Starting phenix.real_space_refine on Sun Jun 29 18:06:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwa_37886/06_2025/8wwa_37886.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwa_37886/06_2025/8wwa_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_37886/06_2025/8wwa_37886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwa_37886/06_2025/8wwa_37886.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwa_37886/06_2025/8wwa_37886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwa_37886/06_2025/8wwa_37886.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.01, per 1000 atoms: 0.58 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: 9.04 Conformation dependent library (CDL) restraints added in 4.8 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: 4.35 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: 12.82 Time building geometry restraints manager: 10.56 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: 4362 0.056 - 0.113: 699 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 896 or resid 1001 thr \ ough 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: 6.710 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: 1.370 Check model and map are aligned: 0.250 Set scattering table: 0.280 Process input model: 76.860 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.160 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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= 0.194 Angle : 0.707 18.169 48266 Z= 0.352 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 : 12.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (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 TRP 0.048 0.002 TRP D 634 HIS 0.010 0.001 HIS A 572 PHE 0.012 0.001 PHE C 817 TYR 0.027 0.001 TYR F 314 ARG 0.008 0.000 ARG E 829 Details of bonding type rmsd hydrogen bonds : bond 0.18422 ( 1387) hydrogen bonds : angle 6.88229 ( 3957) covalent geometry : bond 0.00382 (35511) covalent geometry : angle 0.70676 (48266) *********************** 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 : 3.946 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: 0.8603 (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: C 379 MET cc_start: 0.9229 (mpp) cc_final: 0.8644 (mpp) outliers start: 28 outliers final: 4 residues processed: 294 average time/residue: 0.4681 time to fit residues: 229.5685 Evaluate side-chains 208 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 204 time to evaluate : 3.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 ASN Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain D residue 671 GLU 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 344 optimal weight: 7.9990 chunk 309 optimal weight: 0.8980 chunk 171 optimal weight: 0.0870 chunk 105 optimal weight: 9.9990 chunk 208 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 319 optimal weight: 10.0000 chunk 123 optimal weight: 30.0000 chunk 194 optimal weight: 0.6980 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS A 494 GLN ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 ASN A 871 ASN B 491 HIS D 25 GLN D 260 ASN D 304 HIS D 308 ASN E 296 HIS E 330 ASN E 383 HIS E 867 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.105229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067295 restraints weight = 120878.530| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.47 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1060 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= 0.135 Angle : 0.614 10.148 48266 Z= 0.317 Chirality : 0.041 0.153 5121 Planarity : 0.004 0.055 5996 Dihedral : 14.066 176.556 4979 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.95 % Favored : 92.75 % Rotamer: Outliers : 0.76 % Allowed : 7.40 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 4044 helix: 0.88 (0.12), residues: 1792 sheet: -0.93 (0.26), residues: 411 loop : -1.28 (0.15), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 362 HIS 0.009 0.001 HIS E 383 PHE 0.039 0.001 PHE A 326 TYR 0.021 0.001 TYR C 69 ARG 0.008 0.000 ARG E 829 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 1387) hydrogen bonds : angle 5.38571 ( 3957) covalent geometry : bond 0.00288 (35511) covalent geometry : angle 0.61369 (48266) *********************** 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 266 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 885 GLU cc_start: 0.8674 (tt0) cc_final: 0.7611 (tp30) REVERT: B 294 MET cc_start: 0.6168 (mmm) cc_final: 0.5694 (mmm) REVERT: D 379 MET cc_start: 0.8880 (mpp) cc_final: 0.8472 (mpp) REVERT: D 732 MET cc_start: 0.8236 (mmm) cc_final: 0.7991 (mmm) REVERT: E 362 TRP cc_start: 0.7833 (p-90) cc_final: 0.7222 (p-90) REVERT: E 692 GLU cc_start: 0.8685 (pt0) cc_final: 0.8422 (pm20) REVERT: E 724 GLU cc_start: 0.8278 (mp0) cc_final: 0.7873 (mp0) REVERT: E 834 THR cc_start: 0.8635 (p) cc_final: 0.8278 (p) REVERT: E 864 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: