Starting phenix.real_space_refine on Wed Mar 4 14:14:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m22_30058/03_2026/6m22_30058.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m22_30058/03_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_30058/03_2026/6m22_30058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m22_30058/03_2026/6m22_30058.map" model { file = "/net/cci-nas-00/data/ceres_data/6m22_30058/03_2026/6m22_30058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m22_30058/03_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-dev-5986/lib/python3.9/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 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: 3.32, per 1000 atoms: 0.24 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: 1.28 Conformation dependent library (CDL) restraints added in 625.7 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: 0.47 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: 2.11 Time building geometry restraints manager: 1.62 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: 0.02 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: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.130 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- 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 : 0.010 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 : 14.669 111.579 5372 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 covalent geometry : bond 0.00891 (14302) covalent geometry : angle 1.04549 (19422) SS BOND : bond 0.00532 ( 2) SS BOND : angle 1.90009 ( 4) hydrogen bonds : bond 0.30187 ( 686) hydrogen bonds : angle 9.16658 ( 1992) link_BETA1-4 : bond 0.00883 ( 6) link_BETA1-4 : angle 12.29874 ( 18) link_NAG-ASN : bond 0.13700 ( 10) link_NAG-ASN : angle 15.37932 ( 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 : 0.500 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: 0.6481 time to fit residues: 189.7662 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 : 0.539 ------------------------------------------------------------------------------- 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... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.092418 restraints weight = 19385.810| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.32 r_work: 0.2901 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14320 Z= 0.160 Angle : 0.751 15.941 19474 Z= 0.381 Chirality : 0.046 0.274 2296 Planarity : 0.006 0.073 2390 Dihedral : 9.579 105.336 2294 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.53 % Favored : 91.24 % Rotamer: Outliers : 2.84 % Allowed : 10.83 % 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: -2.35 (0.18), residues: 1758 helix: -0.93 (0.15), residues: 900 sheet: 0.36 (0.39), residues: 170 loop : -2.90 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 557 TYR 0.011 0.001 TYR B 650 PHE 0.012 0.001 PHE B 441 TRP 0.008 0.001 TRP B 397 HIS 0.005 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00338 (14302) covalent geometry : angle 0.70295 (19422) SS BOND : bond 0.00363 ( 2) SS BOND : angle 2.52751 ( 4) hydrogen bonds : bond 0.06383 ( 686) hydrogen bonds : angle 4.33247 ( 1992) link_BETA1-4 : bond 0.00358 ( 6) link_BETA1-4 : angle 3.01415 ( 18) link_NAG-ASN : bond 0.00692 ( 10) link_NAG-ASN : angle 6.34231 ( 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 202 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 567 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6176 (tp30) REVERT: A 703 ASN cc_start: 0.8747 (m-40) cc_final: 0.8107 (t0) REVERT: A 873 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8600 (mtt) REVERT: A 905 MET cc_start: 0.7349 (ptp) cc_final: 0.6876 (ptm) REVERT: A 1062 ARG cc_start: 0.7623 (tpp80) cc_final: 0.7324 (mpp-170) REVERT: B 567 GLU cc_start: 0.6706 (mt-10) cc_final: 0.6169 (tp30) REVERT: B 703 ASN cc_start: 0.8746 (m-40) cc_final: 0.8106 (t0) REVERT: B 873 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8606 (mtt) REVERT: B 905 MET cc_start: 0.7355 (ptp) cc_final: 0.6885 (ptm) REVERT: B 1062 ARG cc_start: 0.7618 (tpp80) cc_final: 0.7321 (mpp-170) outliers start: 42 outliers final: 14 residues processed: 186 average time/residue: 0.6508 time to fit residues: 131.6349 Evaluate side-chains 158 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 29 optimal weight: 0.0050 chunk 108 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1029 ASN B1029 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.092978 restraints weight = 19311.821| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.20 r_work: 0.2916 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2737 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 : 0.643 10.572 19474 Z= 0.327 Chirality : 0.044 0.281 2296 Planarity : 0.005 0.070 2390 Dihedral : 7.906 80.522 2284 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.85 % Favored : 91.92 % Rotamer: Outliers : 1.89 % Allowed : 13.26 % Favored : 84.84 % 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: 0.90 (0.18), residues: 898 sheet: 0.52 (0.39), residues: 170 loop : -2.71 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 820 TYR 0.010 0.001 TYR B 628 PHE 0.012 0.001 PHE B 555 TRP 0.010 0.001 TRP A 649 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00289 (14302) covalent geometry : angle 0.61862 (19422) SS BOND : bond 0.00038 ( 2) SS BOND : angle 1.18705 ( 4) hydrogen bonds : bond 0.04939 ( 686) hydrogen bonds : angle 3.83671 ( 1992) link_BETA1-4 : bond 0.00598 ( 6) link_BETA1-4 : angle 2.25576 ( 18) link_NAG-ASN : bond 0.00585 ( 10) link_NAG-ASN : angle 4.15442 ( 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 180 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8984 (mmm) REVERT: A 422 ASN cc_start: 0.8461 (t0) cc_final: 0.7921 (t0) REVERT: A 429 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7699 (m-30) REVERT: A 703 ASN cc_start: 0.8776 (m-40) cc_final: 0.8132 (t0) REVERT: A 873 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8568 (mtt) REVERT: A 905 MET cc_start: 0.7468 (ptp) cc_final: 0.7163 (ptm) REVERT: A 927 MET cc_start: 0.5295 (OUTLIER) cc_final: 0.5090 (ttt) REVERT: A 1062 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7451 (tpp80) REVERT: B 138 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8990 (mmm) REVERT: B 422 ASN cc_start: 0.8449 (t0) cc_final: 0.7906 (t0) REVERT: B 429 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7698 (m-30) REVERT: B 703 ASN cc_start: 0.8789 (m-40) cc_final: 0.8143 (t0) REVERT: B 873 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8568 (mtt) REVERT: B 905 MET cc_start: 0.7473 (ptp) cc_final: 0.7174 (ptm) REVERT: B 927 MET cc_start: 0.5304 (OUTLIER) cc_final: 0.5103 (ttt) REVERT: B 1062 ARG cc_start: 0.7776 (tpp80) cc_final: 0.7445 (tpp80) outliers start: 28 outliers final: 8 residues processed: 164 average time/residue: 0.6259 time to fit residues: 111.9663 Evaluate side-chains 146 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 429 ASP 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 429 ASP 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: 8.9990 chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.126652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.090569 restraints weight = 19220.419| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.29 r_work: 0.2867 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14320 Z= 0.156 Angle : 0.652 9.797 19474 Z= 0.331 Chirality : 0.045 0.300 2296 Planarity : 0.005 0.064 2390 Dihedral : 6.851 48.369 2284 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.19 % Favored : 91.58 % Rotamer: Outliers : 2.71 % Allowed : 13.13 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1758 helix: 1.48 (0.18), residues: 912 sheet: 0.55 (0.39), residues: 170 loop : -2.65 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 622 TYR 0.014 0.002 TYR B 628 PHE 0.012 0.001 PHE B 555 TRP 0.013 0.001 TRP B 649 HIS 0.004 0.001 HIS B 561 Details of bonding type rmsd covalent geometry : bond 0.00357 (14302) covalent geometry : angle 0.62928 (19422) SS BOND : bond 0.00023 ( 2) SS BOND : angle 0.81113 ( 4) hydrogen bonds : bond 0.05080 ( 686) hydrogen bonds : angle 3.83060 ( 1992) link_BETA1-4 : bond 0.00445 ( 6) link_BETA1-4 : angle 1.95517 ( 18) link_NAG-ASN : bond 0.00370 ( 10) link_NAG-ASN : angle 4.18490 ( 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 178 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.9016 (mmm) REVERT: A 422 ASN cc_start: 0.8433 (t0) cc_final: 0.7955 (t0) REVERT: A 429 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: A 567 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6207 (tp30) REVERT: A 573 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8933 (tt) REVERT: A 873 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8548 (mtt) REVERT: A 905 MET cc_start: 0.7456 (ptp) cc_final: 0.7193 (ptm) REVERT: A 916 LEU cc_start: 0.8002 (mm) cc_final: 0.7305 (mm) REVERT: A 1062 ARG cc_start: 0.7781 (tpp80) cc_final: 0.7507 (tpp80) REVERT: B 138 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.9013 (mmm) REVERT: B 422 ASN cc_start: 0.8437 (t0) cc_final: 0.7958 (t0) REVERT: B 429 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7976 (m-30) REVERT: B 567 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6202 (tp30) REVERT: B 573 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8929 (tt) REVERT: B 873 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8547 (mtt) REVERT: B 905 MET cc_start: 0.7463 (ptp) cc_final: 0.7200 (ptm) REVERT: B 916 LEU cc_start: 0.8002 (mm) cc_final: 0.7309 (mm) REVERT: B 1062 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7511 (tpp80) outliers start: 40 outliers final: 20 residues processed: 163 average