Starting phenix.real_space_refine on Mon Aug 25 07:12:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8slw_40581/08_2025/8slw_40581.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slw_40581/08_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_40581/08_2025/8slw_40581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slw_40581/08_2025/8slw_40581.map" model { file = "/net/cci-nas-00/data/ceres_data/8slw_40581/08_2025/8slw_40581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slw_40581/08_2025/8slw_40581.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 35, 'ASN:plan1': 9, 'PHE:plan': 17, 'ARG:plan': 17, 'GLN:plan1': 13, 'HIS:plan': 8, 'ASP:plan': 27, 'TRP:plan': 3, 'TYR:plan': 5} 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: {'GLU:plan': 35, 'ASN:plan1': 9, 'PHE:plan': 17, 'ARG:plan': 17, 'GLN:plan1': 13, 'HIS:plan': 8, 'ASP:plan': 27, 'TRP:plan': 3, 'TYR:plan': 5} 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: {'GLU:plan': 35, 'ASN:plan1': 9, 'PHE:plan': 17, 'ARG:plan': 17, 'GLN:plan1': 13, 'HIS:plan': 8, 'ASP:plan': 27, 'TRP:plan': 3, 'TYR:plan': 5} 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: {'GLU:plan': 35, 'ASN:plan1': 9, 'PHE:plan': 17, 'ARG:plan': 17, 'GLN:plan1': 13, 'HIS:plan': 8, 'ASP:plan': 27, 'TRP:plan': 3, 'TYR:plan': 5} 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: 6.23, per 1000 atoms: 0.24 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: 2.56 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.01 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: 5.42 Time building geometry restraints manager: 3.28 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.650 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.500 ------------------------------------------------------------------------------- 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 : 14.13 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG D 518 TYR 0.022 0.002 TYR D 587 PHE 0.039 0.002 PHE D 877 TRP 0.014 0.002 TRP C 806 HIS 0.007 0.001 HIS C 612 Details of bonding type rmsd covalent geometry : bond 0.00528 (26532) covalent geometry : angle 0.74250 (36328) hydrogen bonds : bond 0.16619 ( 1685) hydrogen bonds : angle 6.83666 ( 4983) *********************** 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 : 1.045 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: 0.8821 (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: 0.8891 (tp40) REVERT: A 752 LEU cc_start: 0.9279 (mm) cc_final: 0.8981 (mm) REVERT: A 809 CYS cc_start: 0.9249 (t) cc_final: 0.8975 (p) REVERT: A 840 ASP cc_start: 0.8935 (t70) cc_final: 0.8462 (t0) REVERT: A 844 PHE cc_start: 0.9075 (m-10) cc_final: 0.8835 (m-10) REVERT: A 847 ARG cc_start: 0.8678 (tmt170) cc_final: 0.7999 (tpt90) REVERT: A 873 PHE cc_start: 0.8676 (t80) cc_final: 0.7683 (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: 0.7305 (pp) REVERT: B 752 LEU cc_start: 0.9228 (mm) cc_final: 0.8892 (mm) REVERT: B 809 CYS cc_start: 0.9272 (t) cc_final: 0.8960 (p) REVERT: B 847 ARG cc_start: 0.8702 (tmt170) cc_final: 0.7890 (tpt90) REVERT: B 850 HIS cc_start: 0.7927 (t70) cc_final: 0.7699 (t-90) REVERT: B 873 PHE cc_start: 0.8944 (t80) cc_final: 0.7933 (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: 0.8896 (mm) REVERT: C 809 CYS cc_start: 0.9375 (t) cc_final: 0.8939 (p) REVERT: C 840 ASP cc_start: 0.9014 (t70) cc_final: 0.8591 (t0) REVERT: C 844 PHE cc_start: 0.9022 (m-10) cc_final: 0.8754 (m-10) REVERT: C 847 ARG cc_start: 0.8750 (tmt170) cc_final: 0.7950 (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: 0.7533 (m-80) REVERT: D 532 MET cc_start: 0.9317 (ttp) cc_final: 0.9068 (mmm) REVERT: D 539 MET cc_start: 0.8229 (mtm) cc_final: 0.8015 (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: 0.8942 (mm) REVERT: D 809 CYS cc_start: 0.9285 (t) cc_final: 0.8958 (p) REVERT: D 847 ARG cc_start: 0.8768 (tmt170) cc_final: 0.7957 (tpt90) REVERT: D 873 PHE cc_start: 0.8701 (t80) cc_final: 0.7660 (m-80) REVERT: D 953 LEU cc_start: 0.8197 (mt) cc_final: 0.7981 (mp) outliers start: 3 outliers final: 3 residues processed: 593 average time/residue: 0.1780 time to fit residues: 167.0761 Evaluate side-chains 368 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 365 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 284 GLN A 602 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS A 951 ASN A 982 GLN A 998 HIS A1057 GLN B 210 HIS B 214 GLN B 284 GLN ** 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 B1057 GLN 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 C 951 ASN C 982 GLN C1057 GLN D 184 HIS D 284 GLN ** 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 D1057 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.091495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066775 restraints weight = 123852.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.068203 restraints weight = 76426.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069137 restraints weight = 55439.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.069716 restraints weight = 45014.