F 328 LEU cc_start: 0.9604 (mm) cc_final: 0.9147 (tp) REVERT: F 375 LYS cc_start: 0.8917 (tmtt) cc_final: 0.8716 (tptt) REVERT: F 482 ASP cc_start: 0.8940 (m-30) cc_final: 0.8658 (m-30) REVERT: C 18 ARG cc_start: 0.8450 (ttm110) cc_final: 0.8097 (ptp-170) REVERT: C 452 MET cc_start: 0.8692 (ptp) cc_final: 0.8479 (ptm) REVERT: C 651 MET cc_start: 0.8816 (pmm) cc_final: 0.8453 (pmm) REVERT: C 864 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8954 (pm20) outliers start: 28 outliers final: 16 residues processed: 257 average time/residue: 0.4559 time to fit residues: 194.9289 Evaluate side-chains 227 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 3.854 ------------------------------------------------------------------------------- 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 310 LEU Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain D residue 671 GLU 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 367 HIS Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 310 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 20.0000 chunk 146 optimal weight: 0.0570 chunk 295 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 290 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 GLN B 367 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 640 ASN ** 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** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.104933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.066672 restraints weight = 122436.335| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.58 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35511 Z= 0.126 Angle : 0.576 14.762 48266 Z= 0.297 Chirality : 0.040 0.152 5121 Planarity : 0.004 0.055 5996 Dihedral : 13.411 179.221 4977 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.90 % Favored : 92.83 % Rotamer: Outliers : 1.06 % Allowed : 10.88 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 4044 helix: 0.93 (0.12), residues: 1803 sheet: -1.00 (0.26), residues: 419 loop : -1.25 (0.15), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 634 HIS 0.008 0.001 HIS E 383 PHE 0.013 0.001 PHE A 342 TYR 0.040 0.001 TYR C 69 ARG 0.003 0.000 ARG F 301 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 1387) hydrogen bonds : angle 5.04089 ( 3957) covalent geometry : bond 0.00272 (35511) covalent geometry : angle 0.57601 (48266) *********************** 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 262 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 3.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 885 GLU cc_start: 0.8708 (tt0) cc_final: 0.7698 (tp30) REVERT: B 294 MET cc_start: 0.6325 (mmm) cc_final: 0.5912 (mmm) REVERT: B 708 MET cc_start: 0.9091 (mtm) cc_final: 0.8862 (mtm) REVERT: D 651 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8239 (pmm) REVERT: E 335 TYR cc_start: 0.7823 (m-10) cc_final: 0.7615 (m-80) REVERT: E 336 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7292 (mmm160) REVERT: E 362 TRP cc_start: 0.7889 (p-90) cc_final: 0.7263 (p-90) REVERT: E 452 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8417 (ptp) REVERT: E 732 MET cc_start: 0.8764 (mtm) cc_final: 0.8539 (mtt) REVERT: E 864 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: F 328 LEU cc_start: 0.9599 (mm) cc_final: 0.9162 (tp) REVERT: F 482 ASP cc_start: 0.9049 (m-30) cc_final: 0.8737 (m-30) REVERT: C 335 TYR cc_start: 0.8191 (m-10) cc_final: 0.7963 (m-80) REVERT: C 651 MET cc_start: 0.8828 (pmm) cc_final: 0.8453 (pmm) REVERT: C 871 ASN cc_start: 0.8989 (t0) cc_final: 0.8789 (t0) outliers start: 39 outliers final: 25 residues processed: 251 average time/residue: 0.4498 time to fit residues: 188.9941 Evaluate side-chains 231 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 3.776 ------------------------------------------------------------------------------- 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 488 ILE Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain D residue 671 GLU Chi-restraints excluded: chain E residue 383 HIS 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 E residue 864 GLU 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 864 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 216 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 122 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 366 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 277 optimal weight: 0.0040 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN ** A 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 HIS D 308 ASN E 383 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.105675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.067481 restraints weight = 123561.387| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 4.52 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 35511 Z= 0.108 Angle : 0.564 12.702 48266 Z= 0.287 Chirality : 0.040 