Starting phenix.real_space_refine on Sun May 25 00:27:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8slw_40581/05_2025/8slw_40581.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slw_40581/05_2025/8slw_40581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8slw_40581/05_2025/8slw_40581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slw_40581/05_2025/8slw_40581.map" model { file = "/net/cci-nas-00/data/ceres_data/8slw_40581/05_2025/8slw_40581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slw_40581/05_2025/8slw_40581.cif" } resolution = 4.2 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= 0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 84 5.16 5 C 16756 2.51 5 N 4596 2.21 5 O 4520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25964 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 6489 Classifications: {'peptide': 921} Incomplete info: {'truncation_to_alanine': 268} Link IDs: {'PTRANS': 36, 'TRANS': 884} Chain breaks: 12 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1015 Unresolved non-hydrogen angles: 1285 Unresolved non-hydrogen dihedrals: 834 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 27, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 3, 'HIS:plan': 8, 'PHE:plan': 17, 'GLU:plan': 35, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 589 Chain: "B" Number of atoms: 6489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 6489 Classifications: {'peptide': 921} Incomplete info: {'truncation_to_alanine': 268} Link IDs: {'PTRANS': 36, 'TRANS': 884} Chain breaks: 12 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1015 Unresolved non-hydrogen angles: 1285 Unresolved non-hydrogen dihedrals: 834 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 27, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 3, 'HIS:plan': 8, 'PHE:plan': 17, 'GLU:plan': 35, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 589 Chain: "C" Number of atoms: 6489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 6489 Classifications: {'peptide': 921} Incomplete info: {'truncation_to_alanine': 268} Link IDs: {'PTRANS': 36, 'TRANS': 884} Chain breaks: 12 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1015 Unresolved non-hydrogen angles: 1285 Unresolved non-hydrogen dihedrals: 834 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 27, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 3, 'HIS:plan': 8, 'PHE:plan': 17, 'GLU:plan': 35, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 589 Chain: "D" Number of atoms: 6489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 6489 Classifications: {'peptide': 921} Incomplete info: {'truncation_to_alanine': 268} Link IDs: {'PTRANS': 36, 'TRANS': 884} Chain breaks: 12 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1015 Unresolved non-hydrogen angles: 1285 Unresolved non-hydrogen dihedrals: 834 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 27, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 3, 'HIS:plan': 8, 'PHE:plan': 17, 'GLU:plan': 35, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 589 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.42, per 1000 atoms: 0.59 Number of scatterers: 25964 At special positions: 0 Unit cell: (151.2, 151.2, 150.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 84 16.00 O 4520 8.00 N 4596 7.00 C 16756 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: 6.70 Conformation dependent library (CDL) restraints added in 3.6 seconds 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7056 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 8 sheets defined 71.8% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 48 through 61 removed outlier: 3.520A pdb=" N LEU A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 removed outlier: 4.145A pdb=" N VAL A 87 " --> pdb=" O TRP A 83 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 126 removed outlier: 4.154A pdb=" N HIS A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.582A pdb=" N LEU A 151 " --> pdb=" O HIS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 Processing helix chain 'A' and resid 238 through 249 removed outlier: 3.881A pdb=" N ARG A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 4.146A pdb=" N VAL A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.083A pdb=" N HIS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 345 removed outlier: 3.511A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 345 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.537A pdb=" N ALA A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 374 removed outlier: 4.413A pdb=" N GLY A 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 374' Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.764A pdb=" N VAL A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.543A pdb=" N PHE A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 408 through 413' Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 429 through 444 removed outlier: 3.763A pdb=" N GLU A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.518A pdb=" N VAL A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.850A pdb=" N ASP A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 4.137A pdb=" N TYR A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET A 539 " --> pdb=" O TYR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 557 removed outlier: 3.616A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 removed outlier: 3.933A pdb=" N THR A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 589 removed outlier: 3.696A pdb=" N ALA A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 599 removed outlier: 3.848A pdb=" N ALA A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.583A pdb=" N PHE A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.849A pdb=" N ILE A 659 " --> pdb=" O CYS A 655 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 660 " --> pdb=" O PRO A 656 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 655 through 661' Processing helix chain 'A' and resid 717 through 729 removed outlier: 3.738A pdb=" N ALA A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 755 removed outlier: 3.603A pdb=" N VAL A 733 " --> pdb=" O ALA A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 762 removed outlier: 3.627A pdb=" N GLY A 762 " --> pdb=" O PRO A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 787 Processing helix chain 'A' and resid 793 through 804 removed outlier: 4.126A pdb=" N ASP A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 826 removed outlier: 3.856A pdb=" N LYS A 808 " --> pdb=" O ASP A 804 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS A 823 " --> pdb=" O VAL A 819 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 849 removed outlier: 3.826A pdb=" N ARG A 834 " --> pdb=" O PHE A 830 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 849 " --> pdb=" O THR A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 removed outlier: 3.678A pdb=" N ILE A 854 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 868 removed outlier: 4.358A pdb=" N LYS A 861 " --> pdb=" O GLN A 857 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 895 removed outlier: 4.413A pdb=" N PHE A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP A 882 " --> pdb=" O PHE A 878 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 885 " --> pdb=" O VAL A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 916 Proline residue: A 912 - end of helix removed outlier: 3.977A pdb=" N ILE A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 925 Processing helix chain 'A' and resid 951 through 1005 removed outlier: 4.096A pdb=" N ASN A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP A 989 " --> pdb=" O GLN A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 3.810A pdb=" N SER A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A1019 " --> pdb=" O LEU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1071 Processing helix chain 'A' and resid 1072 through 1091 Processing helix chain 'B' and resid 48 through 61 removed outlier: 3.520A pdb=" N LEU B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 removed outlier: 4.145A pdb=" N VAL B 87 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 4.154A pdb=" N HIS B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 removed outlier: 3.582A pdb=" N LEU B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 212 Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.880A pdb=" N ARG B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 removed outlier: 4.146A pdb=" N VAL B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 288 Processing helix chain 'B' and resid 295 through 310 removed outlier: 4.082A pdb=" N HIS B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 345 removed outlier: 3.510A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 345 " --> pdb=" O CYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 363 through 370 removed outlier: 3.537A pdb=" N ALA