378 (t0) cc_final: 0.7898 (t0) REVERT: B 429 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7962 (m-30) REVERT: B 567 GLU cc_start: 0.6589 (mt-10) cc_final: 0.6219 (tp30) REVERT: B 672 GLU cc_start: 0.8920 (tt0) cc_final: 0.8582 (tm-30) REVERT: B 916 LEU cc_start: 0.7973 (mm) cc_final: 0.7317 (mm) REVERT: B 1062 ARG cc_start: 0.7765 (tpp80) cc_final: 0.7462 (tpp80) outliers start: 35 outliers final: 16 residues processed: 160 average time/residue: 0.6629 time to fit residues: 116.0447 Evaluate side-chains 140 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 908 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 46 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 127 optimal weight: 0.0570 chunk 31 optimal weight: 0.8980 chunk 158 optimal weight: 0.4980 chunk 164 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.093973 restraints weight = 19420.248| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.21 r_work: 0.2933 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14320 Z= 0.119 Angle : 0.581 7.554 19474 Z= 0.301 Chirality : 0.044 0.315 2296 Planarity : 0.004 0.066 2390 Dihedral : 5.057 33.579 1900 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.34 % Favored : 92.43 % Rotamer: Outliers : 2.17 % Allowed : 13.80 % Favored : 84.03 % 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: 0.17 (0.21), residues: 1758 helix: 1.83 (0.18), residues: 918 sheet: 0.66 (0.40), residues: 170 loop : -2.67 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 622 TYR 0.011 0.001 TYR A 650 PHE 0.011 0.001 PHE B 555 TRP 0.013 0.001 TRP A 649 HIS 0.003 0.001 HIS A 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (14302) covalent geometry : angle 0.56924 / 0.30 (19422) SS BOND : bond 0.00039 / 0.02 ( 2) SS BOND : angle 0.63395 / 0.38 ( 4) hydrogen bonds : bond 0.04155 / 2.72 ( 686) hydrogen bonds : angle 3.64116 / 2.61 ( 1992) link_BETA1-4 : bond 0.00533 / 0.28 ( 6) link_BETA1-4 : angle 1.39644 / 0.80 ( 18) link_NAG-ASN : bond 0.00383 / 0.19 ( 10) link_NAG-ASN : angle 2.80883 / 1.67 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ASN cc_start: 0.8413 (t0) cc_final: 0.7940 (t0) REVERT: A 429 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8001 (m-30) REVERT: A 567 GLU cc_start: 0.6574 (mt-10) cc_final: 0.6195 (tp30) REVERT: A 672 GLU cc_start: 0.8960 (tt0) cc_final: 0.8629 (tm-30) REVERT: A 907 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7979 (tppt) REVERT: A 916 LEU cc_start: 0.7968 (mm) cc_final: 0.7363 (mm) REVERT: A 1062 ARG cc_start: 0.7791 (tpp80) cc_final: 0.7496 (tpp80) REVERT: B 422 ASN cc_start: 0.8410 (t0) cc_final: 0.7944 (t0) REVERT: B 429 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: B 567 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6197 (tp30) REVERT: B 672 GLU cc_start: 0.8959 (tt0) cc_final: 0.8623 (tm-30) REVERT: B 907 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7981 (tppt) REVERT: B 916 LEU cc_start: 0.7968 (mm) cc_final: 0.7361 (mm) REVERT: B 1062 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7494 (tpp80) outliers start: 32 outliers final: 12 residues processed: 150 average time/residue: 0.6298 time to fit residues: 103.8112 Evaluate side-chains 132 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 588 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 86 optimal weight: 6.9990 chunk 28 optimal weight: 0.0670 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.093908 restraints weight = 19305.093| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.18 r_work: 0.2925 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14320 Z= 0.119 Angle : 0.571 7.607 19474 Z= 0.295 Chirality : 0.043 0.236 2296 Planarity : 0.004 0.063 2390 Dihedral : 4.960 33.259 1900 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.62 % Favored : 92.15 % Rotamer: Outliers : 2.44 % Allowed : 14.88 % Favored : 82.68 % 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: 0.35 (0.21), residues: 1758 helix: 1.98 (0.18), residues: 920 sheet: 0.73 (0.40), residues: 170 loop : -2.61 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 622 TYR 0.010 0.001 TYR B 628 PHE 0.011 0.001 PHE A 555 TRP 0.014 0.001 TRP B 649 HIS 0.003 0.001 HIS A 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14302) covalent geometry : angle 0.56063 / 0.29 (19422) SS BOND : bond 0.00115 / 0.06 ( 2) SS BOND : angle 0.53040 / 0.32 ( 4) hydrogen bonds : bond 0.04136 / 2.71 ( 686) hydrogen bonds : angle 3.61515 / 2.59 ( 1992) link_BETA1-4 : bond 0.00521 / 0.28 ( 6) link_BETA1-4 : angle 1.34100 / 0.77 ( 18) link_NAG-ASN : bond 