0.150 5121 Planarity : 0.004 0.058 5996 Dihedral : 12.827 174.937 4977 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.63 % Favored : 93.10 % Rotamer: Outliers : 1.22 % Allowed : 12.90 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 4044 helix: 1.03 (0.13), residues: 1788 sheet: -1.02 (0.26), residues: 417 loop : -1.25 (0.15), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 362 HIS 0.007 0.001 HIS A 572 PHE 0.010 0.001 PHE E 519 TYR 0.042 0.001 TYR C 69 ARG 0.007 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 1387) hydrogen bonds : angle 4.79570 ( 3957) covalent geometry : bond 0.00223 (35511) covalent geometry : angle 0.56389 (48266) *********************** 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 272 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 3.537 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: A 885 GLU cc_start: 0.8732 (tt0) cc_final: 0.7740 (tp30) REVERT: B 294 MET cc_start: 0.6670 (mmm) cc_final: 0.6231 (mmm) REVERT: D 379 MET cc_start: 0.9109 (mpp) cc_final: 0.8864 (mpp) REVERT: D 631 MET cc_start: 0.8562 (tpt) cc_final: 0.8307 (tpt) REVERT: D 666 LEU cc_start: 0.9371 (mm) cc_final: 0.9049 (mm) REVERT: E 336 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7373 (mmm160) REVERT: E 362 TRP cc_start: 0.7920 (p-90) cc_final: 0.7289 (p-90) REVERT: E 692 GLU cc_start: 0.8756 (pt0) cc_final: 0.8288 (pm20) REVERT: E 732 MET cc_start: 0.8728 (mtm) cc_final: 0.8460 (mtt) REVERT: E 864 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: F 328 LEU cc_start: 0.9574 (mm) cc_final: 0.9175 (tp) REVERT: F 482 ASP cc_start: 0.9017 (m-30) cc_final: 0.8688 (m-30) REVERT: C 640 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8209 (m-40) REVERT: C 651 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8391 (pmm) REVERT: C 871 ASN cc_start: 0.9053 (t0) cc_final: 0.8820 (t0) outliers start: 45 outliers final: 24 residues processed: 259 average time/residue: 0.4787 time to fit residues: 205.8840 Evaluate side-chains 235 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 3.957 ------------------------------------------------------------------------------- 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 417 MET Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain D residue 671 GLU 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 743 ASP 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 661 LEU Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain C residue 254 SER 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 864 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 333 optimal weight: 5.9990 chunk 302 optimal weight: 2.9990 chunk 315 optimal weight: 0.8980 chunk 334 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 294 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 HIS F 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.102972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.064373 restraints weight = 125058.887| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.56 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 35511 Z= 0.215 Angle : 0.618 12.153 48266 Z= 0.320 Chirality : 0.041 0.150 5121 Planarity : 0.004 0.058 5996 Dihedral : 12.444 178.032 4977 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.49 % Favored : 92.24 % Rotamer: Outliers : 1.20 % Allowed : 14.37 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 4044 helix: 1.01 (0.13), residues: 1795 sheet: -1.17 (0.26), residues: 418 loop : -1.23 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 362 HIS 0.007 0.001 HIS A 572 PHE 0.027 0.001 PHE D 342 TYR 0.037 0.001 TYR C 69 ARG 0.008 0.000 ARG B 483 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 1387) hydrogen bonds : angle 4.96321 ( 3957) covalent geometry : bond 0.00481 (35511) covalent geometry : angle 0.61801 (48266) *********************** 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 254 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 GLU cc_start: 0.8450 (mp0) cc_final: 0.8110 (mp0) REVERT: A 885 GLU cc_start: 0.8801 (tt0) cc_final: 0.7800 (tp30) REVERT: B 294 MET cc_start: 0.6626 (mmm) cc_final: 0.6244 (mmm) REVERT: D 631 MET cc_start: 0.8622 (tpt) cc_final: 0.8285 (tpt) REVERT: D 666 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9087 (mm) REVERT: E 336 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7392 (mmm160) REVERT: E 362 TRP cc_start: 0.7896 (p-90) cc_final: 0.7223 (p-90) REVERT: E 452 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8507 (ptp) REVERT: E 481 MET cc_start: 0.9387 (mmm) cc_final: 0.9110 (mmm) REVERT: E 631 MET cc_start: 0.7924 (tmm) cc_final: 0.7598 (tmm) REVERT: E 692 GLU cc_start: 0.8808 (pt0) cc_final: 0.8330 (pm20) REVERT: F 482 ASP cc_start: 0.9094 (m-30) cc_final: 0.8837 (m-30) REVERT: F 651 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8378 (ttm) REVERT: C 651 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8500 (pmm) REVERT: C 871 ASN cc_start: 0.9123 (t0) cc_final: 0.8791 (t0) outliers start: 44 outliers final: 27 residues processed: 244 average time/residue: 0.4339 time to fit residues: 177.2786 Evaluate side-chains 228 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 3.719 ------------------------------------------------------------------------------- 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 488 ILE Chi-restraints excluded: chain D residue 601 LEU 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 367 HIS 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 254 SER 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 816 VAL Chi-restraints excluded: chain C residue 864 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 81 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 378 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 400 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 875 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.102413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.064443 restraints weight = 121864.336| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.54 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 35511 Z= 0.207 Angle : 0.610 12.496 48266 Z= 0.316 Chirality : 0.041 0.159 5121 Planarity : 0.004 0.058 5996 Dihedral : 12.217 179.337 4971 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.15 % Favored : 92.56 % Rotamer: Outliers : 1.66 % Allowed : 14.94 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 4044 helix: 0.98 (0.12), residues: 1796 sheet: -1.19 (0.26), residues: 413 loop : -1.26 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 362 HIS 0.007 0.001 HIS A 572 PHE 0.024 0.001 PHE C 38 TYR 0.033 0.001 TYR C 69 ARG 0.006 0.000 ARG B 483 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 1387) hydrogen bonds : angle 4.93560 ( 3957) covalent geometry : bond 0.00464 (35511) covalent geometry : angle 0.60956 (48266) *********************** 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 266 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 205 time to evaluate : 4.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 885 GLU cc_start: 0.8813 (tt0) cc_final: 0.7847 (tp30) REVERT: B 294 MET cc_start: 0.6571 (mmm) cc_final: 0.6158 (mmm) REVERT: D 631 MET cc_start: 0.8595 (tpt) cc_final: 0.7920 (tpt) REVERT: D 666 LEU cc_start: 0.9421 (mm) cc_final: 0.9123 (mm) REVERT: E 336 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7344 (mmm160) REVERT: E 362 TRP cc_start: 0.7968 (p-90) cc_final: 0.7317 (p-90) REVERT: E 481 MET cc_start: 0.9378 (mmm) cc_final: 0.9079 (mmm) REVERT: E 631 MET cc_start: 0.7920 (tmm) cc_final: 0.7646 (tmm) REVERT: E 692 GLU cc_start: 0.8825 (pt0) cc_final: 0.8322 (pm20) REVERT: F 314 TYR cc_start: 0.7469 (p90) cc_final: 0.7115 (p90) REVERT: F 317 GLU cc_start: 0.5816 (OUTLIER) cc_final: 0.5397 (pm20) REVERT: F 328 LEU cc_start: 0.9598 (mm) cc_final: 0.9263 (tp) REVERT: F 482 ASP cc_start: 0.9093 (m-30) cc_final: 0.8834 (m-30) REVERT: F 693 GLU cc_start: 0.7853 (pm20) cc_final: 0.7526 (pm20) REVERT: C 640 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8320 (m-40) REVERT: C 651 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8546 (pmm) REVERT: C 674 GLU cc_start: 0.7126 (tp30) cc_final: 0.6919 (tp30) REVERT: C 786 MET cc_start: 0.9226 (mpp) cc_final: 0.8597 (mpp) REVERT: C 871 ASN cc_start: 0.9168 (t0) cc_final: 0.8896 (t0) outliers start: 61 outliers final: 36 residues processed: 258 average time/residue: 0.4623 time to fit residues: 201.1542 Evaluate side-chains 239 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 3.914 ------------------------------------------------------------------------------- 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 182 THR 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 669 CYS 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 302 TYR Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 464 VAL 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 254 SER 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 743 ASP Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 864 GLU 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 276 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 274 optimal weight: 0.9980 chunk 190 optimal weight: 9.9990 chunk 284 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 389 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 253 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 C 530 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.103837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.065811 restraints weight = 122024.303| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 4.54 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35511 Z= 0.120 Angle : 0.575 13.510 48266 Z= 0.295 Chirality : 0.040 0.160 5121 Planarity : 0.004 0.059 5996 Dihedral : 12.058 179.972 