Starting phenix.real_space_refine on Tue Aug 26 20:49:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ww8_37884/08_2025/8ww8_37884.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ww8_37884/08_2025/8ww8_37884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ww8_37884/08_2025/8ww8_37884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ww8_37884/08_2025/8ww8_37884.map" model { file = "/net/cci-nas-00/data/ceres_data/8ww8_37884/08_2025/8ww8_37884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ww8_37884/08_2025/8ww8_37884.cif" } resolution = 3.99 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= -0.003 sd= 0.040 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: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 26364 2.51 5 N 6921 2.21 5 O 7445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s 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: 40886 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 6806 Classifications: {'peptide': 854} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 812} Chain breaks: 7 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 281 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 6, 'TRP:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 6796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6796 Classifications: {'peptide': 853} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 811} Chain breaks: 7 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 281 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 6, 'TRP:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 6806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 6806 Classifications: {'peptide': 854} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 812} Chain breaks: 7 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 281 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 6, 'TRP:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "D" Number of atoms: 6824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 856, 6824 Classifications: {'peptide': 856} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 814} Chain breaks: 7 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 281 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 6, 'TRP:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "E" Number of atoms: 6824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 856, 6824 Classifications: {'peptide': 856} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 814} Chain breaks: 7 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 281 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 6, 'TRP:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "F" Number of atoms: 6830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 856, 6830 Classifications: {'peptide': 856} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 814} Chain breaks: 7 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 5, 'TRP:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 9.95, per 1000 atoms: 0.24 Number of scatterers: 40886 At special positions: 0 Unit cell: (168.63, 159.87, 164.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 7445 8.00 N 6921 7.00 C 26364 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: 3.82 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9790 Finding SS restraints... Secondary structure from input PDB file: 236 helices and 38 sheets defined 53.9% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 removed outlier: 4.135A pdb=" N THR A 15 " --> pdb=" O THR A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 34 removed outlier: 3.566A pdb=" N GLU A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 61 through 79 Processing helix chain 'A' and resid 111 through 128 removed outlier: 4.280A pdb=" N ASN A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 180 removed outlier: 3.651A pdb=" N LYS A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 removed outlier: 3.604A pdb=" N GLN A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 297 through 308 removed outlier: 3.531A pdb=" N ASN A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.522A pdb=" N VAL A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 317' Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.581A pdb=" N TRP A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 346 removed outlier: 3.793A pdb=" N ALA A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 346 " --> pdb=" O PHE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.692A pdb=" N TRP A 350 " --> pdb=" O CYS A 346 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 346 through 351' Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 375 through 386 removed outlier: 3.668A pdb=" N MET A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 410 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 466 through 494 removed outlier: 4.295A pdb=" N SER A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 516 removed outlier: 4.107A pdb=" N SER A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 520 through 535 removed outlier: 3.677A pdb=" N PHE