time/residue: 0.5879 time to fit residues: 105.2513 Evaluate side-chains 158 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET 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 573 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain B residue 138 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 429 ASP 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 743 SER Chi-restraints excluded: chain B residue 873 MET 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: 0.9980 chunk 173 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.092651 restraints weight = 19341.977| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.25 r_work: 0.2924 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3147 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= 0.123 Angle : 0.592 7.534 19474 Z= 0.304 Chirality : 0.044 0.330 2296 Planarity : 0.004 0.066 2390 Dihedral : 6.147 46.097 2284 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.28 % Favored : 92.49 % Rotamer: Outliers : 2.71 % Allowed : 14.41 % Favored : 82.88 % 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: 0.18 (0.21), residues: 1758 helix: 1.81 (0.18), residues: 918 sheet: 0.66 (0.40), residues: 170 loop : -2.61 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 622 TYR 0.011 0.001 TYR A 650 PHE 0.012 0.001 PHE B 555 TRP 0.012 0.001 TRP A 649 HIS 0.003 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00268 (14302) covalent geometry : angle 0.57145 (19422) SS BOND : bond 0.00153 ( 2) SS BOND : angle 0.66211 ( 4) hydrogen bonds : bond 0.04346 ( 686) hydrogen bonds : angle 3.70390 ( 1992) link_BETA1-4 : bond 0.00547 ( 6) link_BETA1-4 : angle 1.85252 ( 18) link_NAG-ASN : bond 0.00407 ( 10) link_NAG-ASN : angle 3.71217 ( 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 174 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ASN cc_start: 0.8450 (t0) cc_final: 0.8044 (t0) REVERT: A 429 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: A 567 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6188 (tp30) REVERT: A 672 GLU cc_start: 0.9031 (tt0) cc_final: 0.8697 (tm-30) REVERT: A 703 ASN cc_start: 0.8840 (m-40) cc_final: 0.8335 (t0) REVERT: A 907 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7993 (tppt) REVERT: A 1062 ARG cc_start: 0.7699 (tpp80) cc_final: 0.7473 (tpp80) REVERT: B 422 ASN cc_start: 0.8449 (t0) cc_final: 0.8044 (t0) REVERT: B 429 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7945 (m-30) REVERT: B 567 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6188 (tp30) REVERT: B 672 GLU cc_start: 0.9025 (tt0) cc_final: 0.8684 (tm-30) REVERT: B 703 ASN cc_start: 0.8840 (m-40) cc_final: 0.8338 (t0) REVERT: B 907 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7994 (tppt) REVERT: B 1062 ARG cc_start: 0.7711 (tpp80) cc_final: 0.7484 (tpp80) outliers start: 40 outliers final: 18 residues processed: 162 average time/residue: 0.5730 time to fit residues: 102.1010 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 : 0.531 ------------------------------------------------------------------------------- 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 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 A residue 595 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain B residue 163 THR 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 Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 743 SER 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: 7.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.126602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.090674 restraints weight = 19298.271| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.31 r_work: 0.2871 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3251 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= 0.146 Angle : 0.607 7.846 19474 Z= 0.313 Chirality : 0.044 0.248 2296 Planarity : 0.004 0.061 2390 Dihedral : 5.983 44.360 2284 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.08 % Favored : 91.70 % Rotamer: Outliers : 3.25 % Allowed : 14.68 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.21), residues: 1758 helix: 1.91 (0.18), residues: 920 sheet: 0.69 (0.39), residues: 170 loop : -2.58 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 622 TYR 0.013 0.001 TYR A 628 PHE 0.012 0.001 PHE B 555 TRP 0.014 0.001 TRP B 649 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00336 (14302) covalent geometry : angle 0.58878 (19422) SS BOND : bond 0.00092 ( 2) SS BOND : angle 0.62282 ( 4) hydrogen bonds : bond 0.04788 ( 686) hydrogen bonds : angle 3.74986 ( 1992) link_BETA1-4 : bond 0.00506 ( 6) link_BETA1-4 : angle 1.73112 ( 18) link_NAG-ASN : bond 0.00336 ( 10) link_NAG-ASN : angle 3.58353 ( 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 174 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ASN cc_start: 0.8496 (t0) cc_final: 0.8071 (t0) REVERT: A 429 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: A 567 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6177 (tp30) REVERT: A 573 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8945 (tt) REVERT: A 673 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8737 (ptpp) REVERT: A 1062 ARG cc_start: 0.7784 (tpp80) cc_final: 0.7565 (tpp80) REVERT: B 422 ASN cc_start: 0.8497 (t0) cc_final: 0.8073 (t0) REVERT: B 429 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7978 (m-30) REVERT: B 567 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6177 (tp30) REVERT: B 573 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8945 (tt) REVERT: B 673 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8745 (ptpp) REVERT: B 1062 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7557 (tpp80) outliers start: 48 outliers final: 25 residues processed: 160 average time/residue: 0.5663 time to fit residues: 99.7247 Evaluate side-chains 153 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 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 588 LEU 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 A residue 743 SER 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 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 588 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 743 SER 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: 0.6980 chunk 131 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.128012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.092301 restraints weight = 19311.293| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.30 r_work: 0.2896 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14320 Z= 0.123 Angle : 0.594 7.707 19474 Z= 0.306 Chirality : 0.044 0.364 2296 Planarity : 0.004 0.064 2390 Dihedral : 5.764 44.021 2284 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.30 % Favored : 91.47 % Rotamer: Outliers : 2.64 % Allowed : 16.04 % Favored : 81.33 % 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: 0.43 (0.21), residues: 1758 helix: 2.05 (0.18), residues: 918 sheet: 0.76 (0.39), residues: 170 loop : -2.55 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 622 TYR 0.011 0.001 TYR B 650 PHE 0.011 0.001 PHE B 555 TRP 0.014 0.001 TRP A 864 HIS 0.003 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00270 (14302) covalent geometry : angle 0.57847 (19422) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.54945 ( 4) hydrogen bonds : bond 0.04238 ( 686) hydrogen bonds : angle 3.67727 ( 1992) link_BETA1-4 : bond 0.00544 ( 6) link_BETA1-4 : angle 1.61649 ( 18) link_NAG-ASN : bond 0.00334 ( 10) link_NAG-ASN : angle 3.32007 ( 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 163 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ASN cc_start: 0.8504 (t0) cc_final: 0.8100 (t0) REVERT: A 429 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7976 (m-30) REVERT: A 567 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6106 (tp30) REVERT: A 573 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8946 (tt) REVERT: A 673 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8658 (ptpp) REVERT: A 907 LYS cc_start: 0.8523 (tppt) cc_final: 0.8272 (ttmm) REVERT: A 1062 ARG cc_start: 0.7781 (tpp80) cc_final: 0.7546 (tpp80) REVERT: B 422 ASN cc_start: 0.8490 (t0) cc_final: 0.8091 (t0) REVERT: B 429 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: B 567 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6100 (tp30) REVERT: B 573 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8946 (tt) REVERT: B 673 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8665 (ptpp) REVERT: B 907 LYS cc_start: 0.8520 (tppt) cc_final: 0.8269 (ttmm) REVERT: B 1062 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7542 (tpp80) outliers start: 39 outliers final: 25 residues processed: 153 average time/residue: 0.6312 time to fit residues: 105.7152 Evaluate side-chains 153 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 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 588 LEU 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 A residue 743 SER 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 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 588 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 743 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 89 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.089512 restraints weight = 19306.827| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.26 r_work: 0.2857 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14320 Z= 0.174 Angle : 0.646 8.033 19474 Z= 0.333 Chirality : 0.046 0.326 2296 Planarity : 0.004 0.062 2390 Dihedral : 5.835 45.457 2284 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.19 % Favored : 91.58 % Rotamer: Outliers : 2.57 % Allowed : 16.24 % Favored : 81.19 % 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: 