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.070039 restraints weight = 39460.594| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 26532 Z= 0.299 Angle : 0.744 9.311 36328 Z= 0.390 Chirality : 0.042 0.161 4360 Planarity : 0.005 0.048 4624 Dihedral : 4.580 20.907 3852 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.05 % Allowed : 6.02 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.14), residues: 3580 helix: 0.79 (0.10), residues: 2348 sheet: -0.51 (0.34), residues: 208 loop : -1.60 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 245 TYR 0.024 0.003 TYR A 319 PHE 0.022 0.002 PHE C 583 TRP 0.031 0.002 TRP D 253 HIS 0.007 0.002 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00619 (26532) covalent geometry : angle 0.74443 (36328) hydrogen bonds : bond 0.05079 ( 1685) hydrogen bonds : angle 5.45419 ( 4983) *********************** 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 402 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 401 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ILE cc_start: 0.8754 (mm) cc_final: 0.8454 (mm) REVERT: A 283 LYS cc_start: 0.9153 (tttt) cc_final: 0.8937 (tppt) REVERT: A 333 ILE cc_start: 0.9459 (mt) cc_final: 0.9182 (mm) REVERT: A 577 GLN cc_start: 0.9169 (tp40) cc_final: 0.8750 (tp40) REVERT: A 840 ASP cc_start: 0.9218 (t70) cc_final: 0.9012 (t70) REVERT: A 847 ARG cc_start: 0.8542 (tmt170) cc_final: 0.8266 (tpt90) REVERT: A 873 PHE cc_start: 0.8840 (t80) cc_final: 0.8217 (m-80) REVERT: B 255 ILE cc_start: 0.8598 (mm) cc_final: 0.8202 (mm) REVERT: B 283 LYS cc_start: 0.9207 (tttt) cc_final: 0.8986 (tppt) REVERT: B 577 GLN cc_start: 0.9137 (tp40) cc_final: 0.8648 (tp-100) REVERT: B 752 LEU cc_start: 0.9251 (mm) cc_final: 0.9037 (mm) REVERT: B 847 ARG cc_start: 0.8677 (tmt170) cc_final: 0.8150 (tpt90) REVERT: B 873 PHE cc_start: 0.9100 (t80) cc_final: 0.8533 (m-80) REVERT: C 90 LYS cc_start: 0.9369 (mmpt) cc_final: 0.9128 (mmmt) REVERT: C 255 ILE cc_start: 0.8569 (mm) cc_final: 0.8271 (mm) REVERT: C 532 MET cc_start: 0.9024 (mmm) cc_final: 0.8778 (mmm) REVERT: C 577 GLN cc_start: 0.9160 (tp40) cc_final: 0.8737 (tp40) REVERT: C 847 ARG cc_start: 0.8686 (tmt170) cc_final: 0.8251 (tpt90) REVERT: C 852 PHE cc_start: 0.9188 (m-80) cc_final: 0.8903 (m-80) REVERT: C 873 PHE cc_start: 0.8975 (t80) cc_final: 0.8153 (m-80) REVERT: D 255 ILE cc_start: 0.8709 (mm) cc_final: 0.8419 (mm) REVERT: D 283 LYS cc_start: 0.9149 (tttt) cc_final: 0.8870 (tppt) REVERT: D 418 LEU cc_start: 0.9505 (tt) cc_final: 0.9146 (mt) REVERT: D 557 MET cc_start: 0.8846 (ttm) cc_final: 0.8625 (ttm) REVERT: D 576 GLU cc_start: 0.8774 (tt0) cc_final: 0.8476 (tt0) REVERT: D 577 GLN cc_start: 0.9185 (tp40) cc_final: 0.8780 (tp40) REVERT: D 847 ARG cc_start: 0.8705 (tmt170) cc_final: 0.8309 (tpt90) REVERT: D 852 PHE cc_start: 0.8847 (m-80) cc_final: 0.8092 (m-80) REVERT: D 873 PHE cc_start: 0.8955 (t80) cc_final: 0.8330 (m-80) REVERT: D 1071 ASP cc_start: 0.8750 (m-30) cc_final: 0.8524 (t0) outliers start: 1 outliers final: 0 residues processed: 401 average time/residue: 0.1586 time to fit residues: 104.8115 Evaluate side-chains 300 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 97 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 345 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 294 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 213 optimal weight: 0.7980 overall best weight: 1.7382 ------------------------------------------------------------------------------- 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 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 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 C1057 GLN ** D 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS D1057 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.093422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.068904 restraints weight = 122185.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.070406 restraints weight = 74579.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071298 restraints weight = 53680.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071972 restraints weight = 43532.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.072314 restraints weight = 37954.257| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26532 Z= 0.143 Angle : 0.546 9.580 36328 Z= 0.287 Chirality : 0.037 0.158 4360 Planarity : 0.004 0.047 4624 Dihedral : 4.125 17.781 3852 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.14), residues: 3580 helix: 1.53 (0.11), residues: 2340 sheet: -0.08 (0.33), residues: 236 loop : -0.98 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1083 TYR 0.008 0.001 TYR C 587 PHE 0.025 0.002 PHE B 994 TRP 0.012 0.001 TRP A 723 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00294 (26532) covalent geometry : angle 0.54565 (36328) hydrogen bonds : bond 0.04118 ( 1685) hydrogen bonds : angle 4.71706 ( 4983) *********************** 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 416 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 415 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ILE cc_start: 0.8668 (mm) cc_final: 0.8316 (mm) REVERT: A 283 LYS cc_start: 0.9121 (tttt) cc_final: 0.8908 (tppt) REVERT: A 333 ILE cc_start: 0.9477 (mt) cc_final: 0.9262 (mt) REVERT: A 577 GLN cc_start: 0.9128 (tp40) cc_final: 0.8657 (tp40) REVERT: A 840 ASP cc_start: 0.9176 (t70) cc_final: 0.8888 (t70) REVERT: A 847 ARG cc_start: 0.8501 (tmt170) cc_final: 0.8228 (tpt90) REVERT: A 873 PHE cc_start: 0.8994 (t80) cc_final: 0.8405 (m-80) REVERT: B 255 ILE cc_start: 0.8512 (mm) cc_final: 0.8247 (mm) REVERT: B 283 LYS cc_start: 0.9186 (tttt) cc_final: 0.8962 (tppt) REVERT: B 333 ILE cc_start: 0.9442 (mt) cc_final: 0.9237 (mt) REVERT: B 532 MET cc_start: 0.9112 (mmm) cc_final: 0.8892 (tpp) REVERT: B 577 GLN cc_start: 0.9184 (tp40) cc_final: 0.8858 (tp40) REVERT: B 752 LEU cc_start: 0.9298 (mm) cc_final: 0.9091 (mm) REVERT: B 840 ASP cc_start: 0.9438 (t70) cc_final: 0.9203 (t0) REVERT: B 847 ARG cc_start: 0.8472 (tmt170) cc_final: 0.8207 (tpt90) REVERT: B 873 PHE cc_start: 0.9180 (t80) cc_final: 0.8566 (m-80) REVERT: C 90 LYS cc_start: 0.9181 (mmpt) cc_final: 0.8746 (mmmt) REVERT: C 255 ILE cc_start: 0.8481 (mm) cc_final: 0.8166 (mm) REVERT: C 413 LEU cc_start: 0.9208 (tp) cc_final: 0.8993 (tt) REVERT: C 532 MET cc_start: 0.9162 (mmm) cc_final: 0.8943 (tpp) REVERT: C 577 GLN cc_start: 0.9105 (tp40) cc_final: 0.8632 (tp40) REVERT: C 840 ASP cc_start: 0.9398 (t0) cc_final: 0.9125 (t70) REVERT: C 847 ARG cc_start: 0.8786 (tmt170) cc_final: 0.8242 (tpt90) REVERT: C 852 PHE cc_start: 0.9213 (m-80) cc_final: 0.8916 (m-80) REVERT: C 873 PHE cc_start: 0.9020 (t80) cc_final: 0.8202 (m-80) REVERT: D 255 ILE cc_start: 0.8670 (mm) cc_final: 0.8317 (mm) REVERT: D 283 LYS cc_start: 0.9110 (tttt) cc_final: 0.8832 (tppt) REVERT: D 570 MET cc_start: 0.8659 (ptm) cc_final: 0.8196 (ptp) REVERT: D 577 GLN cc_start: 0.9157 (tp40) cc_final: 0.8675 (tp40) REVERT: D 752 LEU cc_start: 0.9417 (mm) cc_final: 0.9197 (mm) REVERT: D 847 ARG cc_start: 0.8535 (tmt170) cc_final: 0.8175 (tpt90) REVERT: D 852 PHE cc_start: 0.8967 (m-80) cc_final: 0.8248 (m-80) REVERT: D 873 PHE cc_start: 0.9011 (t80) cc_final: 0.8338 (m-80) outliers start: 1 outliers final: 0 residues processed: 416 average time/residue: 0.1612 time to fit residues: 112.3643 Evaluate side-chains 307 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 98 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 203 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 chunk 176 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 286 optimal weight: 30.0000 chunk 276 optimal weight: 60.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- 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 602 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS A1057 GLN ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN B 394 ASN ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS C 210 HIS C 214 GLN C 272 GLN C 394 ASN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 HIS D 214 GLN D 394 ASN ** D 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.089085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065119 restraints weight = 125066.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.066331 restraints weight = 76846.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.067514 restraints weight = 51774.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067461 restraints weight = 44589.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.067506 restraints weight = 41724.603| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 26532 Z= 0.378 Angle : 0.833 11.060 36328 Z= 0.433 Chirality : 0.044 0.200 4360 Planarity : 0.006 0.058 4624 Dihedral : 4.966 19.419 3852 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.33 % Allowed : 5.04 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.14), residues: 3580 helix: 0.75 (0.10), residues: 2332 sheet: 0.06 (0.39), residues: 164 loop : -1.21 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 89 TYR 0.022 0.003 TYR B 587 PHE 0.026 0.003 PHE C 583 TRP 0.024 0.002 TRP C 537 HIS 0.010 0.002 HIS D 423 Details of bonding type rmsd covalent geometry : bond 0.00787 (26532) covalent geometry : angle 0.83340 (36328) hydrogen bonds : bond 0.05151 ( 1685) hydrogen bonds : angle 5.56758 ( 4983) *********************** 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 369 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 362 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ILE cc_start: 0.8797 (mm) cc_final: 0.8554 (mm) REVERT: A 283 LYS cc_start: 0.9173 (tttt) cc_final: 0.8929 (mmtm) REVERT: A 354 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8295 (mt-10) REVERT: A 539 MET cc_start: 0.8172 (mtt) cc_final: 0.7924 (mtt) REVERT: A 577 GLN cc_start: 0.9277 (tp40) cc_final: 0.8755 (tp40) REVERT: A 737 ASN cc_start: 0.9253 (m110) cc_final: 0.8931 (m110) REVERT: A 752 LEU cc_start: 0.9431 (mm) cc_final: 0.9230 (mm) REVERT: A 839 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9119 (tp) REVERT: A 840 ASP cc_start: 0.9234 (t70) cc_final: 0.8888 (t70) REVERT: A 844 PHE cc_start: 0.9006 (m-10) cc_final: 0.8747 (m-10) REVERT: A 847 ARG cc_start: 0.8551 (tmt170) cc_final: 0.8207 (tpt90) REVERT: A 873 PHE cc_start: 0.9131 (t80) cc_final: 0.8447 (m-80) REVERT: B 90 LYS cc_start: 0.9318 (mmpt) cc_final: 0.9109 (mmmt) REVERT: B 255 ILE cc_start: 0.8666 (mm) cc_final: 0.8374 (mm) REVERT: B 283 LYS cc_start: 0.9220 (tttt) cc_final: 0.8977 (mmtm) REVERT: B 354 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8212 (mt-10) REVERT: B 387 MET cc_start: 0.8706 (tpt) cc_final: 0.8401 (tpt) REVERT: B 539 MET cc_start: 0.7940 (mtt) cc_final: 0.7737 (mtt) REVERT: B 577 GLN cc_start: 0.9330 (tp40) cc_final: 0.8494 (tp-100) REVERT: B 752 LEU cc_start: 0.9374 (mm) cc_final: 0.9164 (mm) REVERT: B 847 ARG cc_start: 0.8682 (tmt170) cc_final: 0.8253 (tpt90) REVERT: B 873 PHE cc_start: 0.9265 (t80) cc_final: 0.8554 (m-80) REVERT: C 90 LYS cc_start: 