A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 608 through 620 Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 641 through 654 Processing helix chain 'A' and resid 662 through 668 Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.838A pdb=" N LEU A 683 " --> pdb=" O PHE A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 709 removed outlier: 4.164A pdb=" N LEU A 705 " --> pdb=" O ASN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 783 through 786 Processing helix chain 'A' and resid 787 through 809 removed outlier: 3.510A pdb=" N GLN A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 818 through 833 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 855 through 870 removed outlier: 3.623A pdb=" N VAL A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 887 removed outlier: 3.513A pdb=" N GLN A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 removed outlier: 4.350A pdb=" N TYR A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 944 removed outlier: 3.549A pdb=" N TRP A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.656A pdb=" N GLU B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 79 Processing helix chain 'B' and resid 111 through 128 removed outlier: 4.291A pdb=" N ASN B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 180 removed outlier: 3.536A pdb=" N LYS B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 190 removed outlier: 4.006A pdb=" N GLN B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 288 through 297 Processing helix chain 'B' and resid 297 through 308 removed outlier: 3.684A pdb=" N ASN B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 312 through 317 removed outlier: 3.901A pdb=" N GLU B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 332 Processing helix chain 'B' and resid 335 through 345 removed outlier: 3.626A pdb=" N ALA B 339 " --> pdb=" O TYR B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 353 through 368 Processing helix chain 'B' and resid 374 through 386 removed outlier: 3.936A pdb=" N ILE B 378 " --> pdb=" O THR B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 403 Processing helix chain 'B' and resid 414 through 427 removed outlier: 3.652A pdb=" N ILE B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 494 removed outlier: 4.195A pdb=" N SER B 474 " --> pdb=" O HIS B 470 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 477 " --> pdb=" O ILE B 473 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 479 " --> pdb=" O GLU B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.971A pdb=" N SER B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 520 through 535 removed outlier: 4.030A pdb=" N PHE B 533 " --> pdb=" O ARG B 529 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 608 through 620 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 641 through 654 Processing helix chain 'B' and resid 662 through 668 removed outlier: 4.086A pdb=" N LEU B 666 " --> pdb=" O ASN B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 709 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 779 through 786 removed outlier: 5.912A pdb=" N TYR B 784 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE B 785 " --> pdb=" O HIS B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 809 Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 818 through 833 Processing helix chain 'B' and resid 833 through 842 Processing helix chain 'B' and resid 855 through 870 removed outlier: 3.579A pdb=" N VAL B 859 " --> pdb=" O LEU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 886 removed outlier: 4.063A pdb=" N GLN B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 893 removed outlier: 4.351A pdb=" N TYR B 892 " --> pdb=" O VAL B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 944 Processing helix chain 'C' and resid 12 through 21 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.667A pdb=" N GLU C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 79 Processing helix chain 'C' and resid 111 through 128 removed outlier: 4.189A pdb=" N ASN C 128 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.677A pdb=" N LYS C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 190 removed outlier: 3.739A pdb=" N GLN C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 297 through 308 removed outlier: 3.956A pdb=" N ASN C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 312 through 317 removed outlier: 3.733A pdb=" N VAL C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 312 through 317' Processing helix chain 'C' and resid 317 through 332 Processing helix chain 'C' and resid 335 through 346 Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.666A pdb=" N THR C 352 " --> pdb=" O GLU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 368 Processing helix chain 'C' and resid 374 through 386 removed outlier: 4.068A pdb=" N ILE C 378 " --> pdb=" O THR C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 409 Processing helix chain 'C' and resid 414 through 427 Processing helix chain 'C' and resid 466 through 494 removed outlier: 4.111A pdb=" N SER C 474 " --> pdb=" O HIS C 470 