B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 374 removed outlier: 4.413A pdb=" N GLY B 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 371 through 374' Processing helix chain 'B' and resid 383 through 393 Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.764A pdb=" N VAL B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 removed outlier: 3.542A pdb=" N PHE B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 413 " --> pdb=" O MET B 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 408 through 413' Processing helix chain 'B' and resid 414 through 424 Processing helix chain 'B' and resid 429 through 444 removed outlier: 3.764A pdb=" N GLU B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 477 removed outlier: 3.519A pdb=" N VAL B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.848A pdb=" N ASP B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 removed outlier: 4.137A pdb=" N TYR B 535 " --> pdb=" O GLU B 531 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET B 539 " --> pdb=" O TYR B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 557 removed outlier: 3.615A pdb=" N ALA B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 572 removed outlier: 3.933A pdb=" N THR B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 589 removed outlier: 3.696A pdb=" N ALA B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 589 " --> pdb=" O GLU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 599 removed outlier: 3.849A pdb=" N ALA B 596 " --> pdb=" O ASP B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 618 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.583A pdb=" N PHE B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'B' and resid 645 through 655 Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.849A pdb=" N ILE B 659 " --> pdb=" O CYS B 655 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 660 " --> pdb=" O PRO B 656 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 655 through 661' Processing helix chain 'B' and resid 717 through 729 removed outlier: 3.738A pdb=" N ALA B 729 " --> pdb=" O LYS B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 755 removed outlier: 3.602A pdb=" N VAL B 733 " --> pdb=" O ALA B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.626A pdb=" N GLY B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 787 Processing helix chain 'B' and resid 793 through 804 removed outlier: 4.125A pdb=" N ASP B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 826 removed outlier: 3.856A pdb=" N LYS B 808 " --> pdb=" O ASP B 804 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS B 823 " --> pdb=" O VAL B 819 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ARG B 824 " --> pdb=" O GLY B 820 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 849 removed outlier: 3.826A pdb=" N ARG B 834 " --> pdb=" O PHE B 830 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE B 849 " --> pdb=" O THR B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.677A pdb=" N ILE B 854 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 868 removed outlier: 4.357A pdb=" N LYS B 861 " --> pdb=" O GLN B 857 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 895 removed outlier: 4.413A pdb=" N PHE B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP B 882 " --> pdb=" O PHE B 878 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B 885 " --> pdb=" O VAL B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 916 Proline residue: B 912 - end of helix removed outlier: 3.976A pdb=" N ILE B 916 " --> pdb=" O PRO B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 925 Processing helix chain 'B' and resid 951 through 1005 removed outlier: 4.098A pdb=" N ASN B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1028 removed outlier: 3.811A pdb=" N SER B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B1019 " --> pdb=" O LEU B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1071 Processing helix chain 'B' and resid 1072 through 1091 Processing helix chain 'C' and resid 48 through 61 removed outlier: 3.520A pdb=" N LEU C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 97 removed outlier: 4.145A pdb=" N VAL C 87 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 removed outlier: 4.155A pdb=" N HIS C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 removed outlier: 3.582A pdb=" N LEU C 151 " --> pdb=" O HIS C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 212 Processing helix chain 'C' and resid 238 through 249 removed outlier: 3.881A pdb=" N ARG C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C 246 " --> pdb=" O ARG C 242 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 removed outlier: 4.146A pdb=" N VAL C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'C' and resid 295 through 310 removed outlier: 4.083A pdb=" N HIS C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 345 removed outlier: 3.510A pdb=" N VAL C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER C 343 " --> pdb=" O LYS C 339 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER C 345 " --> pdb=" O CYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 350 No H-bonds generated for 'chain 'C' and resid 348 through 350' Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 363 through 370 removed outlier: 3.538A pdb=" N ALA C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 374 removed outlier: 4.413A pdb=" N GLY C 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 371 through 374' Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.764A pdb=" N VAL C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 401 " --> pdb=" O ASP C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.542A pdb=" N PHE C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 413 " --> pdb=" O MET C 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 408 through 413' Processing helix chain 'C' and resid 414 through 424 Processing helix chain 'C' and resid 429 through 444 removed outlier: 3.763A pdb=" N GLU C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 477 removed outlier: 3.519A pdb=" N VAL C 469 " --> pdb=" O SER C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 527 removed outlier: 3.849A pdb=" N ASP C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 539 removed outlier: 4.137A pdb=" N TYR C 535 " --> pdb=" O GLU C 531 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET C 539 " --> pdb=" O TYR C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 557 removed outlier: 3.616A pdb=" N ALA C 546 " --> pdb=" O GLU C 542 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU C 548 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N CYS C 551 " --> pdb=" O ALA C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 572 removed outlier: 3.933A pdb=" N THR C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 589 removed outlier: 3.696A pdb=" N ALA C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN C 589 " --> pdb=" O GLU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 599 removed outlier: 3.849A pdb=" N ALA C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 618 Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.582A pdb=" N PHE C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 Processing helix chain 'C' and resid 645 through 655 Processing helix chain 'C' and resid 655 through 661 removed outlier: 3.848A pdb=" N ILE C 659 " --> pdb=" O CYS C 655 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 660 " --> pdb=" O PRO C 656 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 655 through 661' Processing helix chain 'C' and resid 717 through 729 removed outlier: 3.737A pdb=" N ALA C 729 " --> pdb=" O LYS C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 755 removed outlier: 3.602A pdb=" N VAL C 733 " --> pdb=" O ALA C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 762 removed outlier: 3.626A pdb=" N GLY C 762 " --> pdb=" O PRO C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 787 Processing helix chain 'C' and resid 793 through 804 removed outlier: 4.126A pdb=" N ASP C 804 " --> pdb=" O LEU C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 826 removed outlier: 3.856A pdb=" N LYS C 808 " --> pdb=" O ASP C 804 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS C 823 " --> pdb=" O VAL C 819 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG C 824 " --> pdb=" O GLY C 820 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET C 825 " --> pdb=" O VAL C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 849 removed outlier: 3.827A pdb=" N ARG C 834 " --> pdb=" O PHE C 830 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE C 849 " --> pdb=" O THR C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 855 removed outlier: 3.678A pdb=" N ILE C 854 " --> pdb=" O ILE C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 868 removed outlier: 4.358A pdb=" N LYS C 861 " --> pdb=" O GLN C 857 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 