Starting phenix.real_space_refine on Sun Jun 22 16:32:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8slw_40581/06_2025/8slw_40581.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slw_40581/06_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_40581/06_2025/8slw_40581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slw_40581/06_2025/8slw_40581.map" model { file = "/net/cci-nas-00/data/ceres_data/8slw_40581/06_2025/8slw_40581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slw_40581/06_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-5710/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: 14.75, per 1000 atoms: 0.57 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: 6.63 Conformation dependent library (CDL) restraints added in 3.5 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: 2.95 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: 9.13 Time building geometry restraints manager: 7.79 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 56.310 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.640 ------------------------------------------------------------------------------- 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 : 3.002 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: 0.3568 time to fit residues: 333.5815 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 : 2.998 ------------------------------------------------------------------------------- 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 = 120604.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071722 restraints weight = 74238.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072705 restraints weight = 53654.999| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2407 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 : 0.581 7.643 36328 Z= 0.312 Chirality : 0.039 0.163 4360 Planarity : 0.005 0.050 4624 Dihedral : 4.124 19.689 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 0.04636 ( 1685) hydrogen bonds : angle 4.96159 ( 4983) covalent geometry : bond 0.00313 (26532) covalent geometry : angle 0.58145 (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 : 2.841 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: 0.8740 (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: 0.9215 (mt) REVERT: A 577 GLN cc_start: 0.9145 (tp40) cc_final: 0.8743 (tp40) REVERT: A 840 ASP cc_start: 0.9225 (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: 0.8538 (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: 0.8653 (tpt) cc_final: 0.8403 (tpp) REVERT: B 577 GLN cc_start: 0.9108 (tp40) cc_final: 0.8779 (tp-100) REVERT: B 847 ARG cc_start: 0.8633 (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: 0.9231 (mt) REVERT: C 401 LEU cc_start: 0.9805 (tp) cc_final: 0.9527 (tt) REVERT: C 577 GLN cc_start: 0.9135 (tp40) cc_final: 0.8825 (tp-100) REVERT: C 840 ASP cc_start: 0.9314 (t70) cc_final: 0.9107 (t70) REVERT: C 847 ARG cc_start: 0.8747 (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: 0.9161 (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: 0.3237 time to fit residues: 252.0787 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 : 2.969 ------------------------------------------------------------------------------- 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: 1.9990 chunk 169 optimal weight: 40.0000 chunk 269 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 296 optimal weight: 0.6980 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: 2.7388 ------------------------------------------------------------------------------- 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 850 HIS B 284 GLN ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS C 184 HIS C 210 HIS C 284 GLN ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS D 184 HIS D 210 HIS ** 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 = 0.3731 r_free = 0.3731 target = 0.093280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.069023 restraints weight = 121136.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.070463 restraints weight = 74947.