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE C 477 " --> pdb=" O ILE C 473 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG C 479 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 516 removed outlier: 4.148A pdb=" N SER C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 520 through 536 Processing helix chain 'C' and resid 539 through 544 Processing helix chain 'C' and resid 591 through 605 Processing helix chain 'C' and resid 607 through 620 Processing helix chain 'C' and resid 621 through 623 No H-bonds generated for 'chain 'C' and resid 621 through 623' Processing helix chain 'C' and resid 641 through 654 Processing helix chain 'C' and resid 662 through 668 removed outlier: 4.296A pdb=" N LEU C 666 " --> pdb=" O ASN C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 684 removed outlier: 3.570A pdb=" N ARG C 682 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 684 " --> pdb=" O MET C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 710 Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.709A pdb=" N ARG C 752 " --> pdb=" O GLY C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 781 Processing helix chain 'C' and resid 782 through 787 removed outlier: 4.355A pdb=" N MET C 786 " --> pdb=" O HIS C 782 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 787 " --> pdb=" O GLU C 783 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 782 through 787' Processing helix chain 'C' and resid 787 through 809 removed outlier: 3.670A pdb=" N GLU C 808 " --> pdb=" O LYS C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 816 Processing helix chain 'C' and resid 818 through 833 Processing helix chain 'C' and resid 833 through 842 Processing helix chain 'C' and resid 855 through 870 removed outlier: 3.849A pdb=" N VAL C 859 " --> pdb=" O LEU C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 886 Processing helix chain 'C' and resid 939 through 944 Processing helix chain 'D' and resid 12 through 21 Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.961A pdb=" N GLU D 28 " --> pdb=" O VAL D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 38 Processing helix chain 'D' and resid 61 through 79 Processing helix chain 'D' and resid 111 through 128 removed outlier: 4.124A pdb=" N ASN D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.623A pdb=" N LYS D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 288 through 297 Processing helix chain 'D' and resid 297 through 308 removed outlier: 3.579A pdb=" N ASN D 308 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 312 through 317 Processing helix chain 'D' and resid 317 through 332 Processing helix chain 'D' and resid 335 through 345 Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.546A pdb=" N THR D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 368 removed outlier: 3.575A pdb=" N ASN D 363 " --> pdb=" O GLU D 359 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 386 removed outlier: 3.828A pdb=" N ILE D 378 " --> pdb=" O THR D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 409 Processing helix chain 'D' and resid 414 through 427 Processing helix chain 'D' and resid 466 through 494 removed outlier: 4.090A pdb=" N SER D 474 " --> pdb=" O HIS D 470 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE D 477 " --> pdb=" O ILE D 473 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER D 478 " --> pdb=" O SER D 474 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 514 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 520 through 536 Processing helix chain 'D' and resid 591 through 605 Processing helix chain 'D' and resid 608 through 621 Processing helix chain 'D' and resid 641 through 654 Processing helix chain 'D' and resid 662 through 668 removed outlier: 3.998A pdb=" N LEU D 666 " --> pdb=" O ASN D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 684 removed outlier: 4.244A pdb=" N LYS D 684 " --> pdb=" O PHE D 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 680 through 684' Processing helix chain 'D' and resid 701 through 709 Processing helix chain 'D' and resid 746 through 751 Processing helix chain 'D' and resid 777 through 783 removed outlier: 3.559A pdb=" N ILE D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 786 No H-bonds generated for 'chain 'D' and resid 784 through 786' Processing helix chain 'D' and resid 787 through 809 Processing helix chain 'D' and resid 812 through 816 Processing helix chain 'D' and resid 818 through 833 Processing helix chain 'D' and resid 833 through 842 Processing helix chain 'D' and resid 855 through 870 removed outlier: 3.673A pdb=" N VAL D 859 " --> pdb=" O LEU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 887 removed outlier: 3.793A pdb=" N SER D 881 " --> pdb=" O ALA D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 891 removed outlier: 3.967A pdb=" N LYS D 891 " --> pdb=" O VAL D 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 888 through 891' Processing helix chain 'D' and resid 939 through 944 removed outlier: 3.693A pdb=" N TRP D 943 " --> pdb=" O LYS D 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 