895 removed outlier: 4.412A pdb=" N PHE C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP C 882 " --> pdb=" O PHE C 878 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 885 " --> pdb=" O VAL C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 916 Proline residue: C 912 - end of helix removed outlier: 3.976A pdb=" N ILE C 916 " --> pdb=" O PRO C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 925 Processing helix chain 'C' and resid 951 through 1005 removed outlier: 4.097A pdb=" N ASN C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP C 989 " --> pdb=" O GLN C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1028 removed outlier: 3.810A pdb=" N SER C1017 " --> pdb=" O PHE C1013 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C1019 " --> pdb=" O LEU C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1043 through 1071 Processing helix chain 'C' and resid 1072 through 1091 Processing helix chain 'D' and resid 48 through 61 removed outlier: 3.519A pdb=" N LEU D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 97 removed outlier: 4.146A pdb=" N VAL D 87 " --> pdb=" O TRP D 83 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 removed outlier: 4.155A pdb=" N HIS D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 removed outlier: 3.582A pdb=" N LEU D 151 " --> pdb=" O HIS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 212 Processing helix chain 'D' and resid 238 through 249 removed outlier: 3.880A pdb=" N ARG D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 4.146A pdb=" N VAL D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 288 Processing helix chain 'D' and resid 295 through 310 removed outlier: 4.083A pdb=" N HIS D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU D 304 " --> pdb=" O VAL D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 345 removed outlier: 3.510A pdb=" N VAL D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER D 345 " --> pdb=" O CYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 363 through 370 removed outlier: 3.537A pdb=" N ALA D 367 " --> pdb=" O ARG D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 374 removed outlier: 4.413A pdb=" N GLY D 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 371 through 374' Processing helix chain 'D' and resid 383 through 393 Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.763A pdb=" N VAL D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU D 401 " --> pdb=" O ASP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 removed outlier: 3.542A pdb=" N PHE D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 413 " --> pdb=" O MET D 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 408 through 413' Processing helix chain 'D' and resid 414 through 424 Processing helix chain 'D' and resid 429 through 444 removed outlier: 3.763A pdb=" N GLU D 433 " --> pdb=" O SER D 429 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 477 removed outlier: 3.519A pdb=" N VAL D 469 " --> pdb=" O SER D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 527 removed outlier: 3.849A pdb=" N ASP D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 4.137A pdb=" N TYR D 535 " --> pdb=" O GLU D 531 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET D 539 " --> pdb=" O TYR D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 557 removed outlier: 3.616A pdb=" N ALA D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU D 548 " --> pdb=" O VAL D 544 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 572 removed outlier: 3.933A pdb=" N THR D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 589 removed outlier: 3.696A pdb=" N ALA D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN D 589 " --> pdb=" O GLU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 599 removed outlier: 3.848A pdb=" N ALA D 596 " --> pdb=" O ASP D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 618 Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.582A pdb=" N PHE D 623 " --> pdb=" O ALA D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 645 through 655 Processing helix chain 'D' and resid 655 through 661 removed outlier: 3.848A pdb=" N ILE D 659 " --> pdb=" O CYS D 655 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D 660 " --> pdb=" O PRO D 656 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 655 through 661' Processing helix chain 'D' and resid 717 through 729 removed outlier: 3.738A pdb=" N ALA D 729 " --> pdb=" O LYS D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 755 removed outlier: 3.602A pdb=" N VAL D 733 " --> pdb=" O ALA D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 762 removed outlier: 3.626A pdb=" N GLY D 762 " --> pdb=" O PRO D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 787 Processing helix chain 'D' and resid 793 through 804 removed outlier: 4.126A pdb=" N ASP D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 826 removed outlier: 3.856A pdb=" N LYS D 808 " --> pdb=" O ASP D 804 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR D 822 " --> pdb=" O ILE D 818 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS D 823 " --> pdb=" O VAL D 819 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG D 824 " --> pdb=" O GLY D 820 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET D 825 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 849 removed outlier: 3.826A pdb=" N ARG D 834 " --> pdb=" O PHE D 830 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE D 849 " --> pdb=" O THR D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 855 removed outlier: 3.677A pdb=" N ILE D 854 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 868 removed outlier: 4.358A pdb=" N LYS D 861 " --> pdb=" O GLN D 857 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 895 removed outlier: 4.412A pdb=" N PHE D 873 " --> pdb=" O MET D 869 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP D 882 " --> pdb=" O PHE D 878 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 885 " --> pdb=" O VAL D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 916 Proline residue: D 912 - end of helix removed outlier: 3.977A pdb=" N ILE D 916 " --> pdb=" O PRO D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 925 Processing helix chain 'D' and resid 951 through 1005 removed outlier: 4.099A pdb=" N ASN D 966 " --> pdb=" O LEU D 962 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP D 989 " --> pdb=" O GLN D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1028 removed outlier: 3.811A pdb=" N SER D1017 " --> pdb=" O PHE D1013 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU D1019 " --> pdb=" O LEU D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1043 through 1071 Processing helix chain 'D' and resid 1072 through 1091 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.620A pdb=" N GLY A 138 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A 188 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA A 140 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 136 removed outlier: 6.446A pdb=" N ALA A 101 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 71 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL A 68 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU A 231 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER A 70 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N LEU A 254 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS A 230 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU A 256 " --> pdb=" O CYS A 230 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU A 232 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP A 253 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR A 319 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE A 255 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.620A pdb=" N GLY B 138 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL B 188 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA B 140 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 136 removed outlier: 6.446A pdb=" N ALA B 101 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 71 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 68 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU B 231 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER B 70 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N LEU B 254 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS B 230 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU B 256 " --> pdb=" O CYS B 230 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU B 232 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP B 253 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR B 319 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE B 255 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.619A pdb=" N GLY C 138 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL C 188 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA C 140 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 