0.9212 (mmpt) cc_final: 0.8870 (mmmt) REVERT: C 255 ILE cc_start: 0.8649 (mm) cc_final: 0.8386 (mm) REVERT: C 354 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8440 (mt-10) REVERT: C 577 GLN cc_start: 0.9221 (tp40) cc_final: 0.8729 (tp40) REVERT: C 752 LEU cc_start: 0.9392 (mm) cc_final: 0.9181 (mm) REVERT: C 847 ARG cc_start: 0.8671 (tmt170) cc_final: 0.8213 (tpt90) REVERT: D 255 ILE cc_start: 0.8863 (mm) cc_final: 0.8574 (mm) REVERT: D 269 LEU cc_start: 0.9371 (mt) cc_final: 0.9148 (pp) REVERT: D 283 LYS cc_start: 0.9200 (tttt) cc_final: 0.8924 (tppt) REVERT: D 354 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8252 (mt-10) REVERT: D 577 GLN cc_start: 0.9272 (tp40) cc_final: 0.8778 (tp40) REVERT: D 752 LEU cc_start: 0.9451 (mm) cc_final: 0.9184 (mm) REVERT: D 809 CYS cc_start: 0.9274 (t) cc_final: 0.8868 (p) REVERT: D 839 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9082 (tp) REVERT: D 847 ARG cc_start: 0.8615 (tmt170) cc_final: 0.8231 (tpt90) REVERT: D 852 PHE cc_start: 0.9060 (m-80) cc_final: 0.8367 (m-80) REVERT: D 873 PHE cc_start: 0.9169 (t80) cc_final: 0.8443 (m-80) outliers start: 7 outliers final: 0 residues processed: 366 average time/residue: 0.1600 time to fit residues: 96.3544 Evaluate side-chains 270 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 268 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 188 optimal weight: 0.6980 chunk 178 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 326 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 322 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 737 ASN ** 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 B1057 GLN C 210 HIS ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.091719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.067413 restraints weight = 122553.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.068846 restraints weight = 75372.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.069768 restraints weight = 54807.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.070306 restraints weight = 44661.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.070699 restraints weight = 39510.528| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26532 Z= 0.177 Angle : 0.591 10.543 36328 Z= 0.306 Chirality : 0.038 0.159 4360 Planarity : 0.004 0.052 4624 Dihedral : 4.384 17.854 3852 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.14), residues: 3580 helix: 1.39 (0.11), residues: 2352 sheet: 0.42 (0.35), residues: 204 loop : -1.03 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1083 TYR 0.013 0.002 TYR C 535 PHE 0.024 0.001 PHE C 289 TRP 0.014 0.001 TRP A 723 HIS 0.005 0.001 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00377 (26532) covalent geometry : angle 0.59106 (36328) hydrogen bonds : bond 0.03946 ( 1685) hydrogen bonds : angle 4.76919 ( 4983) *********************** 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 368 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.125 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: 0.8736 (mm) cc_final: 0.8428 (mm) REVERT: A 539 MET cc_start: 0.7978 (mtt) cc_final: 0.7763 (mtt) REVERT: A 577 GLN cc_start: 0.9129 (tp40) cc_final: 0.8618 (tp40) REVERT: A 847 ARG cc_start: 0.8475 (tmt170) cc_final: 0.8176 (tpt90) REVERT: B 255 ILE cc_start: 0.8510 (mm) cc_final: 0.8187 (mm) REVERT: B 354 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8138 (mt-10) REVERT: B 577 GLN cc_start: 0.9153 (tp40) cc_final: 0.8531 (tp40) REVERT: B 752 LEU cc_start: 0.9390 (mm) cc_final: 0.9169 (mm) REVERT: B 840 ASP cc_start: 0.9466 (t70) cc_final: 0.9259 (t0) REVERT: B 847 ARG cc_start: 0.8600 (tmt170) cc_final: 0.8211 (tpt90) REVERT: C 90 LYS cc_start: 0.9232 (mmpt) cc_final: 0.8877 (mmmt) REVERT: C 255 ILE cc_start: 0.8568 (mm) cc_final: 0.8262 (mm) REVERT: C 418 LEU cc_start: 0.9258 (tt) cc_final: 0.8997 (mt) REVERT: C 577 GLN cc_start: 0.9143 (tp40) cc_final: 0.8595 (tp40) REVERT: C 840 ASP cc_start: 0.9394 (t70) cc_final: 0.9162 (t70) REVERT: C 847 ARG cc_start: 0.8600 (tmt170) cc_final: 0.8179 (tpt90) REVERT: C 1071 ASP cc_start: 0.8706 (t0) cc_final: 0.8456 (t0) REVERT: D 255 ILE cc_start: 0.8700 (mm) cc_final: 0.8422 (mm) REVERT: D 577 GLN cc_start: 0.9160 (tp40) cc_final: 0.8617 (tp40) REVERT: D 752 LEU cc_start: 0.9458 (mm) cc_final: 0.9227 (mm) REVERT: D 840 ASP cc_start: 0.9426 (t70) cc_final: 0.9070 (t70) REVERT: D 847 ARG cc_start: 0.8500 (tmt170) cc_final: 0.8057 (tpt90) REVERT: D 852 PHE cc_start: 0.9105 (m-80) cc_final: 0.8424 (m-80) REVERT: D 873 PHE cc_start: 0.9248 (t80) cc_final: 0.8498 (m-80) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1608 time to fit residues: 97.1648 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 : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 128 optimal weight: 7.9990 chunk 273 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 236 optimal weight: 0.7980 chunk 76 optimal weight: 50.0000 chunk 300 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 361 optimal weight: 0.7980 chunk 332 optimal weight: 9.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- 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 ** 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 184 HIS C 602 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.090072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.065828 restraints weight = 122977.