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.071392 restraints weight = 54426.419| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26532 Z= 0.190 Angle : 0.595 8.443 36328 Z= 0.312 Chirality : 0.038 0.162 4360 Planarity : 0.004 0.049 4624 Dihedral : 4.152 17.267 3852 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: 1.01 (0.14), residues: 3580 helix: 1.50 (0.11), residues: 2332 sheet: -0.16 (0.34), residues: 216 loop : -1.03 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 723 HIS 0.006 0.001 HIS C 184 PHE 0.023 0.002 PHE C 289 TYR 0.015 0.002 TYR D 535 ARG 0.005 0.001 ARG C1083 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 1685) hydrogen bonds : angle 4.77625 ( 4983) covalent geometry : bond 0.00396 (26532) covalent geometry : angle 0.59458 (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 421 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 2.878 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: A 255 ILE cc_start: 0.8761 (mm) cc_final: 0.8441 (mm) REVERT: A 283 LYS cc_start: 0.9108 (tttt) cc_final: 0.8895 (tppt) REVERT: A 357 LEU cc_start: 0.9207 (tp) cc_final: 0.9001 (tp) REVERT: A 434 LEU cc_start: 0.9631 (mt) cc_final: 0.9189 (mt) REVERT: A 577 GLN cc_start: 0.9210 (tp40) cc_final: 0.8529 (tp-100) REVERT: A 809 CYS cc_start: 0.8613 (m) cc_final: 0.8347 (p) REVERT: A 840 ASP cc_start: 0.9200 (t70) cc_final: 0.8911 (t70) REVERT: A 847 ARG cc_start: 0.8698 (tmt170) cc_final: 0.8200 (tpt90) REVERT: A 873 PHE cc_start: 0.8952 (t80) cc_final: 0.8421 (m-80) REVERT: B 90 LYS cc_start: 0.9415 (mmmt) cc_final: 0.9129 (mmmm) REVERT: B 255 ILE cc_start: 0.8573 (mm) cc_final: 0.8282 (mm) REVERT: B 283 LYS cc_start: 0.9196 (tttt) cc_final: 0.8970 (tppt) REVERT: B 401 LEU cc_start: 0.9798 (tp) cc_final: 0.9559 (tt) REVERT: B 577 GLN cc_start: 0.9206 (tp40) cc_final: 0.8549 (tp-100) REVERT: B 752 LEU cc_start: 0.9291 (mm) cc_final: 0.9088 (mm) REVERT: B 840 ASP cc_start: 0.9456 (t70) cc_final: 0.9190 (t0) REVERT: B 847 ARG cc_start: 0.8522 (tmt170) cc_final: 0.8032 (tpt90) REVERT: B 873 PHE cc_start: 0.9160 (t80) cc_final: 0.8567 (m-80) REVERT: C 255 ILE cc_start: 0.8390 (mm) cc_final: 0.8131 (mm) REVERT: C 577 GLN cc_start: 0.9229 (tp40) cc_final: 0.8506 (tp-100) REVERT: C 809 CYS cc_start: 0.8627 (m) cc_final: 0.8257 (p) REVERT: C 840 ASP cc_start: 0.9322 (t70) cc_final: 0.9078 (t70) REVERT: C 847 ARG cc_start: 0.8820 (tmt170) cc_final: 0.8188 (tpt90) REVERT: C 852 PHE cc_start: 0.9145 (m-80) cc_final: 0.8922 (m-80) REVERT: C 873 PHE cc_start: 0.8985 (t80) cc_final: 0.8206 (m-80) REVERT: D 255 ILE cc_start: 0.8701 (mm) cc_final: 0.8350 (mm) REVERT: D 283 LYS cc_start: 0.9096 (tttt) cc_final: 0.8824 (tppt) REVERT: D 401 LEU cc_start: 0.9781 (tp) cc_final: 0.9539 (tt) REVERT: D 570 MET cc_start: 0.8569 (ptm) cc_final: 0.8269 (ptp) REVERT: D 576 GLU cc_start: 0.8690 (tt0) cc_final: 0.8447 (tt0) REVERT: D 577 GLN cc_start: 0.9217 (tp40) cc_final: 0.8551 (tp-100) REVERT: D 752 LEU cc_start: 0.9393 (mm) cc_final: 0.9168 (mm) REVERT: D 847 ARG cc_start: 0.8709 (tmt170) cc_final: 0.8246 (tpt90) REVERT: D 852 PHE cc_start: 0.8805 (m-80) cc_final: 0.8122 (m-80) REVERT: D 873 PHE cc_start: 0.9007 (t80) cc_final: 0.8394 (m-80) REVERT: D 1071 ASP cc_start: 0.8392 (t0) cc_final: 0.8161 (t0) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.3279 time to fit residues: 227.8455 Evaluate side-chains 313 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 2.903 ------------------------------------------------------------------------------- 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: 9.9990 chunk 99 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 346 optimal weight: 3.9990 chunk 103 optimal weight: 0.0000 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 602 ASN ** 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 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.094141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.070110 restraints weight = 121909.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.071588 restraints weight = 74904.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.072483 restraints weight = 54004.984| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26532 Z= 0.122 Angle : 0.526 8.045 36328 Z= 0.274 Chirality : 0.036 0.157 4360 Planarity : 0.004 0.050 4624 Dihedral : 3.908 21.354 3852 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.14 % Allowed : 1.91 % Favored : 97.95 % 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: 1.78 (0.11), residues: 2328 sheet: 0.17 (0.32), residues: 236 loop : -0.89 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 361 HIS 0.007 0.001 HIS B 998 PHE 0.027 0.001 PHE B 994 TYR 0.011 0.001 TYR B 886 ARG 0.007 0.000 ARG B1083 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1685) hydrogen bonds : angle 4.39191 ( 4983) covalent geometry : bond 0.00254 (26532) covalent geometry : angle 0.52638 (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 440 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 437 time to evaluate : 