21 Processing helix chain 'E' and resid 22 through 33 removed outlier: 4.476A pdb=" N ARG E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 39 Processing helix chain 'E' and resid 61 through 78 Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 167 through 180 removed outlier: 3.620A pdb=" N LYS E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 190 Processing helix chain 'E' and resid 251 through 257 Processing helix chain 'E' and resid 288 through 295 removed outlier: 3.649A pdb=" N ILE E 292 " --> pdb=" O HIS E 288 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 310 removed outlier: 4.093A pdb=" N LEU E 303 " --> pdb=" O GLU E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 317 removed outlier: 3.703A pdb=" N VAL E 316 " --> pdb=" O PRO E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 332 removed outlier: 3.625A pdb=" N TRP E 321 " --> pdb=" O GLU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 345 Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.841A pdb=" N THR E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 368 Processing helix chain 'E' and resid 374 through 386 removed outlier: 3.830A pdb=" N ILE E 378 " --> pdb=" O THR E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 409 Processing helix chain 'E' and resid 416 through 427 Processing helix chain 'E' and resid 466 through 494 removed outlier: 3.607A pdb=" N HIS E 470 " --> pdb=" O PRO E 466 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER E 474 " --> pdb=" O HIS E 470 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU E 475 " --> pdb=" O ILE E 471 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER E 478 " --> pdb=" O SER E 474 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG E 479 " --> pdb=" O GLU E 475 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 516 removed outlier: 4.211A pdb=" N SER E 516 " --> pdb=" O GLU E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 519 No H-bonds generated for 'chain 'E' and resid 517 through 519' Processing helix chain 'E' and resid 520 through 535 removed outlier: 3.825A pdb=" N GLN E 530 " --> pdb=" O GLY E 526 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE E 533 " --> pdb=" O ARG E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 605 Processing helix chain 'E' and resid 608 through 622 removed outlier: 3.798A pdb=" N ILE E 622 " --> pdb=" O LEU E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 654 Processing helix chain 'E' and resid 662 through 668 removed outlier: 4.087A pdb=" N LEU E 666 " --> pdb=" O ASN E 662 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 684 removed outlier: 4.000A pdb=" N LEU E 683 " --> pdb=" O PHE E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 709 removed outlier: 3.559A pdb=" N LEU E 705 " --> pdb=" O ASN E 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 752 removed outlier: 3.702A pdb=" N ARG E 752 " --> pdb=" O GLY E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 778 through 783 Processing helix chain 'E' and resid 784 through 786 No H-bonds generated for 'chain 'E' and resid 784 through 786' Processing helix chain 'E' and resid 787 through 809 Processing helix chain 'E' and resid 812 through 816 Processing helix chain 'E' and resid 818 through 833 Processing helix chain 'E' and resid 833 through 842 Processing helix chain 'E' and resid 855 through 870 removed outlier: 3.746A pdb=" N VAL E 859 " --> pdb=" O LEU E 855 " (cutoff:3.500A) Processing helix chain 'E' and resid 878 through 886 Processing helix chain 'E' and resid 887 through 892 Processing helix chain 'E' and resid 939 through 944 Processing helix chain 'F' and resid 12 through 21 Processing helix chain 'F' and resid 24 through 34 removed outlier: 3.641A pdb=" N GLU F 28 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 79 Processing helix chain 'F' and resid 111 through 128 removed outlier: 4.133A pdb=" N ASN F 128 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 180 removed outlier: 3.518A pdb=" N LYS F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 190 Processing helix chain 'F' and resid 251 through 257 Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 297 through 308 removed outlier: 3.756A pdb=" N ASN F 308 " --> pdb=" O HIS F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 312 through 317 removed outlier: 3.522A pdb=" N GLU F 317 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 332 Processing helix chain 'F' and resid 335 through 345 Processing helix chain 'F' and resid 346 through 352 removed outlier: 3.798A pdb=" N THR F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 368 Processing helix chain 'F' and resid 374 through 386 removed outlier: 4.008A pdb=" N ILE F 378 " --> pdb=" O THR F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 410 Processing helix chain 'F' and resid 414 through 427 removed outlier: 3.780A pdb=" N ILE F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 493 removed outlier: 3.989A pdb=" N PHE F 477 " --> pdb=" O ILE F 473 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER F 478 " --> pdb=" O SER F 474 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG F 479 " --> pdb=" O GLU F 475 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER F 493 " --> pdb=" O LYS F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 518 removed outlier: 4.037A pdb=" N TYR F 503 " --> pdb=" O ASN F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 536 removed outlier: 4.294A pdb=" N PHE F 533 " --> pdb=" O ARG F 529 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU F 534 " --> pdb=" O GLN F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 605 Processing helix chain 'F' and resid 608 through 620 Processing helix chain 'F' and resid 621 through 623 No H-bonds generated for 'chain 'F' and resid 621 through 623' Processing helix chain 'F' and resid 641 through 654 Processing helix chain 'F' and resid 662 through 668 removed outlier: 4.255A pdb=" N LEU F 666 " --> pdb=" O ASN F 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 709 Processing helix chain 'F' and resid 746 through 752 Processing helix chain 'F' and resid 777 through 783 removed outlier: 4.003A pdb=" N ILE F 781 " --> pdb=" O ASP F 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 809 Processing helix chain 'F' and resid 812 through 816 Processing helix chain 'F' and resid 818 through 833 Processing helix chain 'F' and resid 834 through 842 Processing helix chain 'F' and resid 855 through 869 Processing helix chain 'F' and resid 878 through 887 Processing helix chain 'F' and resid 888 through 892 removed outlier: 4.463A pdb=" N LYS F 891 " --> pdb=" O VAL F 888 " (cutoff:3.500A) Processing helix chain 'F' and resid 939 through 944 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.991A pdb=" N ILE A 160 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 157 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR A 144 " --> pdb=" O HIS A 157 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 142 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 225 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 145 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LEU A 223 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.526A pdb=" N VAL A 431 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TRP A 442 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 553 Processing sheet with id=AA5, first strand: chain 'A' and resid 634 through 635 Processing sheet with id=AA6, first strand: chain 'A' and resid 658 through 660 removed outlier: 3.883A pdb=" N TYR A 690 " --> pdb=" O SER A 659 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 906 through 908 removed outlier: 3.542A pdb=" N SER A 920 " --> pdb=" O GLU A 845 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.587A pdb=" N THR B 40 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR B 57 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 145 removed outlier: 3.917A pdb=" N PHE B 143 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR B 225 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 145 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU B 223 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 430 through 434 removed outlier: 3.610A pdb=" N ASP B 433 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP B 442 " --> pdb=" O GLU B 463 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 461 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 551 through 553 removed outlier: 3.890A pdb=" N LYS B 566 " --> pdb=" O SER B 559 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 658 through 660 removed outlier: 3.712A pdb=" N SER B 659 " --> pdb=" O TYR B 688 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR B 690 " --> pdb=" O SER B 659 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU B 632 " --> pdb=" O MET B 732 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 736 " --> pdb=" O TRP B 634 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N MET B 631 " --> pdb=" O ARG B 754 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N TYR B 756 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU B 633 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 906 through 908 removed outlier: 3.526A pdb=" N SER B 920 " --> pdb=" O GLU B 845 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 56 through 58 Processing sheet with id=AB6, first strand: chain 'C' and resid 94 through 95 removed outlier: 3.522A pdb=" N HIS C 157 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 144 " --> pdb=" O HIS C 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 142 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE C 143 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR C 225 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU C 145 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU C 223 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.930A pdb=" N TRP C 442 " --> pdb=" O GLU C 463 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 463 " --> pdb=" O TRP C 442 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 550 through 553 Processing sheet with id=AB9, first strand: chain 'C' and