0.33 (0.21), residues: 1758 helix: 1.96 (0.18), residues: 916 sheet: 0.68 (0.39), residues: 170 loop : -2.56 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 622 TYR 0.014 0.002 TYR A 628 PHE 0.011 0.001 PHE B 555 TRP 0.017 0.002 TRP B 864 HIS 0.004 0.001 HIS A 790 Details of bonding type rmsd covalent geometry : bond 0.00411 (14302) covalent geometry : angle 0.63126 (19422) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.69135 ( 4) hydrogen bonds : bond 0.05183 ( 686) hydrogen bonds : angle 3.82223 ( 1992) link_BETA1-4 : bond 0.00471 ( 6) link_BETA1-4 : angle 1.58170 ( 18) link_NAG-ASN : bond 0.00336 ( 10) link_NAG-ASN : angle 3.33801 ( 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 160 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ASN cc_start: 0.8543 (t0) cc_final: 0.8141 (t0) REVERT: A 429 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8034 (m-30) REVERT: A 567 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6192 (tp30) REVERT: A 573 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8963 (tt) REVERT: A 673 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8697 (ptpp) REVERT: A 907 LYS cc_start: 0.8630 (tppt) cc_final: 0.8243 (ttmm) REVERT: A 1062 ARG cc_start: 0.7737 (tpp80) cc_final: 0.7522 (tpp80) REVERT: B 422 ASN cc_start: 0.8544 (t0) cc_final: 0.8150 (t0) REVERT: B 429 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8029 (m-30) REVERT: B 567 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6195 (tp30) REVERT: B 573 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8968 (tt) REVERT: B 673 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8721 (ptpp) REVERT: B 907 LYS cc_start: 0.8628 (tppt) cc_final: 0.8242 (ttmm) REVERT: B 1062 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7512 (tpp80) outliers start: 38 outliers final: 23 residues processed: 154 average time/residue: 0.6357 time to fit residues: 107.2117 Evaluate side-chains 149 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 429 ASP 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 673 LYS Chi-restraints excluded: chain A residue 743 SER 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 429 ASP 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 673 LYS Chi-restraints excluded: chain B residue 743 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 118 optimal weight: 6.9990 chunk 18 optimal weight: 0.0770 chunk 33 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 174 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.091519 restraints weight = 19334.175| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.29 r_work: 0.2877 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3484 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 7.485 19474 Z= 0.310 Chirality : 0.044 0.300 2296 Planarity : 0.004 0.065 2390 Dihedral : 5.636 44.641 2284 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.08 % Favored : 91.70 % Rotamer: Outliers : 2.44 % Allowed : 16.44 % Favored : 81.12 % 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: 2.08 (0.18), residues: 916 sheet: 0.75 (0.40), residues: 170 loop : -2.51 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 622 TYR 0.010 0.001 TYR A 628 PHE 0.011 0.001 PHE B 555 TRP 0.013 0.001 TRP B 649 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00295 (14302) covalent geometry : angle 0.58446 (19422) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.60490 ( 4) hydrogen bonds : bond 0.04451 ( 686) hydrogen bonds : angle 3.71408 ( 1992) link_BETA1-4 : bond 0.00527 ( 6) link_BETA1-4 : angle 1.47336 ( 18) link_NAG-ASN : bond 0.00344 ( 10) link_NAG-ASN : angle 3.14174 ( 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 162 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 HIS cc_start: 0.7014 (OUTLIER) cc_final: 0.6769 (m-70) REVERT: A 422 ASN cc_start: 0.8540 (t0) cc_final: 0.8128 (t0) REVERT: A 429 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: A 567 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6055 (tp30) REVERT: A 573 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8937 (tt) REVERT: A 702 LYS cc_start: 0.7986 (mmpt) cc_final: 0.7755 (mppt) REVERT: A 907 LYS cc_start: 0.8602 (tppt) cc_final: 0.8231 (ttmm) REVERT: A 1062 ARG cc_start: 0.7774 (tpp80) cc_final: 0.7532 (tpp80) REVERT: B 252 HIS cc_start: 0.7022 (OUTLIER) cc_final: 0.6776 (m-70) REVERT: B 422 ASN cc_start: 0.8528 (t0) cc_final: 0.8123 (t0) REVERT: B 429 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8001 (m-30) REVERT: B 567 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6055 (tp30) REVERT: B 573 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8937 (tt) REVERT: B 702 LYS cc_start: 0.7975 (mmpt) cc_final: 0.7741 (mppt) REVERT: B 907 LYS cc_start: 0.8601 (tppt) cc_final: 0.8230 (ttmm) REVERT: B 1062 ARG cc_start: 0.7763 (tpp80) cc_final: 0.7520 (tpp80) outliers start: 