2.991 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 253 TRP cc_start: 0.6508 (m100) cc_final: 0.6262 (m100) REVERT: A 255 ILE cc_start: 0.8676 (mm) cc_final: 0.8293 (mm) REVERT: A 283 LYS cc_start: 0.9102 (tttt) cc_final: 0.8850 (mmtm) REVERT: A 434 LEU cc_start: 0.9601 (mt) cc_final: 0.9139 (mt) REVERT: A 577 GLN cc_start: 0.9260 (tp40) cc_final: 0.8701 (tp40) REVERT: A 737 ASN cc_start: 0.9205 (m110) cc_final: 0.8982 (m-40) REVERT: A 840 ASP cc_start: 0.9245 (t70) cc_final: 0.9032 (t70) REVERT: A 847 ARG cc_start: 0.8605 (tmt170) cc_final: 0.8216 (tpt90) REVERT: A 873 PHE cc_start: 0.8979 (t80) cc_final: 0.8367 (m-80) REVERT: B 90 LYS cc_start: 0.9374 (mmmt) cc_final: 0.8867 (mmmt) REVERT: B 255 ILE cc_start: 0.8440 (mm) cc_final: 0.8165 (mm) REVERT: B 283 LYS cc_start: 0.9174 (tttt) cc_final: 0.8934 (tppt) REVERT: B 387 MET cc_start: 0.8897 (tpt) cc_final: 0.8659 (tpp) REVERT: B 401 LEU cc_start: 0.9760 (tp) cc_final: 0.9499 (tt) REVERT: B 577 GLN cc_start: 0.9289 (tp40) cc_final: 0.8714 (tp40) REVERT: B 752 LEU cc_start: 0.9256 (mm) cc_final: 0.8994 (mm) REVERT: B 840 ASP cc_start: 0.9500 (t70) cc_final: 0.9273 (t0) REVERT: B 847 ARG cc_start: 0.8388 (tmt170) cc_final: 0.7985 (tpt90) REVERT: B 873 PHE cc_start: 0.9166 (t80) cc_final: 0.8647 (m-80) REVERT: C 90 LYS cc_start: 0.9279 (mmmt) cc_final: 0.8999 (mmmt) REVERT: C 255 ILE cc_start: 0.8361 (mm) cc_final: 0.8105 (mm) REVERT: C 413 LEU cc_start: 0.9357 (tp) cc_final: 0.9150 (tt) REVERT: C 577 GLN cc_start: 0.9286 (tp40) cc_final: 0.8865 (tp40) REVERT: C 840 ASP cc_start: 0.9339 (t70) cc_final: 0.9060 (t70) REVERT: C 847 ARG cc_start: 0.8709 (tmt170) cc_final: 0.8143 (tpt90) REVERT: C 852 PHE cc_start: 0.9250 (m-80) cc_final: 0.9016 (m-80) REVERT: D 255 ILE cc_start: 0.8647 (mm) cc_final: 0.8322 (mm) REVERT: D 577 GLN cc_start: 0.9275 (tp40) cc_final: 0.8728 (tp40) REVERT: D 752 LEU cc_start: 0.9384 (mm) cc_final: 0.9116 (mm) REVERT: D 847 ARG cc_start: 0.8549 (tmt170) cc_final: 0.8149 (tpt90) REVERT: D 852 PHE cc_start: 0.9036 (m-80) cc_final: 0.8414 (m-80) REVERT: D 873 PHE cc_start: 0.9058 (t80) cc_final: 0.8419 (m-80) outliers start: 3 outliers final: 0 residues processed: 438 average time/residue: 0.3336 time to fit residues: 239.9807 Evaluate side-chains 305 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 3.134 ------------------------------------------------------------------------------- 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: 0.0470 chunk 93 optimal weight: 4.9990 chunk 346 optimal weight: 8.9990 chunk 170 optimal weight: 40.0000 chunk 152 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 294 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN 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 214 GLN B 394 ASN ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS C 214 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS D 214 GLN D 284 GLN D 394 ASN D 602 ASN ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.091474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.067043 restraints weight = 123050.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.068464 restraints weight = 75817.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069301 restraints weight = 55152.272| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26532 Z= 0.221 Angle : 0.642 8.404 36328 Z= 0.332 Chirality : 0.039 0.159 4360 Planarity : 0.005 0.090 4624 Dihedral : 4.294 16.738 3852 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.09 % Allowed : 2.15 % Favored : 97.76 % 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: 1.24 (0.14), residues: 3580 helix: 1.58 (0.11), residues: 2348 sheet: 0.23 (0.38), residues: 164 loop : -0.74 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 723 HIS 0.007 0.002 HIS A 603 PHE 0.023 0.002 PHE B 583 TYR 0.014 0.002 TYR C 587 ARG 0.006 0.001 ARG B 518 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 1685) hydrogen bonds : angle 4.76664 ( 4983) covalent geometry : bond 0.00462 (26532) covalent geometry : angle 0.64191 (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 376 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ILE cc_start: 0.8754 (mm) cc_final: 0.8407 (mm) REVERT: A 283 LYS cc_start: 0.9142 (tttt) cc_final: 0.8897 (mmtm) REVERT: A 354 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8210 (mt-10) REVERT: A 357 LEU cc_start: 0.9254 (tp) cc_final: 0.9052 (tp) REVERT: A 577 GLN cc_start: 0.9265 (tp40) cc_final: 0.8523 (tp-100) REVERT: A 752 LEU cc_start: 0.9424 (mm) cc_final: 0.9223 (mm) REVERT: A 847 ARG cc_start: 