Starting phenix.real_space_refine on Mon Dec 30 22:51:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m22_30058/12_2024/6m22_30058.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m22_30058/12_2024/6m22_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_30058/12_2024/6m22_30058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m22_30058/12_2024/6m22_30058.map" model { file = "/net/cci-nas-00/data/ceres_data/6m22_30058/12_2024/6m22_30058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m22_30058/12_2024/6m22_30058.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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: 8.63, per 1000 atoms: 0.62 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: 3.67 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.57 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: 4.79 Time building geometry restraints manager: 4.21 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 - 22.32: 8049 22.32 - 44.63: 513 44.63 - 66.95: 60 66.95 - 89.26: 6 89.26 - 111.58: 6 Dihedral angle restraints: 8634 sinusoidal: 3564 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 8631 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: 0.00 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: 1.730 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.760 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.009 0.213 14302 Z= 0.560 Angle : 1.045 13.207 19422 Z= 0.573 Chirality : 0.059 0.330 2296 Planarity : 0.007 0.096 2390 Dihedral : 14.669 111.579 5372 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.002 TRP A 649 HIS 0.008 0.001 HIS B 252 PHE 0.015 0.002 PHE B 555 TYR 0.020 0.002 TYR B 372 ARG 0.009 0.001 ARG B 622 *********************** 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 : 1.594 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: 1.4205 time to fit residues: 417.3913 Evaluate side-chains 154 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 148 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14302 Z= 0.223 Angle : 0.695 8.953 19422 Z= 0.365 Chirality : 0.046 0.308 2296 Planarity : 0.006 0.071 2390 Dihedral : 9.471 105.437 2294 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.87 % Favored : 90.90 % Rotamer: Outliers : 2.84 % Allowed : 11.10 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.18), residues: 1758 helix: -0.80 (0.16), residues: 900 sheet: 0.38 (0.39), residues: 170 loop : -2.87 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 519 HIS 0.005 0.001 HIS A 867 PHE 0.014 0.001 PHE A 441 TYR 0.012 0.002 TYR B 628 ARG 0.006 0.001 ARG B 557 *********************** 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 202 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 703 ASN cc_start: 0.8072 (m-40) cc_final: 0.7542 (t0) REVERT: A 873 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7166 (mtt) REVERT: B 703 ASN cc_start: 0.8086 (m-40) cc_final: 0.7550 (t0) REVERT: B 873 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7162 (mtt) outliers start: 42 outliers final: 14 residues processed: 184 average time/residue: 1.4382 time to fit residues: 288.5925 Evaluate side-chains 156 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 88 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14302 Z= 0.186 Angle : 0.615 10.569 19422 Z= 0.320 Chirality : 0.044 0.255 2296 Planarity : 0.005 0.071 2390 Dihedral : 7.865 79.954 2284 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.17 % Favored : 92.61 % Rotamer: Outliers : 2.30 % Allowed : 12.72 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), residues: 1758 helix: 0.89 (0.18), residues: 898 sheet: 0.56 (0.39), residues: 170 loop : -2.71 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 649 HIS 0.003 0.001 HIS A 115 PHE 0.012 0.001 PHE B 555 TYR 0.011 0.001 TYR B 628 ARG 0.003 0.000 ARG A 820 *********************** 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 194 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 703 ASN cc_start: 0.8121 (m-40) cc_final: 0.7603 (t0) REVERT: A 873 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7203 (mtt) REVERT: B 703 ASN cc_start: 0.8132 (m-40) cc_final: 0.7607 (t0) REVERT: B 873 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7202 (mtt) outliers start: 34 outliers final: 8 residues processed: 172 average time/residue: 1.3689 time to fit residues: 258.1542 Evaluate side-chains 140 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 160 optimal weight: 0.0370 chunk 170 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14302 Z= 0.177 Angle : 0.590 9.655 19422 Z= 0.307 Chirality : 0.044 0.304 2296 Planarity : 0.004 0.065 2390 Dihedral : 6.653 46.352 2284 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.39 % Favored : 92.38 % Rotamer: Outliers : 2.30 % Allowed : 13.26 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1758 helix: 1.54 (0.18), residues: 918 sheet: 0.62 (0.40), residues: 170 loop : -2.62 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 649 HIS 0.003 0.001 HIS A 423 PHE 0.012 0.001 PHE B 555 TYR 0.012 0.001 TYR B 288 ARG 0.005 0.000 ARG A 622 *********************** 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 172 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 916 LEU cc_start: 0.7007 (mm) cc_final: 0.6202 (mm) REVERT: B 916 LEU cc_start: 0.7004 (mm) cc_final: 0.6199 (mm) outliers start: 34 outliers final: 20 residues processed: 160 average time/residue: 1.3960 time to fit residues: 245.6906 Evaluate side-chains 148 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 588 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 927 MET 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 588 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 927 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 145 optimal weight: 0.0970 chunk 117 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14302 Z= 0.327 Angle : 0.665 8.312 19422 Z= 0.348 Chirality : 0.047 0.324 2296 Planarity : 0.005 0.065 2390 Dihedral : 6.413 45.129 2284 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.19 % Favored : 91.58 % Rotamer: Outliers : 2.77 % Allowed : 13.87 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1758 helix: 1.62 (0.18), residues: 914 sheet: 0.79 (0.42), residues: 150 loop : -2.55 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 864 HIS 0.010 0.001 HIS A1048 PHE 0.013 0.002 PHE B 555 TYR 0.015 0.002 TYR A 628 ARG 0.004 0.001 ARG B 705 *********************** 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 171 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 673 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8045 (ptpp) outliers start: 41 outliers final: 16 residues processed: 159 average time/residue: 1.3226 time to fit residues: 231.4715 Evaluate side-chains 141 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 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 673 LYS Chi-restraints excluded: chain A residue 717 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 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 717 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14302 Z= 0.248 Angle : 0.614 8.483 19422 Z= 0.322 Chirality : 0.045 0.340 2296 Planarity : 0.004 0.063 2390 Dihedral : 6.170 45.141 2284 