Starting phenix.real_space_refine on Sun Aug 9 11:37:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwa_37886/08_2026/8wwa_37886.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwa_37886/08_2026/8wwa_37886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwa_37886/08_2026/8wwa_37886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwa_37886/08_2026/8wwa_37886.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwa_37886/08_2026/8wwa_37886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwa_37886/08_2026/8wwa_37886.cif" } resolution = 3.32 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= 0.045 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 P 48 5.49 5 Mg 6 5.21 5 S 154 5.16 5 C 22107 2.51 5 N 5826 2.21 5 O 6367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34508 Number of models: 1 Model: "" Number of chains: 14 Chain: "H" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4960 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 570} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4971 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 571} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 6838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6838 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 41, 'TRANS': 793} Chain breaks: 5 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 4990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4990 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 573} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 4983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4983 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 572} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 6970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6970 Classifications: {'peptide': 852} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 809} Chain breaks: 5 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.16, per 1000 atoms: 0.21 Number of scatterers: 34508 At special positions: 0 Unit cell: (151.11, 155.49, 167.535, 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) S 154 16.00 P 48 15.00 Mg 6 11.99 O 6367 8.00 N 5826 7.00 C 22107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7826 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 33 sheets defined 50.7% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.634A pdb=" N ARG A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 removed outlier: 5.948A pdb=" N GLU A 313 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 320 Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.743A pdb=" N VAL A 325 " --> pdb=" O TRP A 321 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 removed outlier: 3.652A pdb=" N ALA A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.975A pdb=" N TRP A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.850A pdb=" N ILE A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 409 removed outlier: 4.110A pdb=" N GLN A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLY A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N SER A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 402 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 466 through 494 removed outlier: 4.004A pdb=" N SER A 474 " --> pdb=" O HIS A 470 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE A 477 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 516 removed outlier: 4.867A pdb=" N LEU A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 520 through 535 removed outlier: 4.366A pdb=" N PHE A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.674A pdb=" N ARG A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 620 " --> pdb=" O PHE A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 654 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 703 through 709 removed outlier: 3.628A pdb=" N GLU A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 751 removed outlier: 3.557A pdb=" N TRP A 750 " --> pdb=" O ASP A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 783 Processing helix chain 'A' and resid 787 through 808 Processing helix chain 'A' and resid 818 through 831 removed outlier: 3.868A pdb=" N GLU A 822 " --> pdb=" O CYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 856 through 869 removed outlier: 4.404A pdb=" N THR A 860 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TYR A 862 " --> pdb=" O VAL A 858 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU A 864 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TRP A 865 " --> pdb=" O ALA A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 297 through 309 removed outlier: 3.687A pdb=" N LEU B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 317 through 330 Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 346 removed outlier: 3.863A pdb=" N CYS B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.632A pdb=" N LYS B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 removed outlier: 4.290A pdb=" N HIS B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 386 removed outlier: 4.041A pdb=" N ILE B 378 " --> pdb=" O THR B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 409 removed outlier: 3.510A pdb=" N ILE B 393 " --> pdb=" O GLN B 389 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.650A pdb=" N ILE B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 476 removed outlier: 3.656A pdb=" N SER B 474 " --> pdb=" O HIS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 494 removed outlier: 3.884A pdb=" N VAL B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 516 removed outlier: 4.466A pdb=" N LYS B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 520 through 535 removed outlier: 4.192A pdb=" N PHE B 533 " --> pdb=" O ARG B 529 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 641 through 654 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 680 through 684 Processing helix chain 'B' and resid 701 through 710 removed outlier: 3.633A pdb=" N GLU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.638A pdb=" N TRP B 750 " --> pdb=" O ASP B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 781 Processing helix chain 'B' and resid 787 through 808 Processing helix chain 'B' and resid 818 through 831 removed outlier: 3.536A pdb=" N GLU B 822 " --> pdb=" O CYS B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 842 Processing helix chain 'B' and resid 855 through 867 removed outlier: 3.815A pdb=" N TRP B 865 " --> pdb=" O ALA B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 886 removed outlier: 3.504A pdb=" N ASN B 886 " --> pdb=" O GLN B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 893 removed outlier: 3.696A pdb=" N LEU B 893 " --> pdb=" O GLU B 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.722A pdb=" N GLN D 17 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 34 Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 61 through 79 removed outlier: 4.459A pdb=" N GLN D 78 " --> pdb=" O GLN D 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY D 79 " --> pdb=" O CYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 128 removed outlier: 3.565A pdb=" N ASN D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 292 through 296 removed outlier: 3.661A pdb=" N HIS D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 292 through 296' Processing helix chain 'D' and resid 297 through 