134 through 136 removed outlier: 6.447A pdb=" N ALA C 101 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 71 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL C 68 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU C 231 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER C 70 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N LEU C 254 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS C 230 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU C 256 " --> pdb=" O CYS C 230 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU C 232 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP C 253 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N TYR C 319 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE C 255 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.619A pdb=" N GLY D 138 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL D 188 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA D 140 " --> pdb=" O VAL D 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.447A pdb=" N ALA D 101 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 71 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL D 68 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU D 231 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER D 70 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N LEU D 254 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS D 230 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU D 256 " --> pdb=" O CYS D 230 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU D 232 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP D 253 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR D 319 " --> pdb=" O TRP D 253 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE D 255 " --> pdb=" O TYR D 319 " (cutoff:3.500A) 1685 hydrogen bonds defined for protein. 4983 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: 9.59 Time building geometry restraints manager: 7.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4158 1.30 - 1.43: 7136 1.43 - 1.56: 15110 1.56 - 1.68: 0 1.68 - 1.81: 128 Bond restraints: 26532 Sorted by residual: bond pdb=" C ASP C1047 " pdb=" N GLN C1048 " ideal model delta sigma weight residual 1.335 1.399 -0.065 1.25e-02 6.40e+03 2.66e+01 bond pdb=" C ASP D1047 " pdb=" N GLN D1048 " ideal model delta sigma weight residual 1.335 1.399 -0.065 1.25e-02 6.40e+03 2.66e+01 bond pdb=" C PHE B 977 " pdb=" O PHE B 977 " ideal model delta sigma weight residual 1.236 1.178 0.059 1.15e-02 7.56e+03 2.60e+01 bond pdb=" C PHE D 977 " pdb=" O PHE D 977 " ideal model delta sigma weight residual 1.236 1.178 0.059 1.15e-02 7.56e+03 2.60e+01 bond pdb=" C ASP A1047 " pdb=" N GLN A1048 " ideal model delta sigma weight residual 1.335 1.398 -0.064 1.25e-02 6.40e+03 2.59e+01 ... (remaining 26527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 35065 1.76 - 3.51: 1030 3.51 - 5.27: 181 5.27 - 7.02: 48 7.02 - 8.78: 4 Bond angle restraints: 36328 Sorted by residual: angle pdb=" O LEU C 973 " pdb=" C LEU C 973 " pdb=" N ILE C 974 " ideal model delta sigma weight residual 122.07 128.73 -6.66 1.03e+00 9.43e-01 4.18e+01 angle pdb=" O LEU A 973 " pdb=" C LEU A 973 " pdb=" N ILE A 974 " ideal model delta sigma weight residual 122.07 128.72 -6.65 1.03e+00 9.43e-01 4.17e+01 angle pdb=" O LEU D 973 " pdb=" C LEU D 973 " pdb=" N ILE D 974 " ideal model delta sigma weight residual 122.07 128.68 -6.61 1.03e+00 9.43e-01 4.12e+01 angle pdb=" O LEU B 973 " pdb=" C LEU B 973 " pdb=" N ILE B 974 " ideal model delta sigma weight residual 122.07 128.68 -6.61 1.03e+00 9.43e-01 4.11e+01 angle pdb=" N ASN D 987 " pdb=" CA ASN D 987 " pdb=" C ASN D 987 " ideal model delta sigma weight residual 111.07 117.38 -6.31 1.07e+00 8.73e-01 3.47e+01 ... (remaining 36323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 14291 16.77 - 33.54: 907 33.54 - 50.31: 198 50.31 - 67.08: 12 67.08 - 83.85: 12 Dihedral angle restraints: 15420 sinusoidal: 4664 harmonic: 10756 Sorted by residual: dihedral pdb=" N ALA D 988 " pdb=" C ALA D 988 " pdb=" CA ALA D 988 " pdb=" CB ALA D 988 " ideal model delta harmonic sigma weight residual 122.90 132.75 -9.85 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" N ALA B 988 " pdb=" C ALA B 988 " pdb=" CA ALA B 988 " pdb=" CB ALA B 988 " ideal model delta harmonic sigma weight residual 122.90 132.74 -9.84 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" N ALA A 988 " pdb=" C ALA A 988 " pdb=" CA ALA A 988 " pdb=" CB ALA A 988 " ideal model delta harmonic sigma weight residual 122.90 132.73 -9.83 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 15417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4019 0.079 - 0.158: 321 0.158 - 0.237: 12 0.237 - 0.316: 4 0.316 - 0.396: 4 Chirality restraints: 4360 Sorted by residual: chirality pdb=" CA ALA B 988 " pdb=" N ALA B 988 " pdb=" C ALA B 988 " pdb=" CB ALA B 988 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA ALA D 988 " pdb=" N ALA D 988 " pdb=" C ALA D 988 " pdb=" CB ALA D 988 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA ALA C 988 " pdb=" N ALA C 988 " pdb=" C ALA C 988 " pdb=" CB ALA C 988 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 4357 not shown) Planarity restraints: 4624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 981 " -0.017 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C PHE C 981 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE C 981 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN C 982 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 981 " -0.017 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C PHE D 981 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE D 981 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN D 982 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 981 " 0.017 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C PHE A 981 " -0.063 2.00e-02 2.50e+03 pdb=" O PHE A 981 " 0.025 2.00e-02 2.50e+03 pdb=" N GLN A 982 " 0.021 2.00e-02 2.50e+03 ... (remaining 4621 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 388 2.67 - 3.22: 27104 3.22 - 3.78: 39826 3.78 - 4.34: 47871 4.34 - 4.90: 78045 Nonbonded interactions: 193234 Sorted by model distance: nonbonded pdb=" OE2 GLU B 354 " pdb="CA CA B1201 " model vdw 2.107 2.510 nonbonded pdb=" OE2 GLU C 354 " pdb="CA CA C1201 " model vdw 2.107 2.510 nonbonded pdb=" OE2 GLU A 354 " pdb="CA CA A1201 " model vdw 2.107 2.510 nonbonded pdb=" OE2 GLU D 354 " pdb="CA CA D1201 " model vdw 2.108 2.510 nonbonded pdb=" NH1 ARG C 89 " pdb=" CB HIS C 115 " model vdw 2.167 3.520 ... (remaining 193229 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.890 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 57.780 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 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 : 0.005 0.065 26532 Z= 0.293 Angle : 0.743 8.776 36328 Z= 0.486 Chirality : 0.046 0.396 4360 Planarity : 0.005 0.037 4624 Dihedral : 12.136 83.851 8364 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.14 % Allowed : 6.95 % Favored : 92.91 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.13), residues: 3580 helix: -0.02 (0.10), residues: 2260 sheet: -1.11 (0.32), residues: 200 loop : -2.08 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 806 HIS 0.007 0.001 HIS C 612 PHE 0.039 0.002 PHE D 877 TYR 0.022 0.002 TYR D 587 ARG 0.012 0.001 ARG D 518 Details of bonding type rmsd hydrogen bonds : bond 0.16619 ( 1685) hydrogen bonds : angle 6.83666 ( 4983) covalent geometry : bond 0.00528 (26532) covalent geometry : angle 0.74250 (36328) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 591 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ILE cc_start: 0.8078 (pt) cc_final: 0.7812 (pt) REVERT: A 352 LEU cc_start: 0.9061 (mp) cc_final: 0.8822 (tt) REVERT: A 532 MET cc_start: 0.9326 (ttp) cc_final: 0.8971 (mmm) REVERT: A 577 GLN cc_start: 0.9510 (tp40) cc_final: 0.8890 (tp40) REVERT: A 752 LEU cc_start: 0.9279 (mm) cc_final: 0.8979 (mm) REVERT: A 809 CYS cc_start: 0.9249 (t) cc_final: 0.8972 (p) REVERT: A 840 ASP cc_start: 0.8935 (t70) cc_final: 0.8457 (t0) REVERT: A 844 PHE cc_start: 0.9075 (m-10) cc_final: 0.8844 (m-10) REVERT: A 847 ARG cc_start: 0.8678 (tmt170) cc_final: 0.7995 (tpt90) REVERT: A 873 PHE cc_start: 0.8676 (t80) cc_final: 0.7685 (m-80) REVERT: B 224 ILE cc_start: 0.7836 (pt) cc_final: 0.7530 (pt) REVERT: B 316 LEU cc_start: 0.7527 (pt) cc_final: 0.7304 (pp) REVERT: B 752 LEU cc_start: 0.9228 (mm) cc_final: 0.8890 (mm) REVERT: B 809 CYS cc_start: 0.9272 (t) cc_final: 0.8958 (p) REVERT: B 847 ARG cc_start: 0.8702 (tmt170) cc_final: 0.7888 (tpt90) REVERT: B 850 HIS cc_start: 0.7927 (t70) cc_final: 0.7700 (t-90) REVERT: B 873 PHE cc_start: 0.8944 (t80) cc_final: 0.7935 (m-80) REVERT: C 352 LEU cc_start: 0.8959 (mp) cc_final: 0.8650 (tt) REVERT: C 577 GLN cc_start: 0.9463 (tp40) cc_final: 0.8886 (tp40) REVERT: C 752 LEU cc_start: 0.9212 (mm) cc_final: 0.8892 (mm) REVERT: C 809 CYS cc_start: 0.9375 (t) cc_final: 0.8936 (p) REVERT: C 840 ASP cc_start: 0.9014 (t70) cc_final: 0.8586 (t0) REVERT: C 844 PHE cc_start: 0.9022 (m-10) cc_final: 0.8766 (m-10) REVERT: C 847 ARG cc_start: 0.8750 (tmt170) cc_final: 0.7947 (tpt90) REVERT: C 852 PHE cc_start: 0.9208 (m-80) cc_final: 0.8845 (m-80) REVERT: C 873 PHE cc_start: 0.8697 (t80) cc_final: 0.7534 (m-80) REVERT: D 532 MET cc_start: 0.9317 (ttp) cc_final: 0.9067 (mmm) REVERT: D 539 MET cc_start: 0.8229 (mtm) cc_final: 0.8013 (mtm) REVERT: D 577 GLN cc_start: 0.9475 (tp40) cc_final: 0.8918 (tp40) REVERT: D 752 LEU cc_start: 0.9284 (mm) cc_final: 0.8941 (mm) REVERT: D 809 CYS cc_start: 0.9285 (t) cc_final: 0.8955 (p) REVERT: D 847 ARG cc_start: 0.8768 (tmt170) cc_final: 0.7955 (tpt90) REVERT: D 873 PHE cc_start: 0.8701 (t80) cc_final: 0.7662 (m-80) REVERT: D 953 LEU cc_start: 0.8197 (mt) cc_final: 0.7983 (mp) outliers start: 3 outliers final: 3 residues processed: 593 average time/residue: 0.3500 time to fit residues: 325.9158 Evaluate side-chains 363 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 360 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 4.9990 chunk 278 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 149 optimal weight: 20.0000 chunk 288 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 175 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 chunk 334 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS A 951 ASN A 982 GLN A 998 HIS B 210 HIS ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 ASN B 982 GLN B 998 HIS C 184 HIS C 210 HIS ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS C 951 ASN C 982 GLN D 184 HIS D 210 HIS ** D 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS D 951 ASN D 982 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.094581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.070227 restraints weight = 120607.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071721 restraints weight = 74237.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072697 restraints weight = 53652.021| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26532 Z= 0.156 Angle : 0.582 7.642 36328 Z= 0.312 Chirality : 0.039 0.163 4360 Planarity : 0.005 0.050 4624 Dihedral : 4.124 19.687 3852 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3580 helix: 1.14 (0.11), residues: 2368 sheet: -0.53 (0.36), residues: 184 loop : -1.56 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 253 HIS 0.005 0.001 HIS C 184 PHE 0.025 0.002 PHE D 994 TYR 0.024 0.002 TYR D 319 ARG 0.012 0.001 ARG C 867 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 1685) hydrogen bonds : angle 4.96168 ( 4983) covalent geometry : bond 0.00313 (26532) covalent geometry : angle 0.58153 (36328) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ILE cc_start: 0.8741 (mm) cc_final: 0.8447 (mm) REVERT: A 283 LYS cc_start: 0.9072 (tttt) cc_final: 0.8844 (tppt) REVERT: A 434 LEU cc_start: 0.9623 (mt) cc_final: 0.9216 (mt) REVERT: A 577 GLN cc_start: 0.9146 (tp40) cc_final: 0.8743 (tp40) REVERT: A 840 ASP cc_start: 0.9226 (t70) cc_final: 0.9003 (t70) REVERT: A 847 ARG cc_start: 0.8608 (tmt170) cc_final: 0.8218 (tpt90) REVERT: A 873 PHE cc_start: 0.8736 (t80) cc_final: 0.8172 (m-80) REVERT: B 255 ILE cc_start: 0.8539 (mm) cc_final: 0.8194 (mm) REVERT: B 283 LYS cc_start: 0.9162 (tttt) cc_final: 0.8934 (tppt) REVERT: B 387 MET cc_start: 0.8652 (tpt) cc_final: 0.8402 (tpp) REVERT: B 577 GLN cc_start: 0.9109 (tp40) cc_final: 0.8779 (tp-100) REVERT: B 847 ARG cc_start: 0.8634 (tmt170) cc_final: 0.8020 (tpt90) REVERT: B 873 PHE cc_start: 0.8942 (t80) cc_final: 0.8414 (m-80) REVERT: C 333 ILE cc_start: 0.9435 (mt) cc_final: 0.9230 (mt) REVERT: C 401 LEU cc_start: 0.9805 (tp) cc_final: 0.9527 (tt) REVERT: C 577 GLN cc_start: 0.9137 (tp40) cc_final: 0.8826 (tp-100) REVERT: C 840 ASP cc_start: 0.9314 (t70) cc_final: 0.9108 (t70) REVERT: C 847 ARG cc_start: 0.8748 (tmt170) cc_final: 0.8202 (tpt90) REVERT: C 852 PHE cc_start: 0.9146 (m-80) cc_final: 0.8921 (m-80) REVERT: C 873 PHE cc_start: 0.8839 (t80) cc_final: 0.8069 (m-80) REVERT: D 255 ILE cc_start: 0.8704 (mm) cc_final: 0.8380 (mm) REVERT: D 577 GLN cc_start: 0.9162 (tp40) cc_final: 0.8842 (tp-100) REVERT: D 847 ARG cc_start: 0.8744 (tmt170) cc_final: 0.8253 (tpt90) REVERT: D 852 PHE cc_start: 0.8799 (m-80) cc_final: 0.8084 (m-80) REVERT: D 873 PHE cc_start: 0.8747 (t80) cc_final: 0.8146 (m-80) REVERT: D 953 LEU cc_start: 0.8188 (mt) cc_final: 0.7966 (mp) outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.3173 time to fit residues: 245.6937 Evaluate side-chains 323 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 292 optimal weight: 0.9990 chunk 169 optimal weight: 40.0000 chunk 269 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 330 optimal weight: 8.9990 chunk 296 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 chunk 357 optimal weight: 20.0000 chunk 358 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 850 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 ASN B 850 HIS C 184 HIS C 210 HIS C 284 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS D 184 HIS D 210 HIS D 284 GLN ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.092258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.067967 restraints weight = 121950.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.069382 restraints weight = 75687.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.070296 restraints weight = 55100.021| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 26532 Z= 0.231 Angle : 0.642 7.809 36328 Z= 0.337 Chirality : 0.039 0.167 4360 Planarity : 0.005 0.049 4624 Dihedral : 4.322 17.801 3852 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 3580 helix: 1.36 (0.11), residues: 2336 sheet: -0.20 (0.35), residues: 216 loop : -1.08 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 723 HIS 0.007 0.001 HIS C 184 PHE 0.022 0.002 PHE C 289 TYR 0.017 0.002 TYR D 535 ARG 0.005 0.001 ARG D1083 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 1685) hydrogen bonds : angle 4.94248 ( 4983) covalent geometry : bond 0.00486 (26532) covalent geometry : angle 0.64162 (36328) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TRP cc_start: 0.6448 (m100) cc_final: 0.6227 (m100) REVERT: A 255 ILE cc_start: 0.8787 (mm) cc_final: 0.8434 (mm) REVERT: A 283 LYS cc_start: 0.9131 (tttt) cc_final: 0.8919 (tppt) REVERT: A 357 LEU cc_start: 0.9225 (tp) cc_final: 0.9023 (tp) REVERT: A 401 LEU cc_start: 0.9762 (tp) cc_final: 0.9544 (tt) REVERT: A 577 GLN cc_start: 0.9262 (tp40) cc_final: 0.8533 (tp-100) REVERT: A 840 ASP cc_start: 0.9224 (t70) cc_final: 0.8962 (t70) REVERT: A 847 ARG cc_start: 0.8665 (tmt170) cc_final: 0.8242 (tpt90) REVERT: A 873 PHE cc_start: 0.8950 (t80) cc_final: 0.8348 (m-80) REVERT: B 255 ILE cc_start: 0.8626 (mm) cc_final: 0.8334 (mm) REVERT: B 283 LYS cc_start: 0.9212 (tttt) cc_final: 0.8989 (tppt) REVERT: B 387 MET cc_start: 0.8640 (tpt) cc_final: 0.8378 (tpt) REVERT: B 577 GLN cc_start: 0.9241 (tp40) cc_final: 0.8514 (tp-100) REVERT: B 752 LEU cc_start: 0.9309 (mm) cc_final: 0.9093 (mm) REVERT: B 840 ASP cc_start: 0.9455 (t70) cc_final: 0.9205 (t0) REVERT: B 847 ARG cc_start: 0.8428 (tmt170) cc_final: 0.8055 (tpt90) REVERT: B 873 PHE cc_start: 0.9164 (t80) cc_final: 0.8549 (m-80) REVERT: C 255 ILE cc_start: 0.8481 (mm) cc_final: 0.8232 (mm) REVERT: C 570 MET cc_start: 0.8730 (ptm) cc_final: 0.8472 (ptp) REVERT: C 577 GLN cc_start: 0.9236 (tp40) cc_final: 0.8466 (tp-100) REVERT: C 752 LEU cc_start: 0.9363 (mm) cc_final: 0.9158 (mm) REVERT: C 809 CYS cc_start: 0.8746 (m) cc_final: 0.8417 (p) REVERT: C 840 ASP cc_start: 0.9326 (t70) cc_final: 0.9097 (t70) REVERT: C 847 ARG cc_start: 0.8831 (tmt170) cc_final: 0.8179 (tpt90) REVERT: C 852 PHE cc_start: 0.9214 (m-80) cc_final: 0.8880 (m-80) REVERT: C 873 PHE cc_start: 0.8989 (t80) cc_final: 0.8151 (m-80) REVERT: D 255 ILE cc_start: 0.8734 (mm) cc_final: 0.8448 (mm) REVERT: D 283 LYS cc_start: 0.9108 (tttt) cc_final: 0.8835 (tppt) REVERT: D 576 GLU cc_start: 0.8749 (tt0) cc_final: 0.8490 (tt0) REVERT: D 577 GLN cc_start: 0.9248 (tp40) cc_final: 0.8792 (tp40) REVERT: D 752 LEU cc_start: 0.9404 (mm) cc_final: 0.9162 (mm) REVERT: D 847 ARG cc_start: 0.8602 (tmt170) cc_final: 0.8236 (tpt90) REVERT: D 852 PHE cc_start: 0.8898 (m-80) cc_final: 0.8152 (m-80) REVERT: D 873 PHE cc_start: 0.9013 (t80) cc_final: 0.8347 (m-80) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.3188 time to fit residues: 212.5708 Evaluate side-chains 301 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 86 optimal weight: 30.0000 chunk 71 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 237 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 346 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS B 214 GLN B 394 ASN ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS C 214 GLN ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS D 214 GLN D 394 ASN ** D 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.093272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.069100 restraints weight = 122637.