resid 658 through 660 removed outlier: 3.605A pdb=" N TYR C 690 " --> pdb=" O SER C 659 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU C 632 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N SER C 736 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP C 634 " --> pdb=" O SER C 736 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N MET C 631 " --> pdb=" O ARG C 754 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N TYR C 756 " --> pdb=" O MET C 631 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU C 633 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 906 through 908 removed outlier: 3.755A pdb=" N SER C 920 " --> pdb=" O GLU C 845 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 56 through 58 Processing sheet with id=AC3, first strand: chain 'D' and resid 140 through 145 removed outlier: 3.909A pdb=" N THR D 225 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 145 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU D 223 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 430 through 434 removed outlier: 4.173A pdb=" N TRP D 442 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 550 through 553 removed outlier: 3.566A pdb=" N LYS D 566 " --> pdb=" O SER D 559 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 658 through 660 removed outlier: 3.561A pdb=" N SER D 659 " --> pdb=" O TYR D 688 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR D 690 " --> pdb=" O SER D 659 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY D 689 " --> pdb=" O VAL D 733 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ALA D 735 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU D 632 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N SER D 736 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP D 634 " --> pdb=" O SER D 736 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N MET D 631 " --> pdb=" O ARG D 754 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR D 756 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU D 633 " --> pdb=" O TYR D 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 906 through 908 removed outlier: 3.624A pdb=" N VAL D 844 " --> pdb=" O ARG D 907 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AC9, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=AD1, first strand: chain 'E' and resid 93 through 97 removed outlier: 7.379A pdb=" N HIS E 140 " --> pdb=" O PRO E 161 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR E 225 " --> pdb=" O PHE E 143 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU E 145 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU E 223 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 430 through 434 removed outlier: 4.571A pdb=" N TRP E 442 " --> pdb=" O GLU E 463 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU E 463 " --> pdb=" O TRP E 442 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU E 444 " --> pdb=" O ARG E 461 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 550 through 553 Processing sheet with id=AD4, first strand: chain 'E' and resid 658 through 660 removed outlier: 6.638A pdb=" N SER E 659 " --> pdb=" O TYR E 690 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 632 " --> pdb=" O MET E 732 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER E 736 " --> pdb=" O TRP E 634 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 843 through 845 Processing sheet with id=AD6, first strand: chain 'F' and resid 56 through 58 Processing sheet with id=AD7, first strand: chain 'F' and resid 94 through 95 removed outlier: 6.522A pdb=" N PHE F 141 " --> pdb=" O GLY F 226 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLY F 226 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE F 143 " --> pdb=" O LYS F 224 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 430 through 434 removed outlier: 4.662A pdb=" N TRP F 442 " --> pdb=" O GLU F 463 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU F 463 " --> pdb=" O TRP F 442 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 550 through 553 Processing sheet with id=AE1, first strand: chain 'F' and resid 658 through 660 removed outlier: 3.674A pdb=" N SER F 659 " --> pdb=" O TYR F 688 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR F 690 " --> pdb=" O SER F 659 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 906 through 908 removed outlier: 3.610A pdb=" N SER F 920 " --> pdb=" O GLU F 845 " (cutoff:3.500A) 1919 hydrogen bonds defined for protein. 