36 outliers final: 26 residues processed: 160 average time/residue: 0.6158 time to fit residues: 107.7614 Evaluate side-chains 154 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 252 HIS 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 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 588 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 743 SER 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 252 HIS 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 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 588 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 743 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 138 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 163 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.093782 restraints weight = 19419.688| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.21 r_work: 0.2914 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14320 Z= 0.118 Angle : 0.588 8.740 19474 Z= 0.305 Chirality : 0.043 0.287 2296 Planarity : 0.004 0.064 2390 Dihedral : 5.440 44.295 2284 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.62 % Favored : 92.15 % Rotamer: Outliers : 1.89 % Allowed : 17.19 % Favored : 80.92 % 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: 0.65 (0.21), residues: 1758 helix: 2.23 (0.18), residues: 918 sheet: 0.84 (0.40), residues: 170 loop : -2.44 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 622 TYR 0.010 0.001 TYR B 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 covalent geometry : bond 0.00253 (14302) covalent geometry : angle 0.57492 (19422) SS BOND : bond 0.00076 ( 2) SS BOND : angle 0.49201 ( 4) hydrogen bonds : bond 0.03949 ( 686) hydrogen bonds : angle 3.60781 ( 1992) link_BETA1-4 : bond 0.00527 ( 6) link_BETA1-4 : angle 1.44124 ( 18) link_NAG-ASN : bond 0.00312 ( 10) link_NAG-ASN : angle 3.06064 ( 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 152 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ASN cc_start: 0.8561 (t0) cc_final: 0.8120 (t0) REVERT: A 429 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: A 567 GLU cc_start: 0.6613 (mt-10) cc_final: 0.5997 (tp30) REVERT: A 672 GLU cc_start: 0.8930 (tt0) cc_final: 0.8597 (tm-30) REVERT: A 702 LYS cc_start: 0.7942 (mmpt) cc_final: 0.7705 (mppt) REVERT: A 907 LYS cc_start: 0.8575 (tppt) cc_final: 0.8207 (ttmm) REVERT: A 1029 ASN cc_start: 0.6603 (m-40) cc_final: 0.6259 (t0) REVERT: A 1062 ARG cc_start: 0.7847 (tpp80) cc_final: 0.7611 (tpp80) REVERT: B 422 ASN cc_start: 0.8561 (t0) cc_final: 0.8119 (t0) REVERT: B 429 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: B 567 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6001 (tp30) REVERT: B 672 GLU cc_start: 0.8923 (tt0) cc_final: 0.8588 (tm-30) REVERT: B 702 LYS cc_start: 0.7930 (mmpt) cc_final: 0.7693 (mppt) REVERT: B 907 LYS cc_start: 0.8571 (tppt) cc_final: 0.8204 (ttmm) REVERT: B 1029 ASN cc_start: 0.6598 (m-40) cc_final: 0.6256 (t0) REVERT: B 1062 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7602 (tpp80) outliers start: 28 outliers final: 22 residues processed: 150 average time/residue: 0.6418 time to fit residues: 105.2070 Evaluate side-chains 146 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 429 ASP 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 743 SER 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 429 ASP 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 743 SER 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: 0.8980 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.090928 restraints weight = 19394.845| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.34 r_work: 0.2852 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3588 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= 0.149 Angle : 0.623 8.830 19474 Z= 0.323 Chirality : 0.044 0.281 2296 Planarity : 0.004 0.064 2390 Dihedral : 5.539 40.540 2284 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.85 % Favored : 91.92 % Rotamer: Outliers : 2.03 % Allowed : 17.05 % Favored : 80.92 % 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: 0.58 (0.21), residues: 1758 helix: 2.16 (0.18), residues: 920 sheet: 0.80 (0.40), residues: 170 loop : -2.47 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 622 TYR 0.012 0.001 TYR A 628 PHE 0.023 0.001 PHE B 364 TRP 0.014 0.001 TRP A 649 HIS 0.003 0.001 HIS A 790 Details of bonding type rmsd covalent geometry : bond 0.00343 (14302) covalent geometry : angle 0.61070 (19422) SS BOND : bond 0.00055 ( 2) SS BOND : angle 0.54403 ( 4) hydrogen bonds : bond 0.04611 ( 686) hydrogen bonds : angle 3.69750 ( 1992) link_BETA1-4 : bond 0.00581 ( 6) link_BETA1-4 : angle 1.27613 ( 18) link_NAG-ASN : bond 0.00209 ( 10) link_NAG-ASN : angle 3.13428 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5128.84 seconds wall clock time: 87 minutes 49.48 seconds (5269.48 seconds total)