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.070561 restraints weight = 75523.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.071439 restraints weight = 54641.076| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26532 Z= 0.143 Angle : 0.546 8.337 36328 Z= 0.284 Chirality : 0.037 0.161 4360 Planarity : 0.004 0.046 4624 Dihedral : 4.047 19.180 3852 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.14), residues: 3580 helix: 1.69 (0.11), residues: 2348 sheet: 0.05 (0.32), residues: 236 loop : -0.88 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 361 HIS 0.006 0.001 HIS B 998 PHE 0.029 0.001 PHE B 289 TYR 0.011 0.001 TYR D 535 ARG 0.005 0.000 ARG C1083 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 1685) hydrogen bonds : angle 4.50230 ( 4983) covalent geometry : bond 0.00297 (26532) covalent geometry : angle 0.54564 (36328) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 420 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ILE cc_start: 0.8716 (mm) cc_final: 0.8374 (mm) REVERT: A 283 LYS cc_start: 0.9124 (tttt) cc_final: 0.8885 (mmtm) REVERT: A 577 GLN cc_start: 0.9175 (tp40) cc_final: 0.8673 (tp40) REVERT: A 840 ASP cc_start: 0.9210 (t70) cc_final: 0.8932 (t70) REVERT: A 847 ARG cc_start: 0.8522 (tmt170) cc_final: 0.8129 (tpt90) REVERT: A 873 PHE cc_start: 0.9061 (t80) cc_final: 0.8415 (m-80) REVERT: B 255 ILE cc_start: 0.8501 (mm) cc_final: 0.8224 (mm) REVERT: B 283 LYS cc_start: 0.9193 (tttt) cc_final: 0.8965 (tppt) REVERT: B 570 MET cc_start: 0.8967 (ptm) cc_final: 0.8765 (ptp) REVERT: B 577 GLN cc_start: 0.9171 (tp40) cc_final: 0.8750 (tp-100) REVERT: B 847 ARG cc_start: 0.8448 (tmt170) cc_final: 0.8198 (tpt90) REVERT: B 873 PHE cc_start: 0.9253 (t80) cc_final: 0.8575 (m-80) REVERT: C 90 LYS cc_start: 0.9261 (mmmt) cc_final: 0.8956 (mmmt) REVERT: C 255 ILE cc_start: 0.8433 (mm) cc_final: 0.8152 (mm) REVERT: C 413 LEU cc_start: 0.9326 (tp) cc_final: 0.9120 (tt) REVERT: C 577 GLN cc_start: 0.9202 (tp40) cc_final: 0.8468 (tp-100) REVERT: C 840 ASP cc_start: 0.9313 (t70) cc_final: 0.9060 (t70) REVERT: C 847 ARG cc_start: 0.8673 (tmt170) cc_final: 0.8143 (tpt90) REVERT: C 852 PHE cc_start: 0.9220 (m-80) cc_final: 0.8955 (m-80) REVERT: D 255 ILE cc_start: 0.8706 (mm) cc_final: 0.8368 (mm) REVERT: D 577 GLN cc_start: 0.9198 (tp40) cc_final: 0.8697 (tp40) REVERT: D 752 LEU cc_start: 0.9421 (mm) cc_final: 0.9162 (mm) REVERT: D 847 ARG cc_start: 0.8477 (tmt170) cc_final: 0.8131 (tpt90) REVERT: D 852 PHE cc_start: 0.9028 (m-80) cc_final: 0.8407 (m-80) REVERT: D 873 PHE cc_start: 0.9110 (t80) cc_final: 0.8421 (m-80) outliers start: 2 outliers final: 0 residues processed: 422 average time/residue: 0.3293 time to fit residues: 227.3785 Evaluate side-chains 288 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 133 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 346 optimal weight: 0.9990 chunk 170 optimal weight: 40.0000 chunk 152 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 294 optimal weight: 0.3980 chunk 103 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS C 394 ASN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.091768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.067373 restraints weight = 123043.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.068811 restraints weight = 75719.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.069731 restraints weight = 54993.379| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26532 Z= 0.200 Angle : 0.608 8.072 36328 Z= 0.315 Chirality : 0.038 0.157 4360 Planarity : 0.004 0.079 4624 Dihedral : 4.187 16.632 3852 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.09 % Allowed : 2.52 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.14), residues: 3580 helix: 1.66 (0.11), residues: 2352 sheet: 0.49 (0.36), residues: 184 loop : -0.78 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 723 HIS 0.007 0.001 HIS B 147 PHE 0.022 0.002 PHE C 289 TYR 0.016 0.002 TYR A 660 ARG 0.012 0.001 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 1685) hydrogen bonds : angle 4.63199 ( 4983) covalent geometry : bond 0.00422 (26532) covalent geometry : angle 0.60819 (36328) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 383 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ILE cc_start: 0.8774 (mm) cc_final: 0.8462 (mm) REVERT: A 283 LYS cc_start: 0.9142 (tttt) cc_final: 0.8894 (mmtm) REVERT: A 354 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8272 (mt-10) REVERT: A 577 GLN cc_start: 0.9219 (tp40) cc_final: 0.8490 (tp-100) REVERT: A 737 ASN cc_start: 0.9256 (m-40) cc_final: 0.8884 (m110) REVERT: A 847 ARG cc_start: 0.8394 (tmt170) cc_final: 0.8111 (tpt90) REVERT: A 852 PHE cc_start: 0.9070 (m-80) cc_final: 0.8804 (m-80) REVERT: A 873 PHE cc_start: 0.9173 (t80) cc_final: 0.8427 (m-80) REVERT: B 90 LYS cc_start: 0.9257 (mmmt) cc_final: 0.8959 (mmmt) REVERT: B 255 ILE cc_start: 0.8584 (mm) cc_final: 0.8236 (mm) REVERT: B 283 LYS cc_start: 0.9201 (tttt) cc_final: 0.8991 (tppt) REVERT: B 387 MET cc_start: 0.8839 (tpt) cc_final: 0.8550 (tpt) REVERT: B 577 GLN cc_start: 0.9211 (tp40) cc_final: 0.8463 (tp-100) REVERT: B 752 LEU cc_start: 0.9368 (mm) cc_final: 0.9146 (mm) REVERT: B 840 ASP cc_start: 0.9498 (t70) cc_final: 0.9274 (t0) REVERT: B 847 ARG cc_start: 0.8517 (tmt170) cc_final: 0.7875 (tpt90) REVERT: B 873 PHE cc_start: 0.9341 (t80) cc_final: 0.8563 (m-80) REVERT: C 90 LYS cc_start: 0.9282 (mmmt) cc_final: 0.8917 (mmmt) REVERT: C 255 ILE cc_start: 0.8590 (mm) cc_final: 0.8293 (mm) REVERT: C 354 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8296 (mt-10) REVERT: C 418 LEU cc_start: 0.9492 (tt) cc_final: 0.9198 (mt) REVERT: C 577 GLN cc_start: 0.9235 (tp40) cc_final: 0.8435 (tp-100) REVERT: C 840 ASP cc_start: 0.9306 (t70) cc_final: 0.9055 (t0) REVERT: C 847 ARG cc_start: 0.8679 (tmt170) cc_final: 0.8168 (tpt90) REVERT: C 852 PHE cc_start: 0.9261 (m-80) cc_final: 0.8964 (m-80) REVERT: D 255 ILE cc_start: 0.8772 (mm) cc_final: 0.8508 (mm) REVERT: D 576 GLU cc_start: 0.8704 (tt0) cc_final: 0.8455 (tt0) REVERT: D 577 GLN cc_start: 0.9243 (tp40) cc_final: 0.8767 (tp40) REVERT: D 752 LEU cc_start: 0.9433 (mm) cc_final: 0.9212 (mm) REVERT: D 840 ASP cc_start: 0.9397 (t70) cc_final: 0.8980 (t0) REVERT: D 847 ARG cc_start: 0.8438 (tmt170) cc_final: 0.8012 (tpt90) REVERT: D 852 PHE cc_start: 0.9115 (m-80) cc_final: 0.8455 (m-80) REVERT: D 873 PHE cc_start: 0.9200 (t80) cc_final: 0.8406 (m-80) outliers start: 2 outliers final: 0 residues processed: 384 average time/residue: 0.3329 time to fit residues: 211.9993 Evaluate side-chains 281 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 2 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 306 optimal weight: 7.9990 chunk 0 optimal weight: 60.0000 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 297 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS ** D 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.091888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.067743 restraints weight = 123190.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.069189 restraints weight = 75303.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.070137 restraints weight = 54433.044| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26532 Z= 0.187 Angle : 0.588 9.741 36328 Z= 0.304 Chirality : 0.038 0.170 4360 Planarity : 0.004 0.042 4624 Dihedral : 4.167 21.227 3852 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.14), residues: 3580 helix: 1.77 (0.11), residues: 2352 sheet: -0.07 (0.33), residues: 216 loop : -0.84 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 361 HIS 0.005 0.001 HIS A 184 PHE 0.021 0.001 PHE B 289 TYR 0.012 0.002 TYR B 587 ARG 0.006 0.000 ARG B 89 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 1685) hydrogen bonds : angle 4.53370 ( 4983) covalent geometry : bond 0.00393 (26532) covalent geometry : angle 0.58780 (36328) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ILE cc_start: 0.8730 (mm) cc_final: 0.8427 (mm) REVERT: A 283 LYS cc_start: 0.9177 (tttt) cc_final: 0.8912 (mmtm) REVERT: A 354 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8327 (mt-10) REVERT: A 577 GLN cc_start: 0.9186 (tp40) cc_final: 0.8623 (tp40) REVERT: A 737 ASN cc_start: 0.9260 (m-40) cc_final: 0.9030 (m-40) REVERT: A 840 ASP cc_start: 0.9330 (t70) cc_final: 0.9033 (t70) REVERT: A 847 ARG cc_start: 0.8375 (tmt170) cc_final: 0.8105 (tpt90) REVERT: A 852 PHE cc_start: 0.9068 (m-80) cc_final: 0.8829 (m-80) REVERT: A 873 PHE cc_start: 0.9223 (t80) cc_final: 0.8463 (m-80) REVERT: B 90 LYS cc_start: 0.9158 (mmmt) cc_final: 0.8934 (mmmt) REVERT: B 255 ILE cc_start: 0.8490 (mm) cc_final: 0.8118 (mm) REVERT: B 283 LYS cc_start: 0.9222 (tttt) cc_final: 0.9004 (tppt) REVERT: B 418 LEU cc_start: 0.9383 (tt) cc_final: 0.9127 (mt) REVERT: B 