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067217 restraints weight = 76363.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.068135 restraints weight = 55794.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.068683 restraints weight = 45449.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069037 restraints weight = 40046.368| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4659 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= 0.256 Angle : 0.677 10.939 36328 Z= 0.349 Chirality : 0.040 0.193 4360 Planarity : 0.005 0.051 4624 Dihedral : 4.564 18.843 3852 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.14), residues: 3580 helix: 1.22 (0.11), residues: 2364 sheet: 0.09 (0.38), residues: 164 loop : -1.02 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 148 TYR 0.016 0.002 TYR B 587 PHE 0.021 0.002 PHE D 583 TRP 0.027 0.002 TRP A 773 HIS 0.006 0.002 HIS D 603 Details of bonding type rmsd covalent geometry : bond 0.00533 (26532) covalent geometry : angle 0.67709 (36328) hydrogen bonds : bond 0.04189 ( 1685) hydrogen bonds : angle 4.99854 ( 4983) *********************** 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 351 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.998 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 354 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8271 (mt-10) REVERT: A 577 GLN cc_start: 0.9180 (tp40) cc_final: 0.8606 (tp40) REVERT: A 840 ASP cc_start: 0.9279 (t70) cc_final: 0.9033 (t70) REVERT: A 847 ARG cc_start: 0.8499 (tmt170) cc_final: 0.8170 (tpt90) REVERT: A 999 LEU cc_start: 0.9554 (tt) cc_final: 0.9241 (tt) REVERT: B 255 ILE cc_start: 0.8574 (mm) cc_final: 0.8327 (mm) REVERT: B 354 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8268 (mt-10) REVERT: B 387 MET cc_start: 0.8795 (tpt) cc_final: 0.8417 (tpt) REVERT: B 418 LEU cc_start: 0.9493 (tt) cc_final: 0.9036 (mt) REVERT: B 577 GLN cc_start: 0.9222 (tp40) cc_final: 0.8575 (tp40) REVERT: B 752 LEU cc_start: 0.9379 (mm) cc_final: 0.9140 (mm) REVERT: B 847 ARG cc_start: 0.8633 (tmt170) cc_final: 0.8200 (tpt90) REVERT: C 134 VAL cc_start: 0.7968 (m) cc_final: 0.7604 (p) REVERT: C 255 ILE cc_start: 0.8538 (mm) cc_final: 0.8325 (mm) REVERT: C 354 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8306 (mt-10) REVERT: C 418 LEU cc_start: 0.9439 (tt) cc_final: 0.9093 (mt) REVERT: C 577 GLN cc_start: 0.9135 (tp40) cc_final: 0.8569 (tp40) REVERT: C 752 LEU cc_start: 0.9386 (mm) cc_final: 0.9174 (mm) REVERT: C 840 ASP cc_start: 0.9395 (t70) cc_final: 0.9159 (t70) REVERT: C 847 ARG cc_start: 0.8614 (tmt170) cc_final: 0.8179 (tpt90) REVERT: C 999 LEU cc_start: 0.9534 (tt) cc_final: 0.9042 (tt) REVERT: D 255 ILE cc_start: 0.8705 (mm) cc_final: 0.8502 (mm) REVERT: D 354 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8170 (mt-10) REVERT: D 577 GLN cc_start: 0.9215 (tp40) cc_final: 0.8602 (tp40) REVERT: D 752 LEU cc_start: 0.9450 (mm) cc_final: 0.9210 (mm) REVERT: D 847 ARG cc_start: 0.8538 (tmt170) cc_final: 0.8060 (tpt90) REVERT: D 852 PHE cc_start: 0.9118 (m-80) cc_final: 0.8897 (m-80) REVERT: D 873 PHE cc_start: 0.9243 (t80) cc_final: 0.8417 (m-10) REVERT: D 999 LEU cc_start: 0.9544 (tt) cc_final: 0.9196 (tt) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1478 time to fit residues: 85.1767 Evaluate side-chains 275 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 2 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 366 optimal weight: 0.9990 chunk 286 optimal weight: 5.9990 chunk 338 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 314 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 304 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 chunk 296 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 737 ASN D 850 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.091010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067079 restraints weight = 120757.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.068469 restraints weight = 75015.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.069399 restraints weight = 54747.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.069932 restraints weight = 44529.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070339 restraints weight = 39218.087| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26532 Z= 0.187 Angle : 0.599 10.800 36328 Z= 0.309 Chirality : 0.038 0.170 4360 Planarity : 0.004 0.053 4624 Dihedral : 4.379 18.535 3852 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.14), residues: 3580 helix: 1.55 (0.11), residues: 2352 sheet: 0.14 (0.38), residues: 164 loop : -1.00 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 89 TYR 0.013 0.001 TYR B 587 PHE 0.018 0.002 PHE C 289 TRP 0.016 0.002 TRP A 102 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00395 (26532) covalent geometry : angle 0.59902 (36328) hydrogen bonds : bond 0.03863 ( 1685) hydrogen bonds : angle 4.70003 ( 4983) *********************** 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 362 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.957 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 354 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8293 (mt-10) REVERT: A 577 GLN cc_start: 0.9069 (tp40) cc_final: 0.8543 (tp40) REVERT: A 840 ASP cc_start: 0.9264 (t70) cc_final: 0.8986 (t70) REVERT: A 847 ARG cc_start: 0.8427 (tmt170) cc_final: 