4971 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.07 % Favored : 92.63 % Rotamer: Outliers : 1.50 % Allowed : 15.78 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 4044 helix: 1.07 (0.13), residues: 1786 sheet: -1.24 (0.25), residues: 430 loop : -1.22 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 362 HIS 0.006 0.001 HIS A 572 PHE 0.034 0.001 PHE D 342 TYR 0.030 0.001 TYR C 69 ARG 0.005 0.000 ARG B 483 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 1387) hydrogen bonds : angle 4.73183 ( 3957) covalent geometry : bond 0.00263 (35511) covalent geometry : angle 0.57504 (48266) *********************** 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 273 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 3.876 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: A 885 GLU cc_start: 0.8780 (tt0) cc_final: 0.7779 (tp30) REVERT: B 294 MET cc_start: 0.6674 (mmm) cc_final: 0.6273 (mmm) REVERT: D 631 MET cc_start: 0.8641 (tpt) cc_final: 0.8092 (tpt) REVERT: D 666 LEU cc_start: 0.9259 (mm) cc_final: 0.9035 (mm) REVERT: E 336 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7366 (mmm160) REVERT: E 362 TRP cc_start: 0.7998 (p-90) cc_final: 0.7285 (p-90) REVERT: E 481 MET cc_start: 0.9349 (mmm) cc_final: 0.9034 (mmm) REVERT: E 692 GLU cc_start: 0.8734 (pt0) cc_final: 0.8228 (pm20) REVERT: F 314 TYR cc_start: 0.7336 (p90) cc_final: 0.6946 (p90) REVERT: F 317 GLU cc_start: 0.5746 (OUTLIER) cc_final: 0.4886 (pm20) REVERT: F 328 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9236 (tp) REVERT: F 417 MET cc_start: 0.8214 (mtt) cc_final: 0.7968 (mtm) REVERT: F 482 ASP cc_start: 0.9077 (m-30) cc_final: 0.8812 (m-30) REVERT: F 693 GLU cc_start: 0.7801 (pm20) cc_final: 0.7523 (pm20) REVERT: C 640 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8170 (m-40) REVERT: C 651 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8489 (pmm) REVERT: C 871 ASN cc_start: 0.9181 (t0) cc_final: 0.8891 (t0) outliers start: 55 outliers final: 39 residues processed: 264 average time/residue: 0.4411 time to fit residues: 195.3740 Evaluate side-chains 245 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 3.813 ------------------------------------------------------------------------------- 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 557 VAL Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain D residue 182 THR 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 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 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 302 TYR 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 464 VAL 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 254 SER 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 Chi-restraints excluded: chain C residue 864 GLU Chi-restraints excluded: chain C residue 876 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 292 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 365 optimal weight: 0.7980 chunk 338 optimal weight: 30.0000 chunk 226 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 321 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.103915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.065698 restraints weight = 121002.786| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 4.52 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35511 Z= 0.133 Angle : 0.588 20.862 48266 Z= 0.299 Chirality : 0.040 0.173 5121 Planarity : 0.004 0.058 5996 Dihedral : 11.969 179.703 4970 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.17 % Favored : 92.56 % Rotamer: Outliers : 1.41 % Allowed : 16.22 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 4044 helix: 1.09 (0.13), residues: 1787 sheet: -1.23 (0.25), residues: 429 loop : -1.22 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 362 HIS 0.020 0.001 HIS C 491 PHE 0.012 0.001 PHE C 38 TYR 0.028 0.001 TYR C 69 ARG 0.005 0.000 ARG B 513 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 1387) hydrogen bonds : angle 4.69377 ( 3957) covalent geometry : bond 0.00296 (35511) covalent geometry : angle 0.58841 (48266) *********************** 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 266 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 3.772 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: A 885 GLU cc_start: 0.8790 (tt0) cc_final: 0.7768 (tp30) REVERT: B 294 MET cc_start: 0.6652 (mmm) cc_final: 0.6263 (mmm) REVERT: D 631 MET cc_start: 0.8683 (tpt) cc_final: 0.8131 (tpt) REVERT: D 666 LEU cc_start: 0.9403 (mm) cc_final: 0.9088 (mm) REVERT: E 336 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7331 (mmm160) REVERT: E 362 TRP cc_start: 0.7962 (p-90) cc_final: 0.7257 (p-90) REVERT: E 481 MET cc_start: 0.9334 (mmm) cc_final: 0.9037 (mmm) REVERT: F 314 TYR cc_start: 0.7466 (p90) cc_final: 0.7108 (p90) REVERT: F 317 GLU cc_start: 0.5792 (OUTLIER) cc_final: 0.4926 (pm20) REVERT: F 328 