5565 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.92 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6660 1.32 - 1.44: 11716 1.44 - 1.57: 23331 1.57 - 1.69: 0 1.69 - 1.81: 252 Bond restraints: 41959 Sorted by residual: bond pdb=" CA LEU E 39 " pdb=" C LEU E 39 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.26e-02 6.30e+03 4.54e+00 bond pdb=" CA GLU E 28 " pdb=" C GLU E 28 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.28e-02 6.10e+03 4.54e+00 bond pdb=" N GLU E 28 " pdb=" CA GLU E 28 " ideal model delta sigma weight residual 1.459 1.436 0.022 1.16e-02 7.43e+03 3.75e+00 bond pdb=" CA LEU E 27 " pdb=" C LEU E 27 " ideal model delta sigma weight residual 1.524 1.501 0.023 1.27e-02 6.20e+03 3.24e+00 bond pdb=" CD GLN A 74 " pdb=" OE1 GLN A 74 " ideal model delta sigma weight residual 1.231 1.197 0.034 1.90e-02 2.77e+03 3.21e+00 ... (remaining 41954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 55722 1.96 - 3.91: 1055 3.91 - 5.87: 146 5.87 - 7.83: 25 7.83 - 9.79: 5 Bond angle restraints: 56953 Sorted by residual: angle pdb=" CA GLN A 74 " pdb=" CB GLN A 74 " pdb=" CG GLN A 74 " ideal model delta sigma weight residual 114.10 123.89 -9.79 2.00e+00 2.50e-01 2.39e+01 angle pdb=" C GLU A 370 " pdb=" CA GLU A 370 " pdb=" CB GLU A 370 " ideal model delta sigma weight residual 115.79 110.03 5.76 1.19e+00 7.06e-01 2.34e+01 angle pdb=" N GLN A 74 " pdb=" CA GLN A 74 " pdb=" CB GLN A 74 " ideal model delta sigma weight residual 110.39 117.16 -6.77 1.66e+00 3.63e-01 1.66e+01 angle pdb=" CB ARG B 529 " pdb=" CG ARG B 529 " pdb=" CD ARG B 529 " ideal model delta sigma weight residual 111.30 120.51 -9.21 2.30e+00 1.89e-01 1.60e+01 angle pdb=" N ASN F 363 " pdb=" CA ASN F 363 " pdb=" C ASN F 363 " ideal model delta sigma weight residual 111.14 106.94 4.20 1.08e+00 8.57e-01 1.51e+01 ... (remaining 56948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 22349 17.95 - 35.90: 1994 35.90 - 53.85: 441 53.85 - 71.80: 110 71.80 - 89.75: 27 Dihedral angle restraints: 24921 sinusoidal: 9786 harmonic: 15135 Sorted by residual: dihedral pdb=" CA ASN B 251 " pdb=" C ASN B 251 " pdb=" N LEU B 252 " pdb=" CA LEU B 252 " ideal model delta harmonic sigma weight residual -180.00 -155.27 -24.73 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA HIS E 470 " pdb=" C HIS E 470 " pdb=" N ILE E 471 " pdb=" CA ILE E 471 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA HIS F 415 " pdb=" C HIS F 415 " pdb=" N TYR F 416 " pdb=" CA TYR F 416 " ideal model delta harmonic sigma weight residual 180.00 -157.14 -22.86 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 24918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 4301 0.035 - 0.070: 1384 0.070 - 0.105: 417 0.105 - 0.140: 118 0.140 - 0.176: 13 Chirality restraints: 6233 Sorted by residual: chirality pdb=" CA ARG B 529 " pdb=" N ARG B 529 " pdb=" C ARG B 529 " pdb=" CB ARG B 529 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CB THR A 868 " pdb=" CA THR A 868 " pdb=" OG1 THR A 868 " pdb=" CG2 THR A 868 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CB THR D 868 " pdb=" CA THR D 868 " pdb=" OG1 THR D 868 " pdb=" CG2 THR D 868 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 6230 not shown) Planarity restraints: 7232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 112 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO C 113 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 113 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 113 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 22 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C ALA E 22 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA E 22 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU E 23 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 473 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C ILE A 473 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE A 473 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 474 " 0.012 2.00e-02 2.50e+03 ... (remaining 7229 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1278 2.69 - 3.24: 44124 3.24 - 3.79: 71984 3.79 - 4.35: 90704 4.35 - 4.90: 138857 Nonbonded interactions: 346947 Sorted by model distance: nonbonded pdb=" NH1 ARG A 536 " pdb=" O GLN A 537 " model vdw 2.135 3.120 nonbonded pdb=" O ARG D 513 " pdb=" NZ LYS D 517 " model vdw 2.204 3.120 nonbonded pdb=" OD1 ASN A 662 " pdb=" OG SER A 664 " model vdw 2.218 3.040 nonbonded pdb=" O GLU C 340 " pdb=" OG SER C 343 " model vdw 2.219 3.040 nonbonded pdb=" O TYR C 617 " pdb=" OG1 THR C 620 " model vdw 2.227 3.040 ... (remaining 346942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 763 or resid 777 through 949)) selection = chain 'B' selection = (chain 'C' and (resid 11 through 763 or resid 777 through 949)) selection = (chain 'D' and (resid 11 through 763 or resid 777 through 949)) selection = (chain 'E' and (resid 11 through 763 or resid 777 through 949)) selection = (chain 'F' and (resid 11 through 751 or (resid 752 and (name N or name CA or nam \ e C or name O or name CB )) or resid 753 through 763 or resid 777 through 949)) } 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: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 39.520 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.060 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 : 0.003 0.042 41959 Z= 0.152 Angle : 0.643 9.786 56953 Z= 0.362 Chirality : 0.040 0.176 6233 Planarity : 0.004 0.051 7232 Dihedral : 14.854 89.752 15131 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.79 % Favored : 95.01 % Rotamer: Outliers : 3.83 % Allowed : 1.69 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.14 (0.12), residues: 5033 helix: 1.16 (0.11), residues: 