0.8165 (tpt90) REVERT: B 255 ILE cc_start: 0.8439 (mm) cc_final: 0.8205 (mm) REVERT: B 354 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8193 (mt-10) REVERT: B 418 LEU cc_start: 0.9419 (tt) cc_final: 0.8987 (mt) REVERT: B 577 GLN cc_start: 0.9117 (tp40) cc_final: 0.8410 (tp40) REVERT: B 847 ARG cc_start: 0.8617 (tmt170) cc_final: 0.8224 (tpt90) REVERT: B 852 PHE cc_start: 0.9055 (m-80) cc_final: 0.8783 (m-80) REVERT: C 255 ILE cc_start: 0.8455 (mm) cc_final: 0.8231 (mm) REVERT: C 418 LEU cc_start: 0.9382 (tt) cc_final: 0.9039 (mt) REVERT: C 577 GLN cc_start: 0.9041 (tp40) cc_final: 0.8498 (tp40) REVERT: C 752 LEU cc_start: 0.9413 (mm) cc_final: 0.9190 (mm) REVERT: C 840 ASP cc_start: 0.9368 (t70) cc_final: 0.9129 (t70) REVERT: C 847 ARG cc_start: 0.8604 (tmt170) cc_final: 0.8184 (tpt90) REVERT: C 999 LEU cc_start: 0.9490 (tt) cc_final: 0.9176 (tt) REVERT: C 1071 ASP cc_start: 0.8657 (t0) cc_final: 0.8397 (t0) REVERT: D 118 GLN cc_start: 0.8670 (mm110) cc_final: 0.8360 (mp10) REVERT: D 255 ILE cc_start: 0.8531 (mm) cc_final: 0.8328 (mm) REVERT: D 354 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8190 (mt-10) REVERT: D 418 LEU cc_start: 0.9410 (tt) cc_final: 0.9009 (mt) REVERT: D 577 GLN cc_start: 0.9132 (tp40) cc_final: 0.8568 (tp40) REVERT: D 752 LEU cc_start: 0.9450 (mm) cc_final: 0.9187 (mm) REVERT: D 847 ARG cc_start: 0.8465 (tmt170) cc_final: 0.8032 (tpt90) REVERT: D 873 PHE cc_start: 0.9344 (t80) cc_final: 0.8556 (m-80) REVERT: D 999 LEU cc_start: 0.9523 (tt) cc_final: 0.9239 (tt) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.1519 time to fit residues: 90.4655 Evaluate side-chains 275 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 271 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 165 optimal weight: 6.9990 chunk 358 optimal weight: 4.9990 chunk 309 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 50.0000 chunk 103 optimal weight: 0.0470 chunk 229 optimal weight: 3.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.091714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.067164 restraints weight = 123131.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.068632 restraints weight = 75109.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.069589 restraints weight = 54263.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070128 restraints weight = 43911.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.070550 restraints weight = 38717.537| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26532 Z= 0.153 Angle : 0.572 10.080 36328 Z= 0.293 Chirality : 0.037 0.166 4360 Planarity : 0.004 0.051 4624 Dihedral : 4.204 18.943 3852 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.14), residues: 3580 helix: 1.71 (0.11), residues: 2360 sheet: 0.60 (0.37), residues: 184 loop : -0.96 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 85 TYR 0.011 0.001 TYR B 587 PHE 0.017 0.001 PHE C 289 TRP 0.050 0.001 TRP C 60 HIS 0.010 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00325 (26532) covalent geometry : angle 0.57193 (36328) hydrogen bonds : bond 0.03647 ( 1685) hydrogen bonds : angle 4.51761 ( 4983) *********************** 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 369 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 TYR cc_start: 0.8383 (t80) cc_final: 0.7769 (t80) REVERT: A 577 GLN cc_start: 0.9129 (tp40) cc_final: 0.8605 (tp40) REVERT: A 840 ASP cc_start: 0.9250 (t70) cc_final: 0.8975 (t70) REVERT: A 847 ARG cc_start: 0.8432 (tmt170) cc_final: 0.8166 (tpt90) REVERT: A 852 PHE cc_start: 0.9034 (m-80) cc_final: 0.8778 (m-80) REVERT: A 999 LEU cc_start: 0.9526 (tt) cc_final: 0.9308 (tt) REVERT: A 1059 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8298 (mt-10) REVERT: B 242 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.8000 (ttm-80) REVERT: B 255 ILE cc_start: 0.8358 (mm) cc_final: 0.7987 (mm) REVERT: B 354 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8187 (mt-10) REVERT: B 577 GLN cc_start: 0.9081 (tp40) cc_final: 0.8424 (tp40) REVERT: B 840 ASP cc_start: 0.9465 (t70) cc_final: 0.9211 (t70) REVERT: B 847 ARG cc_start: 0.8563 (tmt170) cc_final: 0.8209 (tpt90) REVERT: B 852 PHE cc_start: 0.9060 (m-80) cc_final: 0.8789 (m-80) REVERT: C 134 VAL cc_start: 0.7984 (m) cc_final: 0.7643 (p) REVERT: C 255 ILE cc_start: 0.8371 (mm) cc_final: 0.8132 (mm) REVERT: C 354 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8190 (mt-10) REVERT: C 368 LYS cc_start: 0.9420 (tptp) cc_final: 0.9194 (tppt) REVERT: C 387 MET cc_start: 0.9030 (tpp) cc_final: 0.8696 (tpp) REVERT: C 418 LEU cc_start: 0.9405 (tt) cc_final: 0.9031 (mt) REVERT: C 577 GLN cc_start: 0.9051 (tp40) cc_final: 0.8642 (tp40) REVERT: C 752 LEU cc_start: 0.9397 (mm) cc_final: 0.9180 (mm) REVERT: C 840 ASP cc_start: 0.9332 (t70) cc_final: 0.9102 (t70) REVERT: C 847 ARG cc_start: 0.8635 (tmt170) cc_final: 0.8206 (tpt90) REVERT: C 999 LEU cc_start: 0.9448 (tt) cc_final: 0.8998 (tt) REVERT: C 1071 ASP cc_start: 0.8787 (t0) cc_final: 0.8496 (t0) REVERT: D 118 GLN cc_start: 0.8621 (mm110) cc_final: 0.8327 (mp10) REVERT: D 255 ILE cc_start: 0.8461 (mm) cc_final: 0.8247 (mm) REVERT: D 354 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8133 (mt-10) REVERT: D 418 LEU cc_start: 0.9412 (tt) cc_final: 0.9019 (mt) REVERT: D 577 GLN cc_start: 0.9121 (tp40) cc_final: 0.8490 (tp40) REVERT: D 752 LEU cc_start: 0.9476 (mm) cc_final: 0.9262 (mm) REVERT: D 847 ARG cc_start: 0.8437 (tmt170) cc_final: 0.7986 (tpt90) REVERT: D 999 LEU cc_start: 0.9509 (tt) cc_final: 0.9274 (tt) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.1638 time to fit residues: 98.7833 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 : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 367 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 266 optimal weight: 7.9990 chunk 167 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 951 ASN ** B 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** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.091232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.066788 restraints weight = 124134.