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9319 (tp) REVERT: F 482 ASP cc_start: 0.9040 (m-30) cc_final: 0.8766 (m-30) REVERT: C 258 LEU cc_start: 0.2463 (OUTLIER) cc_final: 0.1803 (pp) REVERT: C 491 HIS cc_start: 0.9308 (OUTLIER) cc_final: 0.8679 (t-90) REVERT: C 640 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8307 (m-40) REVERT: C 651 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8493 (pmm) REVERT: C 871 ASN cc_start: 0.9152 (t0) cc_final: 0.8890 (t0) outliers start: 52 outliers final: 39 residues processed: 255 average time/residue: 0.4441 time to fit residues: 189.5533 Evaluate side-chains 252 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 4.151 ------------------------------------------------------------------------------- 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 367 HIS Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain D residue 182 THR 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 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 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 302 TYR Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 464 VAL 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 254 SER Chi-restraints excluded: chain C residue 258 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 417 MET Chi-restraints excluded: chain C residue 491 HIS 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 876 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 327 optimal weight: 5.9990 chunk 110 optimal weight: 0.0570 chunk 338 optimal weight: 30.0000 chunk 199 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 405 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 792 ASN ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 HIS F 389 GLN 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** C 491 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.102563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064995 restraints weight = 122911.171| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.57 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 35511 Z= 0.236 Angle : 0.654 19.615 48266 Z= 0.335 Chirality : 0.042 0.182 5121 Planarity : 0.004 0.057 5996 Dihedral : 11.988 175.139 4970 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.76 % Favored : 91.94 % Rotamer: Outliers : 1.36 % Allowed : 16.73 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 4044 helix: 1.00 (0.13), residues: 1791 sheet: -1.26 (0.25), residues: 421 loop : -1.27 (0.15), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 362 HIS 0.007 0.001 HIS D 487 PHE 0.039 0.001 PHE D 342 TYR 0.027 0.001 TYR C 69 ARG 0.006 0.000 ARG B 483 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 1387) hydrogen bonds : angle 4.94779 ( 3957) covalent geometry : bond 0.00529 (35511) covalent geometry : angle 0.65374 (48266) *********************** 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 254 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 3.959 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: 0.8869 (tt0) cc_final: 0.7966 (tp30) REVERT: B 513 ARG cc_start: 0.9019 (tpt90) cc_final: 0.8718 (tpp80) REVERT: D 631 MET cc_start: 0.8460 (tpt) cc_final: 0.8072 (tpt) REVERT: E 362 TRP cc_start: 0.8011 (p-90) cc_final: 0.7295 (p-90) REVERT: E 481 MET cc_start: 0.9396 (mmm) cc_final: 0.9082 (mmm) REVERT: E 631 MET cc_start: 0.7882 (tmm) cc_final: 0.7570 (tmm) REVERT: E 732 MET cc_start: 0.9207 (mtm) cc_final: 0.8813 (mtm) REVERT: F 317 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.5476 (pm20) REVERT: F 328 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9307 (tp) REVERT: F 417 MET cc_start: 0.8696 (mtt) cc_final: 0.8301 (mtm) REVERT: F 482 ASP cc_start: 0.9252 (m-30) cc_final: 0.8987 (m-30) REVERT: C 95 MET cc_start: 0.8458 (tmm) cc_final: 0.6911 (mmt) REVERT: C 651 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8564 (pmm) REVERT: C 871 ASN cc_start: 0.9130 (t0) cc_final: 0.8908 (t0) outliers start: 50 outliers final: 38 residues processed: 243 average time/residue: 0.4563 time to fit residues: 189.2743 Evaluate side-chains 237 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain D residue 182 THR 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 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 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 302 TYR Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 464 VAL 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 C residue 21 LEU Chi-restraints excluded: chain C residue 254 SER 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 417 MET Chi-restraints excluded: chain C residue 491 HIS Chi-restraints excluded: chain C residue 630 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 15 optimal weight: 0.7980 chunk 296 optimal weight: 2.9990 chunk 351 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 chunk 341 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 284 