0.8415 (tmt170) cc_final: 0.8129 (tpt90) REVERT: A 873 PHE cc_start: 0.9128 (t80) cc_final: 0.8398 (m-80) REVERT: B 255 ILE cc_start: 0.8546 (mm) cc_final: 0.8206 (mm) REVERT: B 283 LYS cc_start: 0.9204 (tttt) cc_final: 0.8994 (tppt) REVERT: B 387 MET cc_start: 0.8761 (tpt) cc_final: 0.8459 (tpt) REVERT: B 577 GLN cc_start: 0.9254 (tp40) cc_final: 0.8534 (tp-100) REVERT: B 752 LEU cc_start: 0.9365 (mm) cc_final: 0.9140 (mm) REVERT: B 840 ASP cc_start: 0.9475 (t70) cc_final: 0.9264 (t0) REVERT: B 847 ARG cc_start: 0.8283 (tmt170) cc_final: 0.7945 (tpt90) REVERT: B 873 PHE cc_start: 0.9260 (t80) cc_final: 0.8535 (m-80) REVERT: C 90 LYS cc_start: 0.9290 (mmmt) cc_final: 0.8920 (mmmt) REVERT: C 255 ILE cc_start: 0.8628 (mm) cc_final: 0.8331 (mm) REVERT: C 354 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8333 (mt-10) REVERT: C 577 GLN cc_start: 0.9231 (tp40) cc_final: 0.8646 (tp40) REVERT: C 752 LEU cc_start: 0.9352 (mm) cc_final: 0.9146 (mm) REVERT: C 840 ASP cc_start: 0.9356 (t70) cc_final: 0.9141 (t70) REVERT: C 847 ARG cc_start: 0.8687 (tmt170) cc_final: 0.8172 (tpt90) REVERT: C 852 PHE cc_start: 0.9246 (m-80) cc_final: 0.8944 (m-80) REVERT: D 242 ARG cc_start: 0.8102 (ttt-90) cc_final: 0.7900 (ptm160) REVERT: D 255 ILE cc_start: 0.8820 (mm) cc_final: 0.8502 (mm) REVERT: D 576 GLU cc_start: 0.8705 (tt0) cc_final: 0.8462 (tt0) REVERT: D 577 GLN cc_start: 0.9250 (tp40) cc_final: 0.8778 (tp40) REVERT: D 752 LEU cc_start: 0.9438 (mm) cc_final: 0.9221 (mm) REVERT: D 847 ARG cc_start: 0.8449 (tmt170) cc_final: 0.8017 (tpt90) REVERT: D 873 PHE cc_start: 0.9173 (t80) cc_final: 0.8395 (m-80) outliers start: 2 outliers final: 0 residues processed: 376 average time/residue: 0.3374 time to fit residues: 210.4568 Evaluate side-chains 283 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 2.804 ------------------------------------------------------------------------------- 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: 7.9990 chunk 281 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 0 optimal weight: 60.0000 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 297 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 737 ASN 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 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 = 0.3700 r_free = 0.3700 target = 0.091653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.067460 restraints weight = 124948.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.068780 restraints weight = 79398.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.069583 restraints weight = 58938.175| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 0.055 26532 Z= 0.207 Angle : 0.605 9.762 36328 Z= 0.314 Chirality : 0.038 0.171 4360 Planarity : 0.004 0.042 4624 Dihedral : 4.239 21.748 3852 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: 1.37 (0.14), residues: 3580 helix: 1.72 (0.11), residues: 2348 sheet: 0.44 (0.36), residues: 184 loop : -0.84 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 723 HIS 0.005 0.001 HIS A 184 PHE 0.027 0.002 PHE B 289 TYR 0.013 0.002 TYR B 587 ARG 0.004 0.000 ARG B 518 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 1685) hydrogen bonds : angle 4.61404 ( 4983) covalent geometry : bond 0.00435 (26532) covalent geometry : angle 0.60542 (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 372 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ILE cc_start: 0.8729 (mm) cc_final: 0.8364 (mm) REVERT: A 283 LYS cc_start: 0.9175 (tttt) cc_final: 0.8905 (mmtm) REVERT: A 354 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8369 (mt-10) REVERT: A 577 GLN cc_start: 0.9234 (tp40) cc_final: 0.8771 (tp40) REVERT: A 752 LEU cc_start: 0.9407 (mm) cc_final: 0.9186 (mm) REVERT: A 840 ASP cc_start: 0.9349 (t0) cc_final: 0.9138 (t70) REVERT: A 847 ARG cc_start: 0.8410 (tmt170) cc_final: 0.8124 (tpt90) REVERT: A 852 PHE cc_start: 0.9079 (m-80) cc_final: 0.8835 (m-80) REVERT: A 873 PHE cc_start: 0.9219 (t80) cc_final: 0.8492 (m-80) REVERT: B 255 ILE cc_start: 0.8516 (mm) cc_final: 0.8153 (mm) REVERT: B 283 LYS cc_start: 0.9225 (tttt) cc_final: 0.9004 (tppt) REVERT: B 354 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8064 (mt-10) REVERT: B 577 GLN cc_start: 0.9215 (tp40) cc_final: 0.8640 (tp40) REVERT: B 752 LEU cc_start: 0.9358 (mm) cc_final: 0.9134 (mm) REVERT: B 847 ARG cc_start: 0.8394 (tmt170) cc_final: 0.8140 (tpt90) REVERT: C 255 ILE cc_start: 0.8533 (mm) cc_final: 0.8154 (mm) REVERT: C 354 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8311 (mt-10) REVERT: C 418 LEU