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.068248 restraints weight = 75651.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.069206 restraints weight = 54634.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.069735 restraints weight = 44223.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.070169 restraints weight = 39004.457| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26532 Z= 0.184 Angle : 0.606 11.158 36328 Z= 0.310 Chirality : 0.038 0.167 4360 Planarity : 0.004 0.066 4624 Dihedral : 4.246 18.577 3852 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.14), residues: 3580 helix: 1.74 (0.11), residues: 2332 sheet: -0.09 (0.35), residues: 212 loop : -0.94 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 85 TYR 0.012 0.001 TYR C 587 PHE 0.022 0.002 PHE C 877 TRP 0.020 0.002 TRP C 60 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00389 (26532) covalent geometry : angle 0.60611 (36328) hydrogen bonds : bond 0.03761 ( 1685) hydrogen bonds : angle 4.58823 ( 4983) *********************** 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 369 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.014 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 319 TYR cc_start: 0.8425 (t80) cc_final: 0.7773 (t80) REVERT: A 354 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8241 (mt-10) REVERT: A 577 GLN cc_start: 0.9145 (tp40) cc_final: 0.8594 (tp40) REVERT: A 840 ASP cc_start: 0.9252 (t70) cc_final: 0.8976 (t70) REVERT: A 847 ARG cc_start: 0.8420 (tmt170) cc_final: 0.8160 (tpt90) REVERT: A 852 PHE cc_start: 0.9032 (m-80) cc_final: 0.8788 (m-80) REVERT: A 999 LEU cc_start: 0.9528 (tt) cc_final: 0.9307 (tt) REVERT: A 1059 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8345 (mt-10) REVERT: A 1071 ASP cc_start: 0.8105 (t0) cc_final: 0.7875 (t0) REVERT: B 242 ARG cc_start: 0.8239 (ttt-90) cc_final: 0.8035 (ttm170) REVERT: B 255 ILE cc_start: 0.8293 (mm) cc_final: 0.8018 (mm) REVERT: B 354 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 418 LEU cc_start: 0.9417 (tt) cc_final: 0.8983 (mt) REVERT: B 577 GLN cc_start: 0.9113 (tp40) cc_final: 0.8372 (tp40) REVERT: B 840 ASP cc_start: 0.9463 (t70) cc_final: 0.9238 (t70) REVERT: B 847 ARG cc_start: 0.8679 (tmt170) cc_final: 0.8310 (tpt90) REVERT: B 852 PHE cc_start: 0.9068 (m-80) cc_final: 0.8813 (m-80) REVERT: C 134 VAL cc_start: 0.8004 (m) cc_final: 0.7737 (p) REVERT: C 253 TRP cc_start: 0.6487 (m100) cc_final: 0.6266 (m100) REVERT: C 255 ILE cc_start: 0.8319 (mm) cc_final: 0.8064 (mm) REVERT: C 354 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8242 (mt-10) REVERT: C 418 LEU cc_start: 0.9409 (tt) cc_final: 0.9037 (mt) REVERT: C 577 GLN cc_start: 0.9060 (tp40) cc_final: 0.8499 (tp40) REVERT: C 752 LEU cc_start: 0.9401 (mm) cc_final: 0.9166 (mm) REVERT: C 840 ASP cc_start: 0.9325 (t70) cc_final: 0.9123 (t70) REVERT: C 847 ARG cc_start: 0.8647 (tmt170) cc_final: 0.8209 (tpt90) REVERT: C 999 LEU cc_start: 0.9450 (tt) cc_final: 0.9033 (tt) REVERT: C 1071 ASP cc_start: 0.8891 (t0) cc_final: 0.8579 (t0) REVERT: D 118 GLN cc_start: 0.8665 (mm110) cc_final: 0.8362 (mp10) REVERT: D 354 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8216 (mt-10) REVERT: D 418 LEU cc_start: 0.9437 (tt) cc_final: 0.9004 (mt) REVERT: D 577 GLN cc_start: 0.9152 (tp40) cc_final: 0.8526 (tp40) REVERT: D 752 LEU cc_start: 0.9480 (mm) cc_final: 0.9254 (mm) REVERT: D 847 ARG cc_start: 0.8425 (tmt170) cc_final: 0.7981 (tpt90) REVERT: D 999 LEU cc_start: 0.9503 (tt) cc_final: 0.9247 (tt) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.1628 time to fit residues: 98.7023 Evaluate side-chains 280 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 93 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 324 optimal weight: 0.6980 chunk 182 optimal weight: 0.7980 chunk 192 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 259 optimal weight: 50.0000 chunk 232 optimal weight: 0.7980 chunk 158 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 339 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN B 423 HIS B 602 ASN ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 HIS ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 737 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.092584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.068308 restraints weight = 122238.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.069807 restraints weight = 74503.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.070724 restraints weight = 53527.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.071366 restraints weight = 43390.