0.00352 / 0.17 ( 10) link_NAG-ASN : angle 2.59500 / 1.54 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.543 Fit side-chains REVERT: A 422 ASN cc_start: 0.8411 (t0) cc_final: 0.7951 (t0) REVERT: A 429 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8007 (m-30) REVERT: A 567 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6085 (tp30) REVERT: A 573 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8868 (tt) REVERT: A 672 GLU cc_start: 0.8989 (tt0) cc_final: 0.8621 (tm-30) REVERT: A 1062 ARG cc_start: 0.7800 (tpp80) cc_final: 0.7505 (tpp80) REVERT: B 422 ASN cc_start: 0.8411 (t0) cc_final: 0.7952 (t0) REVERT: B 429 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: B 567 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6096 (tp30) REVERT: B 573 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8872 (tt) REVERT: B 672 GLU cc_start: 0.8984 (tt0) cc_final: 0.8611 (tm-30) REVERT: B 1062 ARG cc_start: 0.7786 (tpp80) cc_final: 0.7492 (tpp80) outliers start: 36 outliers final: 12 residues processed: 152 average time/residue: 0.5742 time to fit residues: 96.5657 Evaluate side-chains 138 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 573 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.092722 restraints weight = 19367.907| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.19 r_work: 0.2922 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14320 Z= 0.131 Angle : 0.598 7.929 19474 Z= 0.306 Chirality : 0.045 0.363 2296 Planarity : 0.004 0.064 2390 Dihedral : 4.877 33.331 1896 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.85 % Favored : 91.92 % Rotamer: Outliers : 2.03 % Allowed : 16.51 % Favored : 81.46 % 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: 0.40 (0.21), residues: 1758 helix: 2.06 (0.18), residues: 918 sheet: 0.74 (0.40), residues: 170 loop : -2.62 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 622 TYR 0.011 0.001 TYR B 628 PHE 0.011 0.001 PHE A 555 TRP 0.014 0.001 TRP A 649 HIS 0.003 0.001 HIS A 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14302) covalent geometry : angle 0.58908 / 0.30 (19422) SS BOND : bond 0.00110 / 0.06 ( 2) SS BOND : angle 0.53107 / 0.31 ( 4) hydrogen bonds : bond 0.04374 / 2.87 ( 686) hydrogen bonds : angle 3.66069 / 2.62 ( 1992) link_BETA1-4 : bond 0.00555 / 0.29 ( 6) link_BETA1-4 : angle 1.29537 / 0.74 ( 18) link_NAG-ASN : bond 0.00370 / 0.18 ( 10) link_NAG-ASN : angle 2.51367 / 1.49 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.527 Fit side-chains REVERT: A 422 ASN cc_start: 0.8468 (t0) cc_final: 0.8043 (t0) REVERT: A 429 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: A 567 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6071 (tp30) REVERT: A 573 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8923 (tt) REVERT: A 702 LYS cc_start: 0.8100 (mmpt) cc_final: 0.7656 (mppt) REVERT: A 907 LYS cc_start: 0.8552 (tppt) cc_final: 0.8306 (ttmm) REVERT: A 916 LEU cc_start: 0.8020 (mm) cc_final: 0.7392 (mm) REVERT: A 1062 ARG cc_start: 0.7786 (tpp80) cc_final: 0.7477 (tpp80) REVERT: B 422 ASN cc_start: 0.8455 (t0) cc_final: 0.8029 (t0) REVERT: B 429 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: B 567 GLU cc_start: 0.6676 (mt-10) cc_final: 0.6068 (tp30) REVERT: B 573 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8932 (tt) REVERT: B 702 LYS cc_start: 0.8100 (mmpt) cc_final: 0.7658 (mppt) REVERT: B 907 LYS cc_start: 0.8550 (tppt) cc_final: 0.8306 (ttmm) REVERT: B 916 LEU cc_start: 0.8020 (mm) cc_final: 0.7394 (mm) REVERT: B 1062 ARG cc_start: 0.7781 (tpp80) cc_final: 0.7473 (tpp80) outliers start: 30 outliers final: 18 residues processed: 144 average time/residue: 0.6161 time to fit residues: 97.4597 Evaluate side-chains 142 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 908 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 89 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.088729 restraints weight = 19352.314| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.28 r_work: 0.2833 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14320 Z= 0.178 Angle : 0.650 7.934 19474 Z= 0.335 Chirality : 0.047 0.316 2296 Planarity : 0.004 0.061 2390 Dihedral : 5.151 35.956 1896 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.36 % Favored : 91.41 % Rotamer: Outliers : 2.30 % Allowed : 16.17 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.21), residues: 1758 helix: 1.95 (0.18), residues: 918 sheet: 0.63 (0.39), residues: 170 loop : -2.58 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 622 TYR 0.014 0.002 TYR A 628 PHE 0.012 