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.30 % Favored : 91.47 % Rotamer: Outliers : 2.84 % Allowed : 14.88 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1758 helix: 1.80 (0.18), residues: 914 sheet: 0.79 (0.42), residues: 150 loop : -2.52 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 649 HIS 0.003 0.001 HIS A 790 PHE 0.012 0.001 PHE A 555 TYR 0.013 0.002 TYR A 628 ARG 0.005 0.000 ARG B 622 *********************** 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 170 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 673 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8076 (ptpp) REVERT: B 673 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8068 (ptpp) outliers start: 42 outliers final: 18 residues processed: 156 average time/residue: 1.3398 time to fit residues: 229.3576 Evaluate side-chains 142 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 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 528 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 673 LYS 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 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 528 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 673 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 169 optimal weight: 0.4980 chunk 106 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14302 Z= 0.185 Angle : 0.574 7.677 19422 Z= 0.302 Chirality : 0.043 0.282 2296 Planarity : 0.004 0.064 2390 Dihedral : 5.888 44.979 2284 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.19 % Favored : 91.58 % Rotamer: Outliers : 1.62 % Allowed : 16.10 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1758 helix: 1.99 (0.18), residues: 916 sheet: 0.84 (0.43), residues: 150 loop : -2.49 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 649 HIS 0.003 0.001 HIS A 252 PHE 0.012 0.001 PHE A 555 TYR 0.011 0.001 TYR B 628 ARG 0.007 0.000 ARG A 622 *********************** 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 148 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 673 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8036 (ptpp) REVERT: B 673 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8057 (ptpp) outliers start: 24 outliers final: 18 residues processed: 146 average time/residue: 1.4157 time to fit residues: 227.0088 Evaluate side-chains 140 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 673 LYS 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 350 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 673 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.4980 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 0.0770 chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14302 Z= 0.151 Angle : 0.548 7.530 19422 Z= 0.289 Chirality : 0.042 0.250 2296 Planarity : 0.004 0.064 2390 Dihedral : 5.542 43.988 2284 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.45 % Favored : 92.32 % Rotamer: Outliers : 1.76 % Allowed : 16.10 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1758 helix: 2.14 (0.18), residues: 916 sheet: 0.92 (0.43), residues: 150 loop : -2.45 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 649 HIS 0.002 0.000 HIS A 252 PHE 0.011 0.001 PHE B 555 TYR 0.011 0.001 TYR B 650 ARG 0.007 0.000 ARG B 622 *********************** 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 144 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 140 average time/residue: 1.4375 time to fit residues: 219.9029 Evaluate side-chains 132 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 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 379 THR Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain B residue 242 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 379 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 616 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14302 Z= 0.196 Angle : 0.589 9.283 19422 Z= 0.308 Chirality : 0.043 0.240 2296 Planarity : 0.004 0.064 2390 Dihedral : 5.552 44.903 2284 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.85 % Favored : 91.92 % Rotamer: Outliers : 1.62 % Allowed : 16.64 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1758 helix: 2.17 (0.18), residues: 918 sheet: 0.79 (0.40), residues: 170 loop : -2.46 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 649 HIS 0.003 0.001 HIS B 790 PHE 0.011 0.001 PHE B 555 TYR 0.011 0.001 TYR B 628 ARG 0.008 0.001 ARG A 622 *********************** 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 150 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8319 (tt) REVERT: B 573 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8319 (tt) outliers start: 24 outliers final: 22 residues processed: 148 average time/residue: 1.3802 time to fit residues: 224.2682 Evaluate side-chains 150 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 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 528 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 242 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 379 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 717 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 175 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14302 Z= 0.181 Angle : 0.563 7.521 19422 Z= 0.296 Chirality : 0.043 0.228 2296 Planarity : 0.004 0.065 2390 Dihedral : 5.486 44.719 2284 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.74 % Favored : 92.04 % Rotamer: Outliers : 1.62 % Allowed : 16.71 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1758 helix: 2.20 (0.18), residues: 922 sheet: 0.81 (0.40), residues: 170 loop : -2.39 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 649 HIS 0.002 0.001 HIS A 423 PHE 0.011 0.001 PHE B 555 TYR 0.010 0.001 TYR B 650 ARG 0.008 0.000 ARG B 622 ********************** 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 152 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8323 (tt) REVERT: B 573 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8324 (tt) outliers start: 24 outliers final: 18 residues processed: 150 average time/residue: 1.4349 time to fit residues: 237.3676 Evaluate side-chains 145 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.718 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 242 VAL 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 528 SER Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 616 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.127329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.092715 restraints weight = 19449.453| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.25 r_work: 0.2909 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14302 Z= 0.181 Angle : 0.598 9.875 19422 Z= 0.313 Chirality : 0.043 0.221 2296 Planarity : 0.004 0.064 2390 Dihedral : 5.431 41.755 2284 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.74 % Favored : 92.04 % Rotamer: Outliers : 1.62 % Allowed : 16.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1758 helix: 2.22 (0.18), residues: 922 sheet: 0.82 (0.40), residues: 170 loop : -2.35 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 649 HIS 0.002 0.001 HIS B 790 PHE 0.015 0.001 PHE A 364 TYR 0.010 0.001 TYR A 650 ARG 0.009 0.000 ARG B 622 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4603.39 seconds wall clock time: 84 minutes 20.18 seconds (5060.18 seconds total)