cc_start: 0.9359 (tt) cc_final: 0.9068 (mt) REVERT: C 577 GLN cc_start: 0.9205 (tp40) cc_final: 0.8358 (tp-100) REVERT: C 752 LEU cc_start: 0.9404 (mm) cc_final: 0.9197 (mm) REVERT: C 840 ASP cc_start: 0.9355 (t70) cc_final: 0.9122 (t70) REVERT: C 847 ARG cc_start: 0.8539 (tmt170) cc_final: 0.8123 (tpt90) REVERT: C 852 PHE cc_start: 0.9240 (m-80) cc_final: 0.8960 (m-80) REVERT: D 242 ARG cc_start: 0.8186 (ttt-90) cc_final: 0.7915 (ptm160) REVERT: D 255 ILE cc_start: 0.8709 (mm) cc_final: 0.8435 (mm) REVERT: D 283 LYS cc_start: 0.9105 (tttt) cc_final: 0.8818 (tppt) REVERT: D 319 TYR cc_start: 0.8073 (t80) cc_final: 0.7846 (t80) REVERT: D 576 GLU cc_start: 0.8710 (tt0) cc_final: 0.8454 (tt0) REVERT: D 577 GLN cc_start: 0.9234 (tp40) cc_final: 0.8786 (tp40) REVERT: D 752 LEU cc_start: 0.9424 (mm) cc_final: 0.9199 (mm) REVERT: D 840 ASP cc_start: 0.9395 (t70) cc_final: 0.9027 (t70) REVERT: D 847 ARG cc_start: 0.8319 (tmt170) cc_final: 0.7982 (tpt90) REVERT: D 873 PHE cc_start: 0.9243 (t80) cc_final: 0.8484 (m-80) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.3683 time to fit residues: 228.0134 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 : 2.907 ------------------------------------------------------------------------------- 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: 0.8980 chunk 132 optimal weight: 5.9990 chunk 284 optimal weight: 30.0000 chunk 361 optimal weight: 4.9990 chunk 295 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.090544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066595 restraints weight = 123381.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.068012 restraints weight = 75830.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.068927 restraints weight = 55095.274| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26532 Z= 0.222 Angle : 0.632 9.724 36328 Z= 0.327 Chirality : 0.039 0.180 4360 Planarity : 0.004 0.042 4624 Dihedral : 4.360 17.080 3852 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: 1.21 (0.14), residues: 3580 helix: 1.60 (0.11), residues: 2368 sheet: 0.08 (0.37), residues: 164 loop : -0.90 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 361 HIS 0.005 0.001 HIS B 423 PHE 0.018 0.002 PHE A 583 TYR 0.014 0.002 TYR B 587 ARG 0.004 0.000 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 1685) hydrogen bonds : angle 4.72071 ( 4983) covalent geometry : bond 0.00469 (26532) covalent geometry : angle 0.63231 (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 366 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 2.796 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: A 90 LYS cc_start: 0.9362 (mmmt) cc_final: 0.8877 (mmmt) REVERT: A 255 ILE cc_start: 0.8663 (mm) cc_final: 0.8426 (mm) REVERT: A 283 LYS cc_start: 0.9201 (tttt) cc_final: 0.8957 (mmtm) REVERT: A 354 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8368 (mt-10) REVERT: A 387 MET cc_start: 0.9059 (tpp) cc_final: 0.8729 (tpp) REVERT: A 539 MET cc_start: 0.7893 (mtt) cc_final: 0.7607 (mtt) REVERT: A 577 GLN cc_start: 0.9235 (tp40) cc_final: 0.8720 (tp40) REVERT: A 752 LEU cc_start: 0.9445 (mm) cc_final: 0.9221 (mm) REVERT: A 840 ASP cc_start: 0.9347 (t0) cc_final: 0.9133 (t70) REVERT: A 847 ARG cc_start: 0.8401 (tmt170) cc_final: 0.8105 (tpt90) REVERT: A 852 PHE cc_start: 0.9078 (m-80) cc_final: 0.8837 (m-80) REVERT: A 1071 ASP cc_start: 0.8419 (t0) cc_final: 0.8198 (t0) REVERT: B 114 ARG cc_start: 0.8745 (ptt90) cc_final: 0.8468 (mtt90) REVERT: B 242 ARG cc_start: 0.8275 (ttt-90) cc_final: 0.7844 (ptm-80) REVERT: B 255 ILE cc_start: 0.8522 (mm) cc_final: 0.8257 (mm) REVERT: B 283 LYS cc_start: 0.9216 (tttt) cc_final: 0.8976 (mmtm) REVERT: B 354 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8122 (mt-10) REVERT: B 387 MET cc_start: 0.8859 (tpt) cc_final: 0.8594 (tpt) REVERT: B 847 ARG cc_start: 0.8511 (tmt170) cc_final: 0.7865 (tpt90) REVERT: B 1071 ASP cc_start: 0.8541 (t0) cc_final: 0.8305 (t0) REVERT: C 255 ILE cc_start: 0.8480 (mm) cc_final: 0.8217 (mm) REVERT: C 368 LYS cc_start: 0.9458 (tptp) cc_final: 0.9256 (tppt) REVERT: C 387 MET cc_start: 0.9026 (tpp) cc_final: 0.8772 (tpp) REVERT: C 418 LEU cc_start: 0.9401 (tt) cc_final: 0.9053 (mt) REVERT: C 577 GLN cc_start: 0.9202 (tp40) cc_final: 0.8592 (tp40) REVERT: C 847 ARG cc_start: 0.8581 (tmt170) cc_final: 0.8139 (tpt90) REVERT: C 852 PHE cc_start: 0.9245 (m-80) cc_final: 0.8989 (m-80) REVERT: D 255 ILE cc_start: 0.8693 (mm) cc_final: 0.8459 (mm) REVERT: D 283 LYS cc_start: 0.9109 (tttt) cc_final: 0.8829 (tppt) REVERT: D 319 TYR cc_start: 0.8046 (t80) cc_final: 0.7819 (t80) REVERT: D 354 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8095 (mt-10) REVERT: D 576 GLU cc_start: 0.8691 (tt0) cc_final: 0.8444 (tt0) REVERT: D 577 GLN cc_start: 0.9242 (tp40) cc_final: 0.8786 (tp40) REVERT: D 737 ASN cc_start: 0.9270 (m-40) cc_final: 0.9060 (m-40) REVERT: D 752 LEU cc_start: 0.9447 (mm) cc_final: 0.9207 (mm) REVERT: D 847 ARG cc_start: 0.8406 (tmt170) cc_final: 0.7944 (tpt90) REVERT: D 873 PHE cc_start: 0.9255 (t80) cc_final: 0.8460 (m-10) REVERT: D 1071 ASP cc_start: 0.8456 (t0) cc_final: 0.8249 (t0) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.3459 time to fit residues: 208.4551 Evaluate side-chains 277 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 2.756 ------------------------------------------------------------------------------- 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: 0.6980 chunk 70 optimal weight: 8.9990 chunk 349 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 226 optimal weight: 0.6980 chunk 292 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 337 optimal weight: 0.0050 overall best weight: 1.6798 ------------------------------------------------------------------------------- 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 ** 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 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.092379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.068450 restraints weight = 121123.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.069878 restraints weight = 75000.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.070806 restraints weight = 54565.087| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 26532 Z= 0.132 Angle : 0.559 10.668 36328 Z= 0.285 Chirality : 0.037 0.171 4360 Planarity : 0.004 0.040 4624 Dihedral : 4.089 16.887 3852 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.57 (0.14), residues: 3580 helix: 1.89 (0.11), residues: 2364 sheet: 0.43 (0.36), residues: 184 loop : -0.84 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 253 HIS 0.003 0.001 HIS A 184 PHE 0.016 0.001 PHE B 873 TYR 0.009 0.001 TYR B 587 ARG 0.012 0.000 ARG D 242 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 1685) hydrogen bonds : angle 4.34122 ( 4983) covalent geometry : bond 0.00283 (26532) covalent geometry : angle 0.55863 (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 375 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 2.851 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 255 ILE cc_start: 0.8447 (mm) cc_final: 0.8093 (mm) REVERT: A 319 TYR cc_start: 0.8281 (t80) cc_final: 0.7781 (t80) REVERT: A 387 MET cc_start: 0.9039 (tpp) cc_final: 0.8680 (tpp) REVERT: A 577 GLN cc_start: 0.9164 (tp40) cc_final: 0.8587 (tp40) REVERT: A 840 ASP cc_start: 0.9343 (t0) cc_final: 0.9106 (t70) REVERT: A 847 ARG cc_start: 0.8359 (tmt170) cc_final: 0.8093 (tpt90) REVERT: A 852 PHE cc_start: 0.9063 (m-80) cc_final: 0.8837 (m-80) REVERT: B 242 ARG cc_start: 0.8240 (ttt-90) cc_final: 0.7863 (ptm-80) REVERT: B 255 ILE cc_start: 0.8446 (mm) cc_final: 0.8139 (mm) REVERT: B 283 LYS cc_start: 0.9196 (tttt) cc_final: 0.8954 (mmtm) REVERT: B 354 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8165 (mt-10) REVERT: B 577 GLN cc_start: 0.9161 (tp40) cc_final: 0.8776 (tp-100) REVERT: B 840 ASP cc_start: 0.9457 (t70) cc_final: 0.9226 (t0) REVERT: B 847 ARG cc_start: 0.8323 (tmt170) cc_final: 0.8037 (tpt90) REVERT: B 852 PHE cc_start: 0.9073 (m-80) cc_final: 0.8790 (m-80) REVERT: C 255 ILE cc_start: 0.8367 (mm) cc_final: 0.8097 (mm) REVERT: C 354 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8239 (mt-10) REVERT: C 368 LYS cc_start: 0.9465 (tptp) cc_final: 0.9232 (tppt) REVERT: C 387 MET cc_start: 0.9017 (tpp) cc_final: 0.8655 (tpp) REVERT: C 577 GLN cc_start: 0.9142 (tp40) cc_final: 0.8291 (tp-100) REVERT: C 840 ASP cc_start: 0.9406 (t70) cc_final: 0.9110 (t70) REVERT: C 847 ARG cc_start: 0.8490 (tmt170) cc_final: 0.8072 (tpt90) REVERT: C 852 PHE cc_start: 0.9234 (m-80) cc_final: 0.9018 (m-80) REVERT: D 255 ILE cc_start: 0.8596 (mm) cc_final: 0.8314 (mm) REVERT: D 354 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8071 (mt-10) REVERT: D 576 GLU cc_start: 0.8644 (tt0) cc_final: 0.8391 (tt0) REVERT: D 577 GLN cc_start: 0.9179 (tp40) cc_final: 0.8630 (tp40) REVERT: D 752 LEU cc_start: 0.9451 (mm) cc_final: 0.9217 (mm) REVERT: D 847 ARG cc_start: 0.8360 (tmt170) cc_final: 0.7924 (tpt90) REVERT: D 873 PHE cc_start: 0.9313 (t80) cc_final: 0.8530 (m-80) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.3271 time