309 removed outlier: 3.532A pdb=" N LEU D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 331 removed outlier: 4.484A pdb=" N ASN D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 347 through 353 removed outlier: 4.032A pdb=" N ASN D 351 " --> pdb=" O PRO D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 361 through 367 removed outlier: 4.164A pdb=" N ALA D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 386 removed outlier: 4.127A pdb=" N ILE D 378 " --> pdb=" O THR D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 408 removed outlier: 3.818A pdb=" N ILE D 393 " --> pdb=" O GLN D 389 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR D 405 " --> pdb=" O ILE D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 427 removed outlier: 3.559A pdb=" N ILE D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 476 removed outlier: 3.559A pdb=" N SER D 474 " --> pdb=" O HIS D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 494 removed outlier: 3.821A pdb=" N VAL D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 removed outlier: 3.662A pdb=" N LEU D 501 " --> pdb=" O GLU D 497 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR D 503 " --> pdb=" O ASN D 499 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 520 through 536 removed outlier: 4.048A pdb=" N PHE D 533 " --> pdb=" O ARG D 529 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 605 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.590A pdb=" N THR D 620 " --> pdb=" O PHE D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 654 Processing helix chain 'D' and resid 662 through 666 Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.683A pdb=" N LEU D 683 " --> pdb=" O PHE D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 710 Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.771A pdb=" N TRP D 750 " --> pdb=" O ASP D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 783 removed outlier: 4.012A pdb=" N ILE D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 808 Processing helix chain 'D' and resid 818 through 831 Processing helix chain 'D' and resid 833 through 843 Processing helix chain 'D' and resid 855 through 870 Processing helix chain 'D' and resid 879 through 885 Processing helix chain 'D' and resid 886 through 891 removed outlier: 6.693A pdb=" N LEU D 889 " --> pdb=" O ASN D 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 308 removed outlier: 3.845A pdb=" N ARG E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 332 Processing helix chain 'E' and resid 335 through 346 removed outlier: 3.939A pdb=" N GLU E 340 " --> pdb=" O ARG E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 360 removed outlier: 3.935A pdb=" N LEU E 358 " --> pdb=" O GLY E 354 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS E 360 " --> pdb=" O GLU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 381 removed outlier: 4.039A pdb=" N ILE E 378 " --> pdb=" O THR E 374 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 409 Processing helix chain 'E' and resid 414 through 426 Processing helix chain 'E' and resid 466 through 476 Processing helix chain 'E' and resid 476 through 494 removed outlier: 3.800A pdb=" N VAL E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 516 removed outlier: 4.270A pdb=" N SER E 516 " --> pdb=" O GLU E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 519 No H-bonds generated for 'chain 'E' and resid 517 through 519' Processing helix chain 'E' and resid 520 through 536 removed outlier: 4.186A pdb=" N PHE E 533 " --> pdb=" O ARG E 529 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU E 534 " --> pdb=" O GLN E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 544 Processing helix chain 'E' and resid 591 through 605 Processing helix chain 'E' and resid 607 through 620 removed outlier: 3.792A pdb=" N THR E 620 " --> pdb=" O PHE E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 654 removed outlier: 3.543A pdb=" N LEU E 645 " --> pdb=" O GLY E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 663 through 668 Processing helix chain 'E' and resid 679 through 684 removed outlier: 3.995A pdb=" N LEU E 683 " --> pdb=" O PHE E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 704 through 710 Processing helix chain 'E' and resid 777 through 783 removed outlier: 4.017A pdb=" N ILE E 781 " --> pdb=" O ASP E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 808 Processing helix chain 'E' and resid 818 through 831 Processing helix chain 'E' and resid 833 through 842 Processing helix chain 'E' and resid 857 through 866 removed outlier: 3.559A pdb=" N TYR E 866 " --> pdb=" O TYR E 862 " (cutoff:3.500A) Processing helix chain 'E' and resid 881 through 886 Processing helix chain 'E' and resid 887 through 893 removed outlier: 3.625A pdb=" N TYR E 892 " --> pdb=" O LEU E 889 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 296 Processing helix chain 'F' and resid 300 through 309 Processing helix chain 'F' and resid 318 through 331 removed outlier: 5.389A pdb=" N VAL F 324 " --> pdb=" O LEU F 320 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL F 325 " --> pdb=" O TRP F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 345 Processing helix chain 'F' and resid 358 through 363 removed outlier: 4.499A pdb=" N ASN F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 367 Processing helix chain 'F' and resid 374 through 386 removed outlier: 4.253A pdb=" N ILE F 378 " --> pdb=" O THR F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 409 removed outlier: 3.831A pdb=" N GLU F 392 " --> pdb=" O GLN F 388 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE F 393 " --> pdb=" O GLN F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 426 removed outlier: 4.210A pdb=" N ILE F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 476 Processing helix chain 'F' and resid 476 through 494 removed outlier: 3.887A pdb=" N VAL F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 516 Processing helix chain 'F' and resid 517 through 519 No H-bonds generated for 'chain 'F' and resid 517 through 519' Processing helix chain 'F' and resid 520 through 535 removed outlier: 4.247A pdb=" N PHE F 533 " --> pdb=" O ARG F 529 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU F 534 " --> pdb=" O GLN F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 605 Processing helix chain 'F' and resid 607 through 620 removed outlier: 3.642A pdb=" N THR F 620 " --> pdb=" O PHE F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 654 Processing helix chain 'F' and resid 663 through 668 Processing helix chain 'F' and resid 679 through 684 Processing helix chain 'F' and resid 705 through 710 Processing helix chain 'F' and resid 746 through 752 removed outlier: 4.417A pdb=" N ARG F 752 " --> pdb=" O GLY F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 781 Processing helix chain 'F' and resid 787 through 808 removed outlier: 3.589A pdb=" N GLN F 791 " --> pdb=" O ASP F 787 " (cutoff:3.500A) Processing helix chain 'F' and resid 818 through 831 removed outlier: 3.521A pdb=" N GLU F 822 " --> pdb=" O CYS F 818 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 842 Processing helix chain 'F' and resid 855 through 867 Processing helix chain 'F' and resid 878 through 882 removed outlier: 3.844A pdb=" N SER F 881 " --> pdb=" O LEU F 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 