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071736 restraints weight = 37851.768| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26532 Z= 0.117 Angle : 0.556 9.108 36328 Z= 0.283 Chirality : 0.037 0.165 4360 Planarity : 0.004 0.047 4624 Dihedral : 4.023 19.028 3852 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.15), residues: 3580 helix: 1.83 (0.11), residues: 2384 sheet: 0.13 (0.35), residues: 212 loop : -1.13 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 89 TYR 0.010 0.001 TYR C 741 PHE 0.018 0.001 PHE C 873 TRP 0.025 0.001 TRP C 60 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00250 (26532) covalent geometry : angle 0.55644 (36328) hydrogen bonds : bond 0.03461 ( 1685) hydrogen bonds : angle 4.28847 ( 4983) ********************** 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 382 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.835 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 118 GLN cc_start: 0.8787 (mm110) cc_final: 0.8412 (mm-40) REVERT: A 255 ILE cc_start: 0.7925 (mm) cc_final: 0.7655 (mm) REVERT: A 319 TYR cc_start: 0.8350 (t80) cc_final: 0.7725 (t80) REVERT: A 354 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 368 LYS cc_start: 0.9427 (tptp) cc_final: 0.9219 (tppt) REVERT: A 577 GLN cc_start: 0.9095 (tp40) cc_final: 0.8621 (tp40) REVERT: A 840 ASP cc_start: 0.9238 (t70) cc_final: 0.8949 (t70) REVERT: A 847 ARG cc_start: 0.8329 (tmt170) cc_final: 0.8080 (tpt90) REVERT: A 852 PHE cc_start: 0.8985 (m-80) cc_final: 0.8753 (m-80) REVERT: A 999 LEU cc_start: 0.9481 (tt) cc_final: 0.9207 (tt) REVERT: A 1059 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 1071 ASP cc_start: 0.8211 (t0) cc_final: 0.7938 (t0) REVERT: B 255 ILE cc_start: 0.8150 (mm) cc_final: 0.7867 (mm) REVERT: B 354 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8165 (mt-10) REVERT: B 368 LYS cc_start: 0.9421 (tptp) cc_final: 0.9214 (tppt) REVERT: B 577 GLN cc_start: 0.9008 (tp40) cc_final: 0.8404 (tp40) REVERT: B 840 ASP cc_start: 0.9432 (t70) cc_final: 0.9169 (t70) REVERT: B 847 ARG cc_start: 0.8516 (tmt170) cc_final: 0.8187 (tpt90) REVERT: B 852 PHE cc_start: 0.9030 (m-80) cc_final: 0.8771 (m-80) REVERT: C 134 VAL cc_start: 0.7960 (m) cc_final: 0.7720 (p) REVERT: C 253 TRP cc_start: 0.6487 (m100) cc_final: 0.6254 (m100) REVERT: C 255 ILE cc_start: 0.8111 (mm) cc_final: 0.7824 (mm) REVERT: C 354 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8276 (mt-10) REVERT: C 368 LYS cc_start: 0.9412 (tptp) cc_final: 0.9189 (tppt) REVERT: C 570 MET cc_start: 0.9091 (ptm) cc_final: 0.8803 (ptp) REVERT: C 577 GLN cc_start: 0.9045 (tp40) cc_final: 0.8486 (tp40) REVERT: C 840 ASP cc_start: 0.9308 (t70) cc_final: 0.9058 (t70) REVERT: C 847 ARG cc_start: 0.8580 (tmt170) cc_final: 0.8188 (tpt90) REVERT: C 999 LEU cc_start: 0.9442 (tt) cc_final: 0.8963 (tt) REVERT: C 1071 ASP cc_start: 0.8778 (t0) cc_final: 0.8464 (t0) REVERT: D 114 ARG cc_start: 0.8364 (ptt90) cc_final: 0.7851 (mtt-85) REVERT: D 118 GLN cc_start: 0.8627 (mm110) cc_final: 0.8333 (mp10) REVERT: D 354 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8191 (mt-10) REVERT: D 577 GLN cc_start: 0.9116 (tp40) cc_final: 0.8691 (tp40) REVERT: D 748 PHE cc_start: 0.8537 (t80) cc_final: 0.8247 (t80) REVERT: D 841 PHE cc_start: 0.9286 (t80) cc_final: 0.8861 (t80) REVERT: D 847 ARG cc_start: 0.8315 (tmt170) cc_final: 0.7909 (tpt90) REVERT: D 999 LEU cc_start: 0.9445 (tt) cc_final: 0.9157 (tt) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.1432 time to fit residues: 89.8342 Evaluate side-chains 298 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 18 optimal weight: 7.9990 chunk 252 optimal weight: 0.0270 chunk 151 optimal weight: 10.0000 chunk 283 optimal weight: 8.9990 chunk 322 optimal weight: 9.9990 chunk 333 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 261 optimal weight: 40.0000 chunk 131 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 overall best weight: 5.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 ASN ** 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 951 ASN D 184 HIS ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.088924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.065488 restraints weight = 123652.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.066912 restraints weight = 81256.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067587 restraints weight = 52823.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067770 restraints weight = 47512.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067808 restraints weight = 44066.905| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 26532 Z= 0.335 Angle : 0.778 11.703 36328 Z= 0.403 Chirality : 0.043 0.177 4360 Planarity : 0.005 0.066 4624 Dihedral : 4.744 17.807 3852 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.14), residues: 3580 helix: 1.19 (0.11), residues: 2368 sheet: -0.23 (0.37), residues: 164 loop : -1.11 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 518 TYR 0.024 0.002 TYR C 587 PHE 0.024 0.002 PHE B 583 TRP 0.058 0.003 TRP D 60 HIS 0.007 0.002 HIS D 423 Details of bonding type rmsd covalent geometry : bond 0.00701 (26532) covalent geometry : angle 0.77844 (36328) hydrogen bonds : bond 0.04558 ( 1685) hydrogen bonds : angle 5.19267 ( 4983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4287.22 seconds wall clock time: 74 minutes 48.49 seconds (4488.49 seconds total)