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** C 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.103707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.065293 restraints weight = 122049.836| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.56 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2321 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= 0.119 Angle : 0.615 19.382 48266 Z= 0.310 Chirality : 0.041 0.189 5121 Planarity : 0.004 0.059 5996 Dihedral : 11.897 177.775 4970 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.02 % Favored : 92.71 % Rotamer: Outliers : 1.28 % Allowed : 16.98 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 4044 helix: 1.02 (0.12), residues: 1784 sheet: -1.23 (0.25), residues: 419 loop : -1.23 (0.15), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 362 HIS 0.017 0.001 HIS F 491 PHE 0.046 0.001 PHE C 38 TYR 0.028 0.001 TYR E 315 ARG 0.004 0.000 ARG B 483 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1387) hydrogen bonds : angle 4.71002 ( 3957) covalent geometry : bond 0.00258 (35511) covalent geometry : angle 0.61518 (48266) ********************** 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 263 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 3.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 885 GLU cc_start: 0.8825 (tt0) cc_final: 0.7871 (tp30) REVERT: B 379 MET cc_start: 0.9403 (mmm) cc_final: 0.9195 (mmm) REVERT: B 513 ARG cc_start: 0.8962 (tpt90) cc_final: 0.8621 (tpp80) REVERT: D 631 MET cc_start: 0.8682 (tpt) cc_final: 0.8189 (tpt) REVERT: E 362 TRP cc_start: 0.8004 (p-90) cc_final: 0.7299 (p-90) REVERT: E 481 MET cc_start: 0.9349 (mmm) cc_final: 0.9041 (mmm) REVERT: F 314 TYR cc_start: 0.7432 (p90) cc_final: 0.7142 (p90) REVERT: F 317 GLU cc_start: 0.5833 (OUTLIER) cc_final: 0.4979 (pm20) REVERT: F 328 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9356 (tp) REVERT: F 417 MET cc_start: 0.8169 (mtt) cc_final: 0.7833 (mtm) REVERT: F 482 ASP cc_start: 0.9097 (m-30) cc_final: 0.8823 (m-30) REVERT: F 491 HIS cc_start: 0.9100 (OUTLIER) cc_final: 0.8520 (t-90) REVERT: C 95 MET cc_start: 0.7812 (tmm) cc_final: 0.6862 (mmt) REVERT: C 640 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8224 (m-40) REVERT: C 651 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8484 (pmm) REVERT: C 871 ASN cc_start: 0.9175 (t0) cc_final: 0.8882 (t0) outliers start: 47 outliers final: 36 residues processed: 253 average time/residue: 0.4264 time to fit residues: 180.8284 Evaluate side-chains 248 residues out of total 3706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 3.796 ------------------------------------------------------------------------------- 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 367 HIS Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain D residue 182 THR 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 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 750 TRP Chi-restraints excluded: chain E residue 780 PHE Chi-restraints excluded: chain F residue 302 TYR Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 464 VAL 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 822 GLU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 254 SER 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 417 MET 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 876 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 336 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 356 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 370 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 355 optimal weight: 0.0020 chunk 353 optimal weight: 0.9980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 491 HIS 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** C 491 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.104409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.067789 restraints weight = 123573.107| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 4.45 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 35511 Z= 0.112 Angle : 0.605 19.018 48266 Z= 0.304 Chirality : 0.040 0.171 5121 Planarity : 0.004 0.062 5996 Dihedral : 11.802 179.897 4970 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.17 % Favored : 92.56 % Rotamer: Outliers : 1.31 % Allowed : 17.06 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 4044 helix: 1.08 (0.13), residues: 1782 sheet: -1.09 (0.25), residues: 439 loop : -1.19 (0.15), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 362 HIS 0.007 0.001 HIS F 491 PHE 0.042 0.001 PHE D 342 TYR 0.027 0.001 TYR C 69 ARG 0.014 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 1387) hydrogen bonds : angle 4.60775 ( 3957) covalent geometry : bond 0.00244 (35511) covalent geometry : angle 0.60461 (48266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15885.30 seconds wall clock time: 273 minutes 48.63 seconds (16428.63 seconds total)