21 removed outlier: 3.756A pdb=" N LYS C 19 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 21 " --> pdb=" O GLN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 61 through 78 removed outlier: 3.561A pdb=" N GLU C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 167 through 180 removed outlier: 3.554A pdb=" N LYS C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 190 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.650A pdb=" N LEU C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 317 removed outlier: 4.155A pdb=" N GLU C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 330 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 345 Processing helix chain 'C' and resid 360 through 367 removed outlier: 4.264A pdb=" N ASN C 363 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 386 removed outlier: 4.006A pdb=" N ILE C 378 " --> pdb=" O THR C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 409 removed outlier: 3.609A pdb=" N ILE C 393 " --> pdb=" O GLN C 389 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 409 " --> pdb=" O TYR C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 426 removed outlier: 3.746A pdb=" N ILE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 476 removed outlier: 3.736A pdb=" N SER C 474 " --> pdb=" O HIS C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 494 removed outlier: 3.762A pdb=" N VAL C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 516 removed outlier: 4.684A pdb=" N LYS C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU C 508 " --> pdb=" O TYR C 504 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 520 through 535 removed outlier: 4.216A pdb=" N PHE C 533 " --> pdb=" O ARG C 529 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 605 Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.724A pdb=" N THR C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 654 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 679 through 684 Processing helix chain 'C' and resid 705 through 710 Processing helix chain 'C' and resid 746 through 751 Processing helix chain 'C' and resid 778 through 783 Processing helix chain 'C' and resid 787 through 808 Processing helix chain 'C' and resid 818 through 831 Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.543A pdb=" N VAL C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 867 removed outlier: 3.563A pdb=" N TRP C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 876 through 887 removed outlier: 3.979A pdb=" N LEU C 880 " --> pdb=" O ILE C 876 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER C 881 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLN C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 891 removed outlier: 3.571A pdb=" N LYS C 891 " --> pdb=" O VAL C 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 888 through 891' Processing sheet with id=AA1, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.515A pdb=" N ASP A 433 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP A 442 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.632A pdb=" N VAL A 557 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 660 removed outlier: 3.795A pdb=" N TYR A 690 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A 689 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA A 735 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE A 691 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 632 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N SER A 736 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP A 634 " --> pdb=" O SER A 736 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 713 through 717 removed outlier: 3.707A pdb=" N VAL A 714 " --> pdb=" O PHE A 726 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 761 through 763 removed outlier: 6.255A pdb=" N LYS A 761 " --> pdb=" O LYS A 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 430 through 434 removed outlier: 3.550A pdb=" N TRP B 442 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 550 through 553 removed outlier: 3.682A pdb=" N GLY B 556 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 658 through 660 removed outlier: 3.665A pdb=" N TYR B 690 " --> pdb=" O SER B 659 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY B 689 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ALA B 735 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU B 632 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N SER B 736 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP B 634 " --> pdb=" O SER B 736 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 698 through 699 removed outlier: 6.753A pdb=" N GLU B 698 " --> pdb=" O ILE B 741 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 713 through 717 removed outlier: 3.529A pdb=" N GLU B 724 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 761 through 763 Processing sheet with id=AB3, first strand: chain 'D' and resid 56 through 58 Processing sheet with id=AB4, first strand: chain 'D' and resid 96 through 99 removed outlier: 4.458A pdb=" N LEU D 96 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL D 158 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE D 143 " --> pdb=" O LYS D 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 430 through 434 removed outlier: 3.575A pdb=" N ASP D 433 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 552 through 553 Processing sheet with id=AB7, first strand: chain 'D' and resid 658 through 661 removed outlier: 3.675A pdb=" N TYR D 690 " --> pdb=" O SER D 659 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU D 632 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 430 through 434 removed outlier: 3.570A pdb=" N TRP E 442 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 550 through 553 removed outlier: 3.646A pdb=" N GLY E 556 " --> pdb=" O VAL E 553 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 688 through 691 removed outlier: 6.030A pdb=" N GLY E 689 " --> pdb=" O VAL E 733 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU E 632 " --> pdb=" O ALA E 734 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU E 633 " --> pdb=" O TYR E 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 698 through 699 removed outlier: 6.761A pdb=" N GLU E 698 " --> pdb=" O ILE E 741 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 715 through 717 Processing sheet with id=AC4, first strand: chain 'E' and resid 761 through 762 removed outlier: 6.391A pdb=" N LYS E 761 " --> pdb=" O LYS E 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 430 through 434 Processing sheet with id=AC6, first strand: chain 'F' and resid 550 through 553 Processing sheet with id=AC7, first strand: chain 'F' and resid 658 through 660 removed outlier: 3.724A pdb=" N TYR F 690 " --> pdb=" O SER F 659 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU F 632 " --> pdb=" O ALA F 734 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N SER F 736 " --> pdb=" O LEU F 632 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TRP F 634 " --> pdb=" O SER F 736 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU F 633 " --> pdb=" O TYR F 756 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 713 through 716 Processing sheet with id=AC9, first strand: chain 'C' and resid 39 through 40 removed outlier: 4.469A pdb=" N THR C 57 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.918A pdb=" N LEU C 96 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL C 158 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.571A pdb=" N TRP C 442 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 550 through 553 Processing sheet with id=AD4, first strand: chain 'C' and resid 658 through 661 removed outlier: 3.768A pdb=" N TYR C 690 " --> pdb=" O SER C 659 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 632 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 713 through 717 Processing sheet with id=AD6, first strand: chain 'C' and resid 761 through 762 removed outlier: 6.519A pdb=" N LYS C 761 " --> pdb=" O LYS C 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 1387 hydrogen bonds defined for protein. 