577 GLN cc_start: 0.9218 (tp40) cc_final: 0.8632 (tp40) REVERT: B 752 LEU cc_start: 0.9353 (mm) cc_final: 0.9135 (mm) REVERT: B 847 ARG cc_start: 0.8306 (tmt170) cc_final: 0.8000 (tpt90) REVERT: B 852 PHE cc_start: 0.9080 (m-80) cc_final: 0.8799 (m-80) REVERT: C 255 ILE cc_start: 0.8537 (mm) cc_final: 0.8173 (mm) REVERT: C 354 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8336 (mt-10) REVERT: C 368 LYS cc_start: 0.9467 (tptp) cc_final: 0.9260 (tppt) REVERT: C 418 LEU cc_start: 0.9324 (tt) cc_final: 0.9038 (mt) REVERT: C 577 GLN cc_start: 0.9229 (tp40) cc_final: 0.8438 (tp-100) REVERT: C 840 ASP cc_start: 0.9322 (t70) cc_final: 0.9089 (t70) REVERT: C 847 ARG cc_start: 0.8542 (tmt170) cc_final: 0.8105 (tpt90) REVERT: C 852 PHE cc_start: 0.9276 (m-80) cc_final: 0.8988 (m-80) REVERT: D 255 ILE cc_start: 0.8702 (mm) cc_final: 0.8438 (mm) REVERT: D 283 LYS cc_start: 0.9111 (tttt) cc_final: 0.8836 (tppt) REVERT: D 418 LEU cc_start: 0.9339 (tt) cc_final: 0.8976 (mt) REVERT: D 576 GLU cc_start: 0.8680 (tt0) cc_final: 0.8430 (tt0) REVERT: D 577 GLN cc_start: 0.9214 (tp40) cc_final: 0.8653 (tp40) REVERT: D 752 LEU cc_start: 0.9423 (mm) cc_final: 0.9201 (mm) REVERT: D 847 ARG cc_start: 0.8282 (tmt170) cc_final: 0.7975 (tpt90) REVERT: D 873 PHE cc_start: 0.9256 (t80) cc_final: 0.8458 (m-10) REVERT: D 1071 ASP cc_start: 0.8324 (t0) cc_final: 0.8123 (t0) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.3304 time to fit residues: 203.4514 Evaluate side-chains 275 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 64 optimal weight: 20.0000 chunk 259 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 173 optimal weight: 50.0000 chunk 243 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 284 optimal weight: 30.0000 chunk 361 optimal weight: 5.9990 chunk 295 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 145 optimal weight: 0.1980 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS B 272 GLN ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS C 272 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 737 ASN D 850 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.090020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.065718 restraints weight = 125037.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.067133 restraints weight = 77157.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.068053 restraints weight = 56123.760| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 26532 Z= 0.272 Angle : 0.697 10.452 36328 Z= 0.359 Chirality : 0.041 0.176 4360 Planarity : 0.005 0.042 4624 Dihedral : 4.547 20.725 3852 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.14), residues: 3580 helix: 1.48 (0.11), residues: 2336 sheet: 0.03 (0.37), residues: 164 loop : -1.07 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 537 HIS 0.007 0.002 HIS B 423 PHE 0.020 0.002 PHE A 583 TYR 0.016 0.002 TYR B 587 ARG 0.006 0.001 ARG B 518 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 1685) hydrogen bonds : angle 4.95033 ( 4983) covalent geometry : bond 0.00567 (26532) covalent geometry : angle 0.69709 (36328) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 3.635 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 283 LYS cc_start: 0.9203 (tttt) cc_final: 0.8946 (mmtm) REVERT: A 354 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8414 (mt-10) REVERT: A 577 GLN cc_start: 0.9229 (tp40) cc_final: 0.8855 (tp40) REVERT: A 737 ASN cc_start: 0.9294 (m-40) cc_final: 0.8947 (m110) REVERT: A 752 LEU cc_start: 0.9416 (mm) cc_final: 0.9215 (mm) REVERT: A 840 ASP cc_start: 0.9299 (t70) cc_final: 0.9066 (t70) REVERT: A 847 ARG cc_start: 0.8465 (tmt170) cc_final: 0.8151 (tpt90) REVERT: B 242 ARG cc_start: 0.8291 (ttt-90) cc_final: 0.8029 (ttm-80) REVERT: B 255 ILE cc_start: 0.8519 (mm) cc_final: 0.8258 (mm) REVERT: B 283 LYS cc_start: 0.9220 (tttt) cc_final: 0.8981 (mmtm) REVERT: B 354 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8012 (mt-10) REVERT: B 387 MET cc_start: 0.8802 (tpt) cc_final: 0.8466 (tpt) REVERT: B 840 ASP cc_start: 0.9463 (t0) cc_final: 0.9221 (t0) REVERT: B 847 ARG cc_start: 0.8402 (tmt170) cc_final: 0.8069 (tpt90) REVERT: C 255 ILE cc_start: 0.8529 (mm) cc_final: 0.8219 (mm) REVERT: C 354 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8425 (mt-10) REVERT: C 387 MET cc_start: 0.9020 (tpp) cc_final: 0.8797 (tpp) REVERT: C 418 LEU cc_start: 0.9409 (tt) cc_final: 0.9053 (mt) REVERT: C 577 GLN cc_start: 0.9272 (tp40) cc_final: 0.8709 (tp40) REVERT: C 752 LEU cc_start: 0.9382 (mm) cc_final: 0.9176 (mm) REVERT: C 847 ARG cc_start: 0.8568 (tmt170) cc_final: 0.8143 (tpt90) REVERT: C 852 PHE cc_start: 0.9253 (m-80) cc_final: 0.8984 (m-80) REVERT: D 255 ILE cc_start: 0.8696 (mm) cc_final: 0.8460 (mm) REVERT: D 283 LYS cc_start: 0.9128 (tttt) cc_final: 0.8843 (tppt) REVERT: D 354 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8103 (mt-10) REVERT: D 577 GLN cc_start: 0.9248 (tp40) cc_final: 0.8761 (tp40) REVERT: D 752 LEU cc_start: 0.9449 (mm) cc_final: 0.9195 (mm) REVERT: D 809 CYS cc_start: 0.9310 (t) cc_final: 0.8961 (p) REVERT: D 840 ASP cc_start: 0.9387 (t70) cc_final: 0.9013 (t0) REVERT: D 847 ARG cc_start: 0.8438 (tmt170) cc_final: 0.7913 (tpt90) REVERT: D 873 PHE cc_start: 0.9277 (t80) cc_final: 0.8441 (m-10) REVERT: D 1071 ASP cc_start: 0.8659 (t0) cc_final: 0.8456 (t0) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.3499 time to fit residues: 203.8630 Evaluate side-chains 278 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 328 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 349 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 226 optimal weight: 1.9990 chunk 292 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 337 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 HIS ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS C 423 HIS ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS D 423 HIS ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.093412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069081 restraints weight = 122437.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.070579 restraints weight = 74636.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.071543 restraints weight = 53702.764| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26532 Z= 0.111 Angle : 0.547 10.723 36328 Z= 0.279 Chirality : 0.037 0.170 4360 Planarity : 0.004 0.042 4624 Dihedral : 4.060 22.819 3852 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.14), residues: 3580 helix: 1.96 (0.11), residues: 2340 sheet: 0.55 (0.36), residues: 184 loop : -0.79 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 253 HIS 0.004 0.001 HIS B 625 PHE 0.023 0.001 PHE B 289 TYR 0.008 0.001 TYR B 886 ARG 0.005 0.000 ARG D1083 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 1685) hydrogen bonds : angle 4.22006 ( 4983) covalent geometry : bond 0.00231 (26532) covalent geometry : angle 0.54652 (36328) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ILE cc_start: 0.8342 (mm) cc_final: 0.8131 (mm) REVERT: A 368 LYS cc_start: 0.9445 (tptp) cc_final: 0.9223 (tppt) REVERT: A 387 MET cc_start: 0.9122 (tpp) cc_final: 0.8675 (tpp) REVERT: A 577 GLN cc_start: 0.9217 (tp40) cc_final: 0.8775 (tp40) REVERT: A 737 ASN cc_start: 0.9240 (m-40) cc_final: 0.9010 (m-40) REVERT: A 840 ASP cc_start: 0.9297 (t70) cc_final: 0.9009 (t70) REVERT: A 847 ARG cc_start: 0.8364 (tmt170) cc_final: 0.8103 (tpt90) REVERT: A 852 PHE cc_start: 0.9129 (m-80) cc_final: 0.8879 (m-80) REVERT: B 242 ARG cc_start: 0.8231 (ttt-90) cc_final: 0.7974 (ttm-80) REVERT: B 255 ILE cc_start: 0.8281 (mm) cc_final: 0.8016 (mm) REVERT: B 319 TYR cc_start: 0.7966 (t80) cc_final: 0.7572 (t80) REVERT: B 354 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 368 LYS cc_start: 0.9465 (tptp) cc_final: 0.9257 (tppt) REVERT: B 387 MET cc_start: 0.8962 (tpt) cc_final: 0.8691 (tpp) REVERT: B 577 GLN cc_start: 0.9120 (tp40) cc_final: 0.8610 (tp40) REVERT: B 752 LEU cc_start: 0.9368 (mm) cc_final: 0.8969 (mp) REVERT: B 847 ARG cc_start: 0.8305 (tmt170) cc_final: 0.8029 (tpt90) REVERT: B 852 PHE cc_start: 0.9066 (m-80) cc_final: 0.8791 (m-80) REVERT: C 255 ILE cc_start: 0.8155 (mm) cc_final: 0.7878 (mm) REVERT: C 368 LYS cc_start: 0.9451 (tptp) cc_final: 0.9216 (tppt) REVERT: C 387 MET cc_start: 0.9005 (tpp) cc_final: 0.8628 (tpp) REVERT: C 577 GLN cc_start: 0.9154 (tp40) cc_final: 0.8437 (tp-100) REVERT: C 840 ASP cc_start: 0.9393 (t70) cc_final: 0.9079 (t70) REVERT: C 847 ARG cc_start: 0.8478 (tmt170) cc_final: 0.8064 (tpt90) REVERT: C 852 PHE cc_start: 0.9276 (m-80) cc_final: 0.9038 (m-80) REVERT: D 255 ILE cc_start: 0.8367 (mm) cc_final: 0.8166 (mm) REVERT: D 354 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8056 (mt-10) REVERT: D 577 GLN cc_start: 0.9118 (tp40) cc_final: 0.8568 (tp40) REVERT: D 847 ARG cc_start: 0.8297 (tmt170) cc_final: 0.7883 (tpt90) REVERT: D 873 PHE cc_start: 0.9324 (t80) cc_final: 0.8529 (m-80) REVERT: D 1071 ASP cc_start: 0.8596 (t0) cc_final: 0.8363 (t0) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.3249 time to fit residues: 201.2424 Evaluate side-chains 288 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 99 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 265 optimal weight: 50.0000 chunk 51 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS C 184 HIS C 284 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.091980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.067797 restraints weight = 125202.