0.001 PHE A 605 TRP 0.016 0.002 TRP A 649 HIS 0.004 0.001 HIS B 790 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (14302) covalent geometry : angle 0.64118 / 0.33 (19422) SS BOND : bond 0.00092 / 0.05 ( 2) SS BOND : angle 0.70699 / 0.41 ( 4) hydrogen bonds : bond 0.05342 / 3.50 ( 686) hydrogen bonds : angle 3.84719 / 2.74 ( 1992) link_BETA1-4 : bond 0.00515 / 0.26 ( 6) link_BETA1-4 : angle 1.33476 / 0.74 ( 18) link_NAG-ASN : bond 0.00359 / 0.17 ( 10) link_NAG-ASN : angle 2.64889 / 1.56 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 HIS cc_start: 0.6941 (OUTLIER) cc_final: 0.6726 (m-70) REVERT: A 287 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7268 (ptt-90) REVERT: A 422 ASN cc_start: 0.8525 (t0) cc_final: 0.8069 (t0) REVERT: A 429 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8029 (m-30) REVERT: A 567 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6218 (tp30) REVERT: A 573 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8946 (tt) REVERT: A 873 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8391 (mtp) REVERT: A 907 LYS cc_start: 0.8634 (tppt) cc_final: 0.8244 (ttmm) REVERT: A 1062 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7529 (tpp80) REVERT: B 252 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.6713 (m-70) REVERT: B 287 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7275 (ptt-90) REVERT: B 422 ASN cc_start: 0.8520 (t0) cc_final: 0.8068 (t0) REVERT: B 429 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: B 567 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6217 (tp30) REVERT: B 573 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8948 (tt) REVERT: B 873 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8382 (mtp) REVERT: B 907 LYS cc_start: 0.8636 (tppt) cc_final: 0.8245 (ttmm) REVERT: B 1062 ARG cc_start: 0.7814 (tpp80) cc_final: 0.7517 (tpp80) outliers start: 34 outliers final: 14 residues processed: 147 average time/residue: 0.6118 time to fit residues: 98.7430 Evaluate side-chains 138 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 873 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 118 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.126730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.090963 restraints weight = 19439.566| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.28 r_work: 0.2876 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14320 Z= 0.132 Angle : 0.598 7.508 19474 Z= 0.308 Chirality : 0.044 0.301 2296 Planarity : 0.004 0.064 2390 Dihedral : 5.044 36.919 1896 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.96 % Favored : 91.81 % Rotamer: Outliers : 2.03 % Allowed : 16.37 % Favored : 81.60 % 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: 0.47 (0.21), residues: 1758 helix: 2.10 (0.18), residues: 916 sheet: 0.90 (0.43), residues: 150 loop : -2.50 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 622 TYR 0.010 0.001 TYR B 628 PHE 0.011 0.001 PHE A 555 TRP 0.012 0.001 TRP A 649 HIS 0.003 0.001 HIS B 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14302) covalent geometry : angle 0.58947 / 0.31 (19422) SS BOND : bond 0.00099 / 0.05 ( 2) SS BOND : angle 0.64568 / 0.39 ( 4) hydrogen bonds : bond 0.04478 / 2.94 ( 686) hydrogen bonds : angle 3.70095 / 2.65 ( 1992) link_BETA1-4 : bond 0.00567 / 0.29 ( 6) link_BETA1-4 : angle 1.19223 / 0.67 ( 18) link_NAG-ASN : bond 0.00404 / 0.19 ( 10) link_NAG-ASN : angle 2.53431 / 1.49 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.563 Fit side-chains REVERT: A 287 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7219 (ptt-90) REVERT: A 422 ASN cc_start: 0.8525 (t0) cc_final: 0.8082 (t0) REVERT: A 429 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: A 567 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6110 (tp30) REVERT: A 573 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8926 (tt) REVERT: A 873 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8361 (mtp) REVERT: A 907 LYS cc_start: 0.8609 (tppt) cc_final: 0.8225 (ttmm) REVERT: A 1062 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7520 (tpp80) REVERT: B 287 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7226 (ptt-90) REVERT: B 422 ASN cc_start: 0.8517 (t0) cc_final: 0.8074 (t0) REVERT: B 429 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: B 567 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6104 (tp30) REVERT: B 573 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8933 (tt) REVERT: B 873 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8375 (mtp) REVERT: B 907 LYS cc_start: 0.8608 (tppt) cc_final: 0.8225 (ttmm) REVERT: B 1062 ARG cc_start: 0.7807 (tpp80) cc_final: 0.7503 (tpp80) outliers start: 30 outliers final: 12 residues processed: 144 average time/residue: 0.6282 time to fit residues: 99.3415 Evaluate side-chains 138 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 873 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 138 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 163 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.091472 restraints weight = 19535.294| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.27 r_work: 0.2873 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14320 Z= 0.126 Angle : 0.588 7.744 19474 Z= 0.303 Chirality : 0.044 0.284 2296 Planarity : 0.004 0.065 2390 Dihedral : 4.945 36.192 1896 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.08 % Favored : 91.70 % Rotamer: Outliers : 1.62 % Allowed : 17.12 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1758 helix: 2.17 (0.18), residues: 922 sheet: 0.80 (0.40), residues: 170 loop : -2.49 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 622 TYR 0.011 0.001 TYR B 628 PHE 0.011 0.001 PHE A 555 TRP 0.014 0.001 TRP B 864 HIS 0.003 0.001 HIS B 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (14302) covalent geometry : angle 0.57960 / 0.30 (19422) SS BOND : bond 0.00091 / 0.05 ( 2) SS BOND : angle 0.54599 / 0.32 ( 4) hydrogen bonds : bond 0.04298 / 2.82 ( 686) hydrogen bonds : angle 3.64974 / 2.61 ( 1992) link_BETA1-4 : bond 0.00438 / 0.23 ( 6) link_BETA1-4 : angle 1.15729 / 0.65 ( 18) link_NAG-ASN : bond 0.00408 / 0.20 ( 10) link_NAG-ASN : angle 2.51337 / 1.49 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.579 Fit side-chains REVERT: A 252 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6744 (m-70) REVERT: A 422 ASN cc_start: 0.8543 (t0) cc_final: 0.8113 (t0) REVERT: A 429 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: A 567 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6080 (tp30) REVERT: A 573 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8923 (tt) REVERT: A 873 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8370 (mtp) REVERT: A 907 LYS cc_start: 0.8601 (tppt) cc_final: 0.8237 (ttmm) REVERT: A 1029 ASN cc_start: 0.6544 (m-40) cc_final: 0.6192 (t0) REVERT: A 1062 ARG cc_start: 0.7816 (tpp80) cc_final: 0.7510 (tpp80) REVERT: B 252 HIS cc_start: 0.6988 (OUTLIER) cc_final: 0.6733 (m-70) REVERT: B 422 ASN cc_start: 0.8541 (t0) cc_final: 0.8107 (t0) REVERT: B 429 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: B 567 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6072 (tp30) REVERT: B 573 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8930 (tt) REVERT: B 873 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8373 (mtp) REVERT: B 907 LYS cc_start: 0.8595 (tppt) cc_final: 0.8229 (ttmm) REVERT: B 1029 ASN cc_start: 0.6538 (m-40) cc_final: 0.6189 (t0) REVERT: B 1062 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7509 (tpp80) outliers start: 24 outliers final: 10 residues processed: 138 average time/residue: 0.7084 time to fit residues: 106.4865 Evaluate side-chains 132 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 873 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.091675 restraints weight = 19455.926| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.26 r_work: 0.2867 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14320 Z= 0.128 Angle : 0.605 9.374 19474 Z= 0.312 Chirality : 0.044 0.275 2296 Planarity : 0.004 0.065 2390 Dihedral : 4.908 35.499 1896 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.96 % Favored : 91.81 % Rotamer: Outliers : 1.49 % Allowed : 17.86 % Favored : 80.65 % 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: 0.62 (0.21), residues: 1758 helix: 2.20 (0.18), residues: 922 sheet: 0.80 (0.40), residues: 170 loop : -2.48 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 622 TYR 0.011 0.001 TYR B 628 PHE 0.011 0.001 PHE A 555 TRP 0.013 0.001 TRP B 649 HIS 0.003 0.001 HIS A 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (14302) covalent geometry : angle 0.59692 / 0.31 (19422) SS BOND : bond 0.00070 / 0.04 ( 2) SS BOND : angle 0.50914 / 0.30 ( 4) hydrogen bonds : bond 0.04278 / 2.81 ( 686) hydrogen bonds : angle 3.63505 / 2.61 ( 1992) link_BETA1-4 : bond 0.00456 / 0.24 ( 6) link_BETA1-4 : angle 1.13900 / 0.64 ( 18) link_NAG-ASN : bond 0.00353 / 0.17 ( 10) link_NAG-ASN : angle 2.46964 / 1.46 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5075.76 seconds wall clock time: 87 minutes 16.87 seconds (5236.87 seconds total)