3957 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: 8.43 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10676 1.34 - 1.46: 7045 1.46 - 1.58: 17442 1.58 - 1.70: 88 1.70 - 1.82: 260 Bond restraints: 35511 Sorted by residual: bond pdb=" O3A ANP B1001 " pdb=" PB ANP B1001 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O3A ANP E1001 " pdb=" PB ANP E1001 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" O3A ANP D1001 " pdb=" PB ANP D1001 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" O3A ANP C1002 " pdb=" PB ANP C1002 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" O3A ANP A1001 " pdb=" PB ANP A1001 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.12e+01 ... (remaining 35506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 48006 3.63 - 7.27: 215 7.27 - 10.90: 37 10.90 - 14.54: 2 14.54 - 18.17: 6 Bond angle restraints: 48266 Sorted by residual: angle pdb=" PB ANP E1001 " pdb=" N3B ANP E1001 " pdb=" PG ANP E1001 " ideal model delta sigma weight residual 126.95 108.78 18.17 3.00e+00 1.11e-01 3.67e+01 angle pdb=" PB ANP B1001 " pdb=" N3B ANP B1001 " pdb=" PG ANP B1001 " ideal model delta sigma weight residual 126.95 109.21 17.74 3.00e+00 1.11e-01 3.50e+01 angle pdb=" PB ANP D1001 " pdb=" N3B ANP D1001 " pdb=" PG ANP D1001 " ideal model delta sigma weight residual 126.95 109.35 17.60 3.00e+00 1.11e-01 3.44e+01 angle pdb=" PB ANP F1001 " pdb=" N3B ANP F1001 " pdb=" PG ANP F1001 " ideal model delta sigma weight residual 126.95 109.42 17.53 3.00e+00 1.11e-01 3.41e+01 angle pdb=" PB ANP C1002 " pdb=" N3B ANP C1002 " pdb=" PG ANP C1002 " ideal model delta sigma weight residual 126.95 109.82 17.13 3.00e+00 1.11e-01 3.26e+01 ... (remaining 48261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 20447 34.92 - 69.83: 618 69.83 - 104.75: 70 104.75 - 139.67: 2 139.67 - 174.58: 5 Dihedral angle restraints: 21142 sinusoidal: 9021 harmonic: 12121 Sorted by residual: dihedral pdb=" CA GLU A 395 " pdb=" C GLU A 395 " pdb=" N GLN A 396 " pdb=" CA GLN A 396 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LYS E 371 " pdb=" C LYS E 371 " pdb=" N LYS E 372 " pdb=" CA LYS E 372 " ideal model delta harmonic sigma weight residual -180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" O1A ANP F1001 " pdb=" O3A ANP F1001 " pdb=" PA ANP F1001 " pdb=" PB ANP F1001 " ideal model delta sinusoidal sigma weight residual 83.11 -83.63 166.74 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 21139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4342 0.056 - 0.113: 719 0.113 - 0.169: 53 0.169 - 0.225: 1 0.225 - 0.281: 6 Chirality restraints: 5121 Sorted by residual: chirality pdb=" C3' ANP B1001 " pdb=" C2' ANP B1001 " pdb=" C4' ANP B1001 " pdb=" O3' ANP B1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C3' ANP F1001 " pdb=" C2' ANP F1001 " pdb=" C4' ANP F1001 " pdb=" O3' ANP F1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' ANP A1001 " pdb=" C2' ANP A1001 " pdb=" C4' ANP A1001 " pdb=" O3' ANP A1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 5118 not shown) Planarity restraints: 5996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 634 " 0.022 2.00e-02 2.50e+03 1.76e-02 7.79e+00 pdb=" CG TRP D 634 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP D 634 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP D 634 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 634 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 634 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 634 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 634 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 634 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 634 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 341 " -0.020 2.00e-02 2.50e+03 1.72e-02 7.37e+00 pdb=" CG TRP B 341 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 341 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 341 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 341 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 341 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 341 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 341 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 341 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 341 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 341 " -0.021 2.00e-02 2.50e+03 1.72e-02 7.36e+00 pdb=" CG TRP C 341 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP C 341 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP C 341 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 341 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 341 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 341 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 341 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 341 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 341 " -0.004 2.00e-02 2.50e+03 ... (remaining 5993 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 471 2.60 - 3.17: 31117 3.17 - 3.75: 56839 3.75 - 4.32: 74841 4.32 - 4.90: 118428 Nonbonded interactions: 281696 Sorted by model distance: nonbonded pdb=" O2G ANP A1001 " pdb="MG MG A1002 " model vdw 2.023 2.170 nonbonded pdb=" N3B ANP F1001 " pdb="MG MG F1002 " model vdw 2.052 2.250 nonbonded pdb="MG MG C1001 " pdb=" O1A ANP C1002 " model vdw 2.061 2.170 nonbonded pdb=" O2A ANP F1001 " pdb="MG MG F1002 " model vdw 2.061 2.170 nonbonded pdb=" O3A ANP D1001 " pdb="MG MG D1002 " model vdw 2.080 2.170 ... (remaining 281691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 291 through 843 or resid 854 through 1002)) selection = (chain 'B' and (resid 291 through 843 or resid 854 through 896 or resid 1001 thr \ ough 1002)) selection = (chain 'E' and (resid 291 through 843 or resid 854 through 896 or resid 1001 thr \ ough 1002)) selection = (chain 'F' and (resid 291 through 843 or resid 854 through 896 or resid 1001 thr \ ough 1002)) } ncs_group { reference = (chain 'C' and (resid 11 through 713 or resid 724 through 844 or resid 852 throu \ gh 897)) selection = (chain 'D' and resid 11 through 897) } 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: 3.930 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.280 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.004 0.146 35511 Z= 0.215 Angle : 0.717 18.169 48266 Z= 0.385 Chirality : 0.041 0.281 5121 Planarity : 0.004 0.052 5996 Dihedral : 16.850 174.583 13316 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.02 % Favored : 92.58 % Rotamer: Outliers : 0.76 % Allowed : 0.90 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.45 (0.14), residues: 4044 helix: 0.87 (0.13), residues: 1766 sheet: -0.96 (0.27), residues: 405 loop : -1.27 (0.15), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 829 TYR 0.027 0.001 TYR F 314 PHE 0.012 0.001 PHE C 817 TRP 0.048 0.002 TRP D 634 HIS 0.010 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.21 (35511) covalent geometry : angle 0.71683 / 0.39 (48266) hydrogen bonds : bond 0.18422 / 16.24 ( 1387) hydrogen bonds : angle 6.88229 / 5.61 ( 3957) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 885 GLU cc_start: 0.8603 (tt0) cc_final: 0.7456 (tp30) REVERT: D 336 ARG cc_start: 0.9275 (mpt180) cc_final: 0.8951 (mmp80) REVERT: E 362 TRP cc_start: 0.7718 (p-90) cc_final: 0.7139 (p-90) REVERT: E 724 GLU cc_start: 0.8379 (mp0) cc_final: 0.8103 (mp0) REVERT: F 328 LEU cc_start: 0.9553 (mm) cc_final: 0.9029 (tp) REVERT: F 375 LYS cc_start: 0.8940 (tmtt) cc_final: 0.8730 (tptt) REVERT: F 482 ASP cc_start: 0.8803 (m-30) cc_final: 0.8533 (m-30) REVERT: C 379 MET cc_start: 0.9229 (mpp) cc_final: 0.8644 (mpp) outliers start: 28 outliers final: 3 residues processed: 294 average time/residue: 0.2006 time to fit residues: 98.7095 Evaluate side-chains 207 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 ASN Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain E residue 864 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.0170 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 ASN A 871 ASN ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN D 260 ASN D 304 HIS D 308 ASN ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 HIS E 330 ASN E 383 HIS E 867 ASN F 640 ASN ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 871 ASN C 218 HIS ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.104732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.066460 restraints weight = 123418.134| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.65 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35511 Z= 0.155 Angle : 0.630 10.602 48266 Z= 0.328 Chirality : 0.042 0.194 5121 Planarity : 0.004 0.055 5996 Dihedral : 14.253 176.180 4976 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.07 % Favored : 92.63 % Rotamer: Outliers : 0.73 % Allowed : 7.78 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.48 (0.14), residues: 4044 helix: 0.80 (0.12), residues: 1807 sheet: -0.96 (0.27), residues: 395 loop : -1.29 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 513 TYR 0.021 0.001 TYR D 335 PHE 0.032 0.001 PHE A 326 TRP 0.034 0.002 TRP D 362 HIS 0.009 0.001 HIS D 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (35511) covalent geometry : angle 0.63008 / 0.33 (48266) hydrogen bonds : bond 0.04959 / 4.37 ( 1387) hydrogen bonds : angle 5.47912 / 4.50 ( 3957) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.6183 (mmm) cc_final: 0.5726 (mmm) REVERT: B 513 ARG cc_start: 0.8926 (tpt90) cc_final: 0.8699 (tpp-160) REVERT: D 379 MET cc_start: 0.8904 (mpp) cc_final: 0.8486 (mpp) REVERT: D 631 MET cc_start: 0.9076 (tmm) cc_final: 0.8812 (tmm) REVERT: D 732 MET cc_start: 0.8287 (mmm) cc_final: 0.8025 (mmm) REVERT: E 362 TRP cc_start: 0.7841 (p-90) cc_final: 0.7248 (p-90) REVERT: E 692 GLU cc_start: 0.8737 (pt0) cc_final: 0.8422 (pm20) REVERT: E 724 GLU cc_start: 0.8296 (mp0) cc_final: 0.7932 (mp0) REVERT: E 864 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: F 328 LEU cc_start: 0.9597 (mm) cc_final: 0.9141 (tp) REVERT: F 375 LYS cc_start: 0.8939 (tmtt) cc_final: 0.8672 (tptp) REVERT: F 482 ASP cc_start: 0.9020 (m-30) cc_final: 0.8727 (m-30) REVERT: C 651 MET cc_start: 0.8831 (pmm) cc_final: 0.8464 (pmm) REVERT: C 786 MET cc_start: 0.9226 (mpp) cc_final: 0.8595 (mpp) outliers start: 27 outliers final: 16 residues processed: 248 average time/residue: 0.2070 time to fit residues: 85.8314 Evaluate side-chains 222 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 864 GLU Chi-restraints excluded: chain F residue 302 TYR Chi-restraints excluded: chain F residue 367 HIS Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 864 GLU Chi-restraints excluded: chain C residue 872 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 170 optimal weight: 0.0010 chunk 82 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 403 optimal weight: 8.9990 chunk 398 optimal weight: 0.7980 chunk 368 optimal weight: 0.9980 chunk 280 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 343 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 351 optimal weight: 10.0000 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS A 832 GLN B 491 HIS B 792 ASN D 304 HIS D 308 ASN E 330 ASN E 383 HIS ** F 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS C 260 ASN ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.104765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066487 restraints weight = 122563.149| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.57 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35511 Z= 0.134 Angle : 0.590 17.523 48266 Z= 0.304 Chirality : 0.041 0.191 5121 Planarity : 0.004 0.055 5996 Dihedral : 13.724 177.796 4973 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.92 % Favored : 92.80 % Rotamer: Outliers : 0.93 % Allowed : 10.91 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.42 (0.14), residues: 4044 helix: 0.90 (0.12), residues: 1804 sheet: -1.04 (0.26), residues: 420 loop : -1.27 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 647 TYR 0.024 0.001 TYR C 69 PHE 0.013 0.001 PHE A 342 TRP 0.022 0.001 TRP D 634 HIS 0.011 0.001 HIS E 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (35511) covalent geometry : angle 0.58970 / 0.30 (48266) hydrogen bonds : bond 0.04273 / 3.73 ( 1387) hydrogen bonds : angle 5.13989 / 4.24 ( 3957) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.6366 (mmm) cc_final: 0.5943 (mmm) REVERT: D 379 MET cc_start: 0.8910 (mpp) cc_final: 0.8572 (mpp) REVERT: D 651 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8505 (pmm) REVERT: D 732 MET cc_start: 0.8254 (mmm) cc_final: 0.7926 (mmm) REVERT: E 336 ARG cc_start: 0.8144 (mmm160) cc_final: 0.7283 (mmm160) REVERT: E 362 TRP cc_start: 0.7868 (p-90) cc_final: 0.7249 (p-90) REVERT: E 631 MET cc_start: 0.7917 (tmm) cc_final: 0.7445 (tmm) REVERT: E 692 GLU cc_start: 0.8680 (pt0) cc_final: 0.8336 (pm20) REVERT: E 724 GLU cc_start: 0.8177 (mp0) cc_final: 0.7910 (mp0) REVERT: E 864 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: F 328 LEU cc_start: 0.9594 (mm) cc_final: 0.9140 (tp) REVERT: F 482 ASP cc_start: 0.8987 (m-30) cc_final: 0.8695 (m-30) REVERT: C 452 MET cc_start: 0.8662 (ptp) cc_final: 0.8445 (ptm) REVERT: C 651 MET cc_start: 0.8799 (pmm) cc_final: 0.8445 (pmm) REVERT: C 871 ASN cc_start: 0.9013 (t0) cc_final: 0.8799 (t0) outliers start: 34 outliers final: 20 residues processed: 241 average time/residue: 0.2067 time to fit residues: 83.9630 Evaluate side-chains 226 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain E residue 864 GLU Chi-restraints excluded: chain F residue 367 HIS Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 864 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 344 optimal weight: 10.0000 chunk 201 optimal weight: 0.1980 chunk 398 optimal weight: 0.