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069170 restraints weight = 79124.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070064 restraints weight = 58256.341| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26532 Z= 0.169 Angle : 0.595 8.880 36328 Z= 0.306 Chirality : 0.038 0.166 4360 Planarity : 0.004 0.041 4624 Dihedral : 4.111 23.083 3852 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.14), residues: 3580 helix: 1.93 (0.11), residues: 2340 sheet: 0.49 (0.36), residues: 184 loop : -0.77 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 60 HIS 0.007 0.001 HIS C 612 PHE 0.019 0.002 PHE B 289 TYR 0.012 0.001 TYR C 587 ARG 0.012 0.000 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 1685) hydrogen bonds : angle 4.39271 ( 4983) covalent geometry : bond 0.00356 (26532) covalent geometry : angle 0.59505 (36328) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8339 (mt-10) REVERT: A 577 GLN cc_start: 0.9327 (tp40) cc_final: 0.8957 (tp40) REVERT: A 737 ASN cc_start: 0.9273 (m-40) cc_final: 0.9053 (m-40) REVERT: A 840 ASP cc_start: 0.9290 (t70) cc_final: 0.9005 (t70) REVERT: A 847 ARG cc_start: 0.8379 (tmt170) cc_final: 0.8113 (tpt90) REVERT: A 852 PHE cc_start: 0.9084 (m-80) cc_final: 0.8806 (m-80) REVERT: B 242 ARG cc_start: 0.8312 (ttt-90) cc_final: 0.8024 (ttm-80) REVERT: B 255 ILE cc_start: 0.8369 (mm) cc_final: 0.8048 (mm) REVERT: B 319 TYR cc_start: 0.8035 (t80) cc_final: 0.7639 (t80) REVERT: B 387 MET cc_start: 0.8940 (tpt) cc_final: 0.8615 (tpt) REVERT: B 840 ASP cc_start: 0.9432 (t70) cc_final: 0.9120 (t0) REVERT: B 847 ARG cc_start: 0.8318 (tmt170) cc_final: 0.8038 (tpt90) REVERT: B 852 PHE cc_start: 0.9081 (m-80) cc_final: 0.8810 (m-80) REVERT: B 1071 ASP cc_start: 0.8327 (t0) cc_final: 0.8076 (t0) REVERT: C 255 ILE cc_start: 0.8332 (mm) cc_final: 0.8061 (mm) REVERT: C 354 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8330 (mt-10) REVERT: C 368 LYS cc_start: 0.9473 (tptp) cc_final: 0.9257 (tppt) REVERT: C 418 LEU cc_start: 0.9367 (tt) cc_final: 0.8994 (mt) REVERT: C 577 GLN cc_start: 0.9112 (tp40) cc_final: 0.8528 (tp40) REVERT: C 840 ASP cc_start: 0.9381 (t70) cc_final: 0.9120 (t70) REVERT: C 847 ARG cc_start: 0.8476 (tmt170) cc_final: 0.8066 (tpt90) REVERT: C 852 PHE cc_start: 0.9252 (m-80) cc_final: 0.9008 (m-80) REVERT: D 255 ILE cc_start: 0.8537 (mm) cc_final: 0.8289 (mm) REVERT: D 354 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8258 (mt-10) REVERT: D 418 LEU cc_start: 0.9428 (tt) cc_final: 0.8995 (mt) REVERT: D 576 GLU cc_start: 0.8693 (tt0) cc_final: 0.8428 (tt0) REVERT: D 577 GLN cc_start: 0.9222 (tp40) cc_final: 0.8850 (tp40) REVERT: D 752 LEU cc_start: 0.9406 (mm) cc_final: 0.9191 (mm) REVERT: D 847 ARG cc_start: 0.8327 (tmt170) cc_final: 0.7880 (tpt90) REVERT: D 873 PHE cc_start: 0.9257 (t80) cc_final: 0.8514 (m-80) REVERT: D 1071 ASP cc_start: 0.8698 (t0) cc_final: 0.8485 (t0) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.3344 time to fit residues: 199.8999 Evaluate side-chains 284 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 323 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 236 optimal weight: 0.9990 chunk 349 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 273 optimal weight: 0.9980 chunk 317 optimal weight: 0.0070 chunk 355 optimal weight: 20.0000 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS C 184 HIS ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.092754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.068679 restraints weight = 123673.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.070049 restraints weight = 78035.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.070935 restraints weight = 57547.019| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26532 Z= 0.134 Angle : 0.569 12.232 36328 Z= 0.289 Chirality : 0.038 0.168 4360 Planarity : 0.004 0.041 4624 Dihedral : 4.021 23.720 3852 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.14), residues: 3580 helix: 1.99 (0.11), residues: 2336 sheet: 0.58 (0.36), residues: 184 loop : -0.79 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 60 HIS 0.006 0.001 HIS C 625 PHE 0.023 0.001 PHE A 877 TYR 0.008 0.001 TYR B 587 ARG 0.009 0.000 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 1685) hydrogen bonds : angle 4.24961 ( 4983) covalent geometry : bond 0.00283 (26532) covalent geometry : angle 0.56901 (36328) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 TYR cc_start: 0.8339 (t80) cc_final: 0.7792 (t80) REVERT: A 354 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8356 (mt-10) REVERT: A 368 LYS cc_start: 0.9470 (tptp) cc_final: 0.9262 (tppt) REVERT: A 577 GLN cc_start: 0.9300 (tp40) cc_final: 0.8808 (tp40) REVERT: A 737 ASN cc_start: 0.9255 (m-40) cc_final: 0.9041 (m-40) REVERT: A 840 ASP cc_start: 0.9282 (t70) cc_final: 0.9006 (t70) REVERT: A 847 ARG cc_start: 0.8347 (tmt170) cc_final: 0.8091 (tpt90) REVERT: A 852 PHE cc_start: 0.9053 (m-80) cc_final: 0.8783 (m-80) REVERT: B 242 ARG cc_start: 0.8285 (ttt-90) cc_final: 0.8026 (ttm170) REVERT: B 255 ILE cc_start: 0.8298 (mm) cc_final: 0.7977 (mm) REVERT: B 319 TYR cc_start: 0.7936 (t80) cc_final: 0.7503 (t80) REVERT: B 354 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8139 (mt-10) REVERT: B 368 LYS cc_start: 0.9461 (tptp) cc_final: 0.9259 (tppt) REVERT: B 577 GLN cc_start: 0.9163 (tp40) cc_final: 0.8766 (tp-100) REVERT: B 752 LEU cc_start: 0.9357 (mm) cc_final: 0.9151 (mm) REVERT: B 840 ASP cc_start: 0.9426 (t70) cc_final: 0.9124 (t0) REVERT: B 847 ARG cc_start: 0.8262 (tmt170) cc_final: 0.7997 (tpt90) REVERT: B 852 PHE cc_start: 0.9077 (m-80) cc_final: 0.8831 (m-80) REVERT: B 1071 ASP cc_start: 0.8335 (t0) cc_final: 0.8093 (t0) REVERT: C 90 LYS cc_start: 0.9304 (mmmt) cc_final: 0.9079 (mmmt) REVERT: C 255 ILE cc_start: 0.8227 (mm) cc_final: 0.7943 (mm) REVERT: C 354 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8346 (mt-10) REVERT: C 368 LYS cc_start: 0.9455 (tptp) cc_final: 0.9224 (tppt) REVERT: C 387 MET cc_start: 0.8986 (tpp) cc_final: 0.8642 (tpp) REVERT: C 577 GLN cc_start: 0.9068 (tp40) cc_final: 0.8541 (tp40) REVERT: C 840 ASP cc_start: 0.9383 (t70) cc_final: 0.9088 (t70) REVERT: C 847 ARG cc_start: 0.8503 (tmt170) cc_final: 0.8081 (tpt90) REVERT: C 852 PHE cc_start: 0.9249 (m-80) cc_final: 0.9027 (m-80) REVERT: D 255 ILE cc_start: 0.8375 (mm) cc_final: 0.8161 (mm) REVERT: D 354 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8177 (mt-10) REVERT: D 418 LEU cc_start: 0.9400 (tt) cc_final: 0.8959 (mt) REVERT: D 570 MET cc_start: 0.8886 (ptm) cc_final: 0.8643 (ptp) REVERT: D 576 GLU cc_start: 0.8650 (tt0) cc_final: 0.8390 (tt0) REVERT: D 577 GLN cc_start: 0.9200 (tp40) cc_final: 0.8632 (tp40) REVERT: D 752 LEU cc_start: 0.9408 (mm) cc_final: 0.9182 (mm) REVERT: D 847 ARG cc_start: 0.8270 (tmt170) cc_final: 0.7834 (tpt90) REVERT: D 1071 ASP cc_start: 0.8666 (t0) cc_final: 0.8448 (t0) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.3299 time to fit residues: 200.2574 Evaluate side-chains 286 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 204 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 326 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 312 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 951 ASN ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS D 272 GLN ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.090235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.065944 restraints weight = 123327.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.067375 restraints weight = 76044.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.068315 restraints weight = 55344.141| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26532 Z= 0.237 Angle : 0.674 12.195 36328 Z= 0.346 Chirality : 0.040 0.184 4360 Planarity : 0.004 0.041 4624 Dihedral : 4.370 23.237 3852 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3580 helix: 1.61 (0.11), residues: 2368 sheet: 0.33 (0.36), residues: 184 loop : -1.04 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 60 HIS 0.007 0.002 HIS C 625 PHE 0.031 0.002 PHE D 877 TYR 0.016 0.002 TYR B 587 ARG 0.010 0.001 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 1685) hydrogen bonds : angle 4.69705 ( 4983) covalent geometry : bond 0.00500 (26532) covalent geometry : angle 0.67407 (36328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8200.05 seconds wall clock time: 143 minutes 43.50 seconds (8623.50 seconds total)