to fit residues: 201.5969 Evaluate side-chains 283 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 2.788 ------------------------------------------------------------------------------- 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: 9.9990 chunk 265 optimal weight: 50.0000 chunk 51 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 234 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 overall best weight: 4.7586 ------------------------------------------------------------------------------- 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 850 HIS B 612 HIS ** 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 272 GLN ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.089749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065506 restraints weight = 125135.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066950 restraints weight = 76503.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.067877 restraints weight = 55417.084| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 26532 Z= 0.284 Angle : 0.721 9.589 36328 Z= 0.376 Chirality : 0.042 0.172 4360 Planarity : 0.005 0.044 4624 Dihedral : 4.598 17.274 3852 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: 0.88 (0.14), residues: 3580 helix: 1.37 (0.11), residues: 2380 sheet: -0.13 (0.36), residues: 164 loop : -1.10 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 60 HIS 0.008 0.002 HIS B 612 PHE 0.022 0.002 PHE B 583 TYR 0.018 0.002 TYR C 530 ARG 0.008 0.001 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 1685) hydrogen bonds : angle 5.01464 ( 4983) covalent geometry : bond 0.00594 (26532) covalent geometry : angle 0.72077 (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 350 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 2.976 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 284 GLN cc_start: 0.8995 (mp10) cc_final: 0.8752 (mp10) REVERT: A 354 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8374 (mt-10) REVERT: A 577 GLN cc_start: 0.9257 (tp40) cc_final: 0.8896 (tp40) REVERT: A 847 ARG cc_start: 0.8511 (tmt170) cc_final: 0.8225 (tpt90) REVERT: A 852 PHE cc_start: 0.9090 (m-80) cc_final: 0.8843 (m-80) REVERT: B 242 ARG cc_start: 0.8332 (ttt-90) cc_final: 0.7968 (ptm-80) REVERT: B 255 ILE cc_start: 0.8528 (mm) cc_final: 0.8285 (mm) REVERT: B 283 LYS cc_start: 0.9211 (tttt) cc_final: 0.8977 (mmtm) REVERT: B 354 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8260 (mt-10) REVERT: B 387 MET cc_start: 0.8840 (tpt) cc_final: 0.8469 (tpt) REVERT: B 418 LEU cc_start: 0.9436 (tt) cc_final: 0.9023 (mt) REVERT: B 840 ASP cc_start: 0.9466 (t70) cc_final: 0.9252 (t0) REVERT: B 847 ARG cc_start: 0.8430 (tmt170) cc_final: 0.8099 (tpt90) REVERT: C 253 TRP cc_start: 0.6439 (m100) cc_final: 0.6230 (m100) REVERT: C 255 ILE cc_start: 0.8399 (mm) cc_final: 0.8165 (mm) REVERT: C 354 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8382 (mt-10) REVERT: C 577 GLN cc_start: 0.9220 (tp40) cc_final: 0.8588 (tp40) REVERT: C 840 ASP cc_start: 0.9372 (t70) cc_final: 0.9168 (t70) REVERT: C 847 ARG cc_start: 0.8593 (tmt170) cc_final: 0.8177 (tpt90) REVERT: C 852 PHE cc_start: 0.9232 (m-80) cc_final: 0.8991 (m-80) REVERT: D 319 TYR cc_start: 0.7995 (t80) cc_final: 0.7582 (t80) REVERT: D 354 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8268 (mt-10) REVERT: D 577 GLN cc_start: 0.9271 (tp40) cc_final: 0.8861 (tp40) REVERT: D 752 LEU cc_start: 0.9458 (mm) cc_final: 0.9189 (mm) REVERT: D 809 CYS cc_start: 0.9286 (t) cc_final: 0.8946 (p) REVERT: D 847 ARG cc_start: 0.8465 (tmt170) cc_final: 0.7933 (tpt90) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.3524 time to fit residues: 201.9381 Evaluate side-chains 266 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 3.622 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 317 optimal weight: 9.9990 chunk 355 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 951 ASN ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 HIS ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS C 184 HIS ** C 629 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.090949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.066973 restraints weight = 121986.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068392 restraints weight = 75083.