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 304 HIS D 308 ASN ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN E 383 HIS E 770 ASN ** F 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 HIS ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.104205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.066015 restraints weight = 121832.266| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 4.73 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35511 Z= 0.162 Angle : 0.591 13.315 48266 Z= 0.305 Chirality : 0.041 0.189 5121 Planarity : 0.004 0.057 5996 Dihedral : 13.271 178.649 4973 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.20 % Favored : 92.53 % Rotamer: Outliers : 1.31 % Allowed : 12.63 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.37 (0.14), residues: 4044 helix: 0.99 (0.12), residues: 1797 sheet: -1.05 (0.26), residues: 409 loop : -1.29 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 513 TYR 0.024 0.001 TYR C 69 PHE 0.016 0.001 PHE A 342 TRP 0.032 0.001 TRP D 362 HIS 0.007 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (35511) covalent geometry : angle 0.59125 / 0.30 (48266) hydrogen bonds : bond 0.04038 / 3.52 ( 1387) hydrogen bonds : angle 5.00071 / 4.13 ( 3957) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 885 GLU cc_start: 0.8777 (tt0) cc_final: 0.7795 (tp30) REVERT: B 294 MET cc_start: 0.6394 (mmm) cc_final: 0.5992 (mmm) REVERT: D 651 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8419 (pmm) REVERT: E 336 ARG cc_start: 0.8088 (mmm160) cc_final: 0.7281 (mmm160) REVERT: E 362 TRP cc_start: 0.7905 (p-90) cc_final: 0.7312 (p-90) REVERT: E 631 MET cc_start: 0.7927 (tmm) cc_final: 0.7600 (tmm) REVERT: E 724 GLU cc_start: 0.8197 (mp0) cc_final: 0.7923 (mp0) REVERT: F 328 LEU cc_start: 0.9559 (mm) cc_final: 0.9120 (tp) REVERT: C 335 TYR cc_start: 0.8073 (m-10) cc_final: 0.7823 (m-80) REVERT: C 651 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8452 (pmm) REVERT: C 871 ASN cc_start: 0.9043 (t0) cc_final: 0.8820 (t0) outliers start: 48 outliers final: 27 residues processed: 248 average time/residue: 0.2064 time to fit residues: 85.8727 Evaluate side-chains 230 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain E residue 390 TYR Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain F residue 367 HIS Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 872 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 58 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 345 optimal weight: 20.0000 chunk 314 optimal weight: 0.9980 chunk 304 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 191 optimal weight: 0.0770 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 330 ASN E 383 HIS ** F 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.104839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.066782 restraints weight = 122228.785| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 4.64 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35511 Z= 0.115 Angle : 0.571 13.731 48266 Z= 0.294 Chirality : 0.041 0.196 5121 Planarity : 0.004 0.058 5996 Dihedral : 12.825 174.657 4970 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.82 % Favored : 92.90 % Rotamer: Outliers : 1.17 % Allowed : 13.96 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.38 (0.14), residues: 4044 helix: 0.96 (0.13), residues: 1800 sheet: -1.05 (0.26), residues: 409 loop : -1.29 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 513 TYR 0.055 0.001 TYR C 69 PHE 0.025 0.001 PHE C 38 TRP 0.025 0.001 TRP D 362 HIS 0.011 0.001 HIS E 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (35511) covalent geometry : angle 0.57082 / 0.29 (48266) hydrogen bonds : bond 0.03715 / 3.24 ( 1387) hydrogen bonds : angle 4.84541 / 4.02 ( 3957) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.6564 (mmm) cc_final: 0.6196 (mmm) REVERT: D 379 MET cc_start: 0.9068 (mpp) cc_final: 0.8862 (mpp) REVERT: D 631 MET cc_start: 0.8641 (tpt) cc_final: 0.8432 (tpt) REVERT: D 651 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8226 (pmm) REVERT: D 666 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9066 (mm) REVERT: E 336 ARG cc_start: 0.8137 (mmm160) cc_final: 0.7326 (mmm160) REVERT: E 362 TRP cc_start: 0.7945 (p-90) cc_final: 0.7334 (p-90) REVERT: E 481 MET cc_start: 0.9300 (mmm) cc_final: 0.9064 (mmm) REVERT: E 724 GLU cc_start: 0.8192 (mp0) cc_final: 0.7992 (mp0) REVERT: F 328 LEU cc_start: 0.9562 (mm) cc_final: 0.9141 (tp) REVERT: F 482 ASP cc_start: 0.8912 (m-30) cc_final: 0.8562 (m-30) REVERT: C 335 TYR cc_start: 0.8104 (m-10) cc_final: 0.7845 (m-80) REVERT: C 640 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8182 (m-40) REVERT: C 651 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8453 (pmm) REVERT: C 871 ASN cc_start: 0.9063 (t0) cc_final: 0.8779 (t0) outliers start: 43 outliers final: 28 residues processed: 245 average time/residue: 0.2011 time to fit residues: 83.3782 Evaluate side-chains 237 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain E residue 390 TYR Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain F residue 367 HIS Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 640 ASN Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 816 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 364 optimal weight: 4.9990 chunk 354 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 403 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 337 optimal weight: 3.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 727 GLN D 51 ASN ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 HIS ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.102430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.064122 restraints weight = 124213.958| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 4.54 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 35511 Z= 0.257 Angle : 0.650 12.712 48266 Z= 0.336 Chirality : 0.042 0.185 5121 Planarity : 0.004 0.058 5996 Dihedral : 12.621 177.790 4970 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.59 % Favored : 92.14 % Rotamer: Outliers : 1.44 % Allowed : 14.50 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.42 (0.14), residues: 4044 helix: 0.97 (0.13), residues: 1796 sheet: -1.17 (0.25), residues: 425 loop : -1.31 (0.15), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 752 TYR 0.048 0.001 TYR C 69 PHE 0.031 0.001 PHE D 342 TRP 0.024 0.002 TRP C 634 HIS 0.029 0.001 HIS E 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.26 (35511) covalent geometry : angle 0.64967 / 0.34 (48266) hydrogen bonds : bond 0.04180 / 3.67 ( 1387) hydrogen bonds : angle 5.02786 / 4.20 ( 3957) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 885 GLU cc_start: 0.8805 (tt0) cc_final: 0.7832 (tp30) REVERT: B 294 MET cc_start: 0.6562 (mmm) cc_final: 0.6159 (mmm) REVERT: D 19 LYS cc_start: 0.6418 (mttt) cc_final: 0.6206 (mmtp) REVERT: D 362 TRP cc_start: 0.9196 (t60) cc_final: 0.8945 (t60) REVERT: D 631 MET cc_start: 0.8624 (tpt) cc_final: 0.8366 (tpt) REVERT: D 651 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8293 (pmm) REVERT: E 336 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7260 (mmm160) REVERT: E 362 TRP cc_start: 0.7886 (p-90) cc_final: 0.7245 (p-90) REVERT: E 452 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8560 (ptp) REVERT: E 631 MET cc_start: 0.7941 (tmm) cc_final: 0.7636 (tmm) REVERT: F 317 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.5343 (pm20) REVERT: F 482 ASP cc_start: 0.9073 (m-30) cc_final: 0.8771 (m-30) REVERT: F 651 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8375 (ttm) REVERT: C 335 TYR cc_start: 0.8119 (m-10) cc_final: 0.7818 (m-80) REVERT: C 640 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8325 (m-40) REVERT: C 651 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8536 (pmm) REVERT: C 871 ASN cc_start: 0.9143 (t0) cc_final: 0.8836 (t0) outliers start: 53 outliers final: 30 residues processed: 244 average time/residue: 0.2052 time to fit residues: 84.9138 Evaluate side-chains 231 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 473 ILE Chi-restraints excluded: chain F residue 651 MET Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 640 ASN Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 876 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 304 optimal weight: 0.9980 chunk 378 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 252 optimal weight: 0.0980 chunk 219 optimal weight: 0.7980 chunk 281 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 377 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 279 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS E 491 HIS ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN C 218 HIS ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.105364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.066531 restraints weight = 125977.844| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 4.61 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35511 Z= 0.110 Angle : 0.587 14.377 48266 Z= 0.300 Chirality : 0.041 0.224 5121 Planarity : 0.004 0.060 5996 Dihedral : 12.427 175.964 4970 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.82 % Favored : 92.90 % Rotamer: Outliers : 1.36 % Allowed : 15.54 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 4044 helix: 1.01 (0.13), residues: 1797 sheet: -1.18 (0.26), residues: 419 loop : -1.26 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 76 TYR 0.044 0.001 TYR C 69 PHE 0.020 0.001 PHE F 342 TRP 0.024 0.001 TRP C 362 HIS 0.007 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (35511) covalent geometry : angle 0.58730 / 0.30 (48266) hydrogen bonds : bond 0.03704 / 3.24 ( 1387) hydrogen bonds : angle 4.76789 / 3.95 ( 3957) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.6580 (mmm) cc_final: 0.6213 (mmm) REVERT: B 379 MET cc_start: 0.9432 (mmm) cc_final: 0.9229 (mmm) REVERT: D 362 TRP cc_start: 0.9211 (t60) cc_final: 0.8951 (t60) REVERT: D 631 MET cc_start: 0.8749 (tpt) cc_final: 0.8406 (tpt) REVERT: D 651 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8217 (pmm) REVERT: D 666 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9019 (mm) REVERT: E 336 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7248 (mmm160) REVERT: E 362 TRP cc_start: 0.7982 (p-90) cc_final: 0.7312 (p-90) REVERT: E 481 MET cc_start: 0.9313 (mmm) cc_final: 0.9052 (mmm) REVERT: F 314 TYR cc_start: 0.7333 (p90) cc_final: 0.7107 (p90) REVERT: F 328 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9230 (tp) REVERT: F 482 ASP cc_start: 0.8992 (m-30) cc_final: 0.8711 (m-30) REVERT: C 335 TYR cc_start: 0.8158 (m-10) cc_final: 0.7923 (m-80) REVERT: C 452 MET cc_start: 0.8648 (ptp) cc_final: 0.8392 (ptm) REVERT: C 640 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8250 (m-40) REVERT: C 651 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8466 (pmm) REVERT: C 871 ASN cc_start: 0.9179 (t0) cc_final: 0.8817 (t0) outliers start: 50 outliers final: 31 residues processed: 260 average time/residue: 0.2064 time to fit residues: 91.2128 Evaluate side-chains 245 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain E residue 390 TYR Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 491 HIS Chi-restraints excluded: chain C residue 640 ASN Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 816 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 400 optimal weight: 2.9990 chunk 387 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 chunk 369 optimal weight: 0.9980 chunk 332 optimal weight: 4.9990 chunk 390 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 251 optimal weight: 0.1980 chunk 280 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN E 491 HIS ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.104151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065785 restraints weight = 123109.993| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.46 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35511 Z= 0.125 Angle : 0.586 14.337 48266 Z= 0.302 Chirality : 0.041 0.218 5121 Planarity : 0.004 0.059 5996 Dihedral : 12.337 176.069 4970 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.20 % Favored : 92.53 % Rotamer: Outliers : 1.09 % Allowed : 16.11 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.34 (0.14), residues: 4044 helix: 1.02 (0.13), residues: 1796 sheet: -1.17 (0.25), residues: 418 loop : -1.25 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 67 TYR 0.040 0.001 TYR C 69 PHE 0.036 0.001 PHE D 342 TRP 0.025 0.001 TRP C 362 HIS 0.026 0.001 HIS C 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (35511) covalent geometry : angle 0.58630 / 0.30 (48266) hydrogen bonds : bond 0.03645 / 3.17 ( 1387) hydrogen bonds : angle 4.75616 / 3.94 ( 3957) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.6661 (mmm) cc_final: 0.6275 (mmm) REVERT: B 379 MET cc_start: 0.9418 (mmm) cc_final: 0.9215 (mmm) REVERT: D 362 TRP cc_start: 0.9202 (t60) cc_final: 0.8938 (t60) REVERT: D 631 MET cc_start: 0.8723 (tpt) cc_final: 0.8399 (tpt) REVERT: D 666 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9069 (mm) REVERT: E 336 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7271 (mmm160) REVERT: E 362 TRP cc_start: 0.7959 (p-90) cc_final: 0.7280 (p-90) REVERT: E 481 MET cc_start: 0.9333 (mmm) cc_final: 0.9064 (mmm) REVERT: F 314 TYR cc_start: 0.7304 (p90) cc_final: 0.6890 (p90) REVERT: F 317 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.4863 (pm20) REVERT: F 328 LEU cc_start: 0.9629 (mm) cc_final: 0.9270 (tp) REVERT: F 482 ASP cc_start: 0.9055 (m-30) cc_final: 0.8760 (m-30) REVERT: C 335 TYR cc_start: 0.8142 (m-10) cc_final: 0.7897 (m-80) REVERT: C 452 MET cc_start: 0.8656 (ptp) cc_final: 0.8388 (ptm) REVERT: C 640 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8251 (m-40) REVERT: C 651 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8473 (pmm) REVERT: C 871 ASN cc_start: 0.9181 (t0) cc_final: 0.8890 (t0) outliers start: 40 outliers final: 30 residues processed: 242 average time/residue: 0.2055 time to fit residues: 84.6424 Evaluate side-chains 243 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 491 HIS Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 392 GLU Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 640 ASN Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 876 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 42 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS E 491 HIS ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.104396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.065792 restraints weight = 124106.758| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 4.66 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35511 Z= 0.113 Angle : 0.577 13.973 48266 Z= 0.296 Chirality : 0.040 0.196 5121 Planarity : 0.004 0.059 5996 Dihedral : 12.212 176.963 4970 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.05 % Favored : 92.68 % Rotamer: Outliers : 1.12 % Allowed : 16.11 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 4044 helix: 1.05 (0.13), residues: 1790 sheet: -1.12 (0.25), residues: 412 loop : -1.24 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 18 TYR 0.038 0.001 TYR C 69 PHE 0.022 0.001 PHE E 519 TRP 0.030 0.001 TRP C 362 HIS 0.007 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (35511) covalent geometry : angle 0.57727 / 0.30 (48266) hydrogen bonds : bond 0.03492 / 3.05 ( 1387) hydrogen bonds : angle 4.66481 / 3.87 ( 3957) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.6658 (mmm) cc_final: 0.6256 (mmm) REVERT: D 362 TRP cc_start: 0.9203 (t60) cc_final: 0.8907 (t60) REVERT: D 631 MET cc_start: 0.8769 (tpt) cc_final: 0.8376 (tpt) REVERT: D 666 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9012 (mm) REVERT: E 336 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7361 (mmm160) REVERT: E 362 TRP cc_start: 0.7961 (p-90) cc_final: 0.7272 (p-90) REVERT: E 379 MET cc_start: 0.9207 (mmm) cc_final: 0.8988 (mmm) REVERT: E 481 MET cc_start: 0.9306 (mmm) cc_final: 0.9051 (mmm) REVERT: F 314 TYR cc_start: 0.7321 (p90) cc_final: 0.6909 (p90) REVERT: F 317 GLU cc_start: 0.5767 (OUTLIER) cc_final: 0.4906 (pm20) REVERT: F 328 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9303 (tp) REVERT: F 417 MET cc_start: 0.8008 (mtt) cc_final: 0.7695 (mtm) REVERT: F 482 ASP cc_start: 0.9054 (m-30) cc_final: 0.8751 (m-30) REVERT: F 693 GLU cc_start: 0.7868 (pm20) cc_final: 0.7287 (pm20) REVERT: C 335 TYR cc_start: 0.8121 (m-10) cc_final: 0.7871 (m-80) REVERT: C 452 MET cc_start: 0.8663 (ptp) cc_final: 0.8386 (ptm) REVERT: C 640 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8248 (m-40) REVERT: C 651 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8469 (pmm) REVERT: C 871 ASN cc_start: 0.9178 (t0) cc_final: 0.8880 (t0) outliers start: 41 outliers final: 32 residues processed: 245 average time/residue: 0.2018 time to fit residues: 84.2755 Evaluate side-chains 244 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 491 HIS Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain E residue 390 TYR Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 392 GLU Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 822 GLU Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 640 ASN Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 816 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 368 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 148 optimal weight: 0.0050 chunk 94 optimal weight: 5.9990 chunk 402 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 307 optimal weight: 6.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 51 ASN D 875 HIS E 491 HIS ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.104891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.067235 restraints weight = 123658.359| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.50 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 35511 Z= 0.106 Angle : 0.579 14.225 48266 Z= 0.294 Chirality : 0.040 0.215 5121 Planarity : 0.004 0.059 5996 Dihedral : 12.124 177.454 4970 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.90 % Favored : 92.83 % Rotamer: Outliers : 1.01 % Allowed : 16.44 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.28 (0.14), residues: 4044 helix: 1.08 (0.13), residues: 1776 sheet: -1.10 (0.25), residues: 412 loop : -1.22 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 513 TYR 0.037 0.001 TYR C 69 PHE 0.043 0.001 PHE D 342 TRP 0.031 0.001 TRP C 362 HIS 0.007 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (35511) covalent geometry : angle 0.57945 / 0.29 (48266) hydrogen bonds : bond 0.03385 / 2.97 ( 1387) hydrogen bonds : angle 4.62174 / 3.83 ( 3957) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8088 Ramachandran restraints generated. 4044 Oldfield, 0 Emsley, 4044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.6597 (mmm) cc_final: 0.6229 (mmm) REVERT: D 362 TRP cc_start: 0.9204 (t60) cc_final: 0.8926 (t60) REVERT: D 631 MET cc_start: 0.8738 (tpt) cc_final: 0.8207 (tpt) REVERT: D 666 LEU cc_start: 0.9399 (mm) cc_final: 0.9083 (mm) REVERT: E 336 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7296 (mmm160) REVERT: E 362 TRP cc_start: 0.7980 (p-90) cc_final: 0.7314 (p-90) REVERT: E 379 MET cc_start: 0.9200 (mmm) cc_final: 0.8973 (mmm) REVERT: E 481 MET cc_start: 0.9324 (mmm) cc_final: 0.9073 (mmm) REVERT: F 314 TYR cc_start: 0.7329 (p90) cc_final: 0.6916 (p90) REVERT: F 317 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.4938 (pm20) REVERT: F 328 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9309 (tp) REVERT: F 417 MET cc_start: 0.8078 (mtt) cc_final: 0.7768 (mtm) REVERT: F 482 ASP cc_start: 0.9079 (m-30) cc_final: 0.8765 (m-30) REVERT: F 693 GLU cc_start: 0.7838 (pm20) cc_final: 0.7252 (pm20) REVERT: C 452 MET cc_start: 0.8629 (ptp) cc_final: 0.8353 (ptm) REVERT: C 640 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8260 (m-40) REVERT: C 651 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8450 (pmm) REVERT: C 871 ASN cc_start: 0.9164 (t0) cc_final: 0.8885 (t0) outliers start: 37 outliers final: 28 residues processed: 247 average time/residue: 0.2104 time to fit residues: 87.5252 Evaluate side-chains 242 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 491 HIS Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain E residue 390 TYR Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 633 LEU Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 392 GLU Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 822 GLU Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 640 ASN Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 816 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 16 optimal weight: 2.9990 chunk 399 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 191 optimal weight: 6.9990 chunk 49 optimal weight: 0.0570 chunk 257 optimal weight: 5.9990 chunk 361 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 306 optimal weight: 1.9990 chunk 1 optimal weight: 40.0000 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 875 HIS ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.104016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.066277 restraints weight = 124696.804| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 4.62 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35511 Z= 0.139 Angle : 0.598 13.451 48266 Z= 0.303 Chirality : 0.041 0.199 5121 Planarity : 0.004 0.059 5996 Dihedral : 12.095 178.865 4970 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.27 % Favored : 92.46 % Rotamer: Outliers : 0.98 % Allowed : 16.68 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.26 (0.14), residues: 4044 helix: 1.10 (0.13), residues: 1789 sheet: -1.08 (0.25), residues: 417 loop : -1.23 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 483 TYR 0.035 0.001 TYR C 69 PHE 0.034 0.001 PHE C 38 TRP 0.030 0.001 TRP C 362 HIS 0.006 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (35511) covalent geometry : angle 0.59761 / 0.30 (48266) hydrogen bonds : bond 0.03499 / 3.08 ( 1387) hydrogen bonds : angle 4.64689 / 3.86 ( 3957) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7787.66 seconds wall clock time: 135 minutes 28.62 seconds (8128.62 seconds total)