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.069325 restraints weight = 54638.087| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26532 Z= 0.181 Angle : 0.612 11.066 36328 Z= 0.317 Chirality : 0.039 0.197 4360 Planarity : 0.004 0.084 4624 Dihedral : 4.359 17.385 3852 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 1.22 (0.14), residues: 3580 helix: 1.65 (0.11), residues: 2364 sheet: 0.25 (0.36), residues: 184 loop : -1.06 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 60 HIS 0.011 0.001 HIS B 612 PHE 0.017 0.002 PHE C 877 TYR 0.011 0.001 TYR B 587 ARG 0.006 0.000 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 1685) hydrogen bonds : angle 4.61527 ( 4983) covalent geometry : bond 0.00385 (26532) covalent geometry : angle 0.61154 (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 341 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 3.495 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 118 GLN cc_start: 0.8793 (mm110) cc_final: 0.8457 (mm-40) REVERT: A 319 TYR cc_start: 0.8317 (t80) cc_final: 0.7696 (t80) REVERT: A 354 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8232 (mt-10) REVERT: A 577 GLN cc_start: 0.9274 (tp40) cc_final: 0.8918 (tp40) REVERT: A 840 ASP cc_start: 0.9305 (t70) cc_final: 0.9033 (t70) REVERT: A 847 ARG cc_start: 0.8434 (tmt170) cc_final: 0.8170 (tpt90) REVERT: A 852 PHE cc_start: 0.9072 (m-80) cc_final: 0.8828 (m-80) REVERT: B 255 ILE cc_start: 0.8444 (mm) cc_final: 0.8153 (mm) REVERT: B 354 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8157 (mt-10) REVERT: B 847 ARG cc_start: 0.8393 (tmt170) cc_final: 0.8057 (tpt90) REVERT: C 253 TRP cc_start: 0.6418 (m100) cc_final: 0.6195 (m100) REVERT: C 255 ILE cc_start: 0.8283 (mm) cc_final: 0.8035 (mm) REVERT: C 354 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8399 (mt-10) REVERT: C 368 LYS cc_start: 0.9441 (tptp) cc_final: 0.9231 (tppt) REVERT: C 387 MET cc_start: 0.8998 (tpp) cc_final: 0.8676 (tpp) REVERT: C 418 LEU cc_start: 0.9412 (tt) cc_final: 0.9024 (mt) REVERT: C 577 GLN cc_start: 0.9193 (tp40) cc_final: 0.8698 (tp40) REVERT: C 840 ASP cc_start: 0.9381 (t70) cc_final: 0.9148 (t70) REVERT: C 847 ARG cc_start: 0.8580 (tmt170) cc_final: 0.8126 (tpt90) REVERT: C 852 PHE cc_start: 0.9225 (m-80) cc_final: 0.8984 (m-80) REVERT: D 118 GLN cc_start: 0.8662 (mm110) cc_final: 0.8429 (mp10) REVERT: D 229 LEU cc_start: 0.9361 (tp) cc_final: 0.9158 (tt) REVERT: D 319 TYR cc_start: 0.7943 (t80) cc_final: 0.7506 (t80) REVERT: D 354 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8229 (mt-10) REVERT: D 576 GLU cc_start: 0.8639 (tt0) cc_final: 0.8391 (tt0) REVERT: D 577 GLN cc_start: 0.9196 (tp40) cc_final: 0.8882 (tp40) REVERT: D 752 LEU cc_start: 0.9505 (mm) cc_final: 0.9303 (mm) REVERT: D 847 ARG cc_start: 0.8447 (tmt170) cc_final: 0.7971 (tpt90) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.3437 time to fit residues: 193.1623 Evaluate side-chains 269 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 2.790 ------------------------------------------------------------------------------- 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: 0.0670 chunk 94 optimal weight: 6.9990 chunk 326 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 306 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 312 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 chunk 273 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 overall best weight: 1.6922 ------------------------------------------------------------------------------- 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 284 GLN B 602 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 C 951 ASN ** 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 = 0.3696 r_free = 0.3696 target = 0.091780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.067738 restraints weight = 120844.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069174 restraints weight = 74943.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.070117 restraints weight = 54460.045| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26532 Z= 0.136 Angle : 0.578 11.832 36328 Z= 0.297 Chirality : 0.037 0.169 4360 Planarity : 0.004 0.102 4624 Dihedral : 4.135 17.032 3852 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 1.49 (0.14), residues: 3580 helix: 1.86 (0.11), residues: 2364 sheet: 0.49 (0.37), residues: 184 loop : -1.00 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 60 HIS 0.004 0.001 HIS A 625 PHE 0.021 0.001 PHE B 877 TYR 0.008 0.001 TYR B 587 ARG 0.007 0.000 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 1685) hydrogen bonds : angle 4.36762 ( 4983) covalent geometry : bond 0.00292 (26532) covalent geometry : angle 0.57785 (36328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8352.93 seconds wall clock time: 144 minutes 58.75 seconds (8698.75 seconds total)