2404 sheet: -0.59 (0.25), residues: 452 loop : -0.93 (0.14), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 529 TYR 0.020 0.001 TYR A 302 PHE 0.016 0.001 PHE E 511 TRP 0.023 0.001 TRP D 802 HIS 0.015 0.001 HIS E 415 Details of bonding type rmsd covalent geometry : bond 0.00262 (41959) covalent geometry : angle 0.64300 (56953) hydrogen bonds : bond 0.16565 ( 1919) hydrogen bonds : angle 6.41084 ( 5565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 259 time to evaluate : 1.630 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 82 MET cc_start: 0.8655 (tpt) cc_final: 0.8376 (tmm) REVERT: B 708 MET cc_start: 0.8861 (mmp) cc_final: 0.8606 (mmm) REVERT: C 211 TYR cc_start: 0.5608 (t80) cc_final: 0.4958 (t80) REVERT: C 728 MET cc_start: 0.5879 (ptt) cc_final: 0.4538 (mmt) REVERT: D 81 LEU cc_start: 0.7409 (pt) cc_final: 0.7200 (pt) REVERT: D 82 MET cc_start: 0.5385 (mpp) cc_final: 0.5174 (mpp) REVERT: D 379 MET cc_start: 0.9286 (mpp) cc_final: 0.8988 (mpp) REVERT: E 45 LYS cc_start: 0.1740 (OUTLIER) cc_final: 0.1419 (pttt) REVERT: E 53 ILE cc_start: 0.5916 (OUTLIER) cc_final: 0.5581 (mt) REVERT: E 98 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: E 126 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6088 (tp) REVERT: E 131 VAL cc_start: 0.3678 (OUTLIER) cc_final: 0.3439 (m) REVERT: E 132 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5633 (mt) REVERT: E 183 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8627 (m) REVERT: E 189 GLU cc_start: 0.4165 (OUTLIER) cc_final: 0.3619 (mt-10) REVERT: E 205 SER cc_start: 0.6166 (OUTLIER) cc_final: 0.5795 (t) REVERT: E 213 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.7256 (p) REVERT: E 250 TYR cc_start: 0.4554 (OUTLIER) cc_final: 0.4244 (m-80) REVERT: E 413 LEU cc_start: 0.8945 (mm) cc_final: 0.8595 (mt) REVERT: E 631 MET cc_start: 0.8881 (tpt) cc_final: 0.8666 (tpt) REVERT: E 732 MET cc_start: 0.9085 (mmm) cc_final: 0.8673 (mmm) REVERT: F 482 ASP cc_start: 0.8985 (m-30) cc_final: 0.8754 (m-30) REVERT: F 681 MET cc_start: 0.8947 (pmm) cc_final: 0.8685 (pmm) outliers start: 165 outliers final: 49 residues processed: 419 average time/residue: 0.2395 time to fit residues: 167.7117 Evaluate side-chains 247 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 187 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain D residue 578 GLN Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain E residue 791 GLN Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 900 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.0470 chunk 132 optimal weight: 9.9990 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 overall best weight: 3.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN A 836 HIS ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 HIS B 363 ASN ** B 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS C 363 ASN C 410 ASN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 HIS ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 549 HIS ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 ASN ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 GLN E 549 HIS ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN F 578 GLN F 836 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.072084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.050532 restraints weight = 397060.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.050442 restraints weight = 300343.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.049816 restraints weight = 241745.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.049682 restraints weight = 210325.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.049652 restraints weight = 176784.039| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41959 Z= 0.163 Angle : 0.621 10.782 56953 Z= 0.322 Chirality : 0.042 0.248 6233 Planarity : 0.005 0.057 7232 Dihedral : 7.135 99.163 5660 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.48 % Favored : 94.38 % Rotamer: Outliers : 2.09 % Allowed : 9.24 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.24 (0.12), residues: 5033 helix: 1.21 (0.11), residues: 2435 sheet: -0.71 (0.24), residues: 496 loop : -0.83 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 267 TYR 0.032 0.002 TYR E 302 PHE 0.024 0.002 PHE E 477 TRP 0.018 0.001 TRP B 442 HIS 0.009 0.001 HIS E 415 Details of bonding type rmsd covalent geometry : bond 0.00345 (41959) covalent geometry : angle 0.62133 (56953) hydrogen bonds : bond 0.04524 ( 1919) hydrogen bonds : angle 5.35563 ( 5565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 200 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.8538 (ppp) cc_final: 0.8290 (ppp) REVERT: A 452 MET cc_start: 0.7705 (ppp) cc_final: 0.7497 (ppp) REVERT: A 486 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8711 (pp20) REVERT: A 499 ASN cc_start: 0.9347 (t0) cc_final: 0.8995 (m110) REVERT: A 631 MET cc_start: 0.8955 (tpp) cc_final: 0.8728 (tpp) REVERT: B 72 LEU cc_start: 0.9010 (mt) cc_final: 0.8461 (pp) REVERT: B 379 MET cc_start: 0.9280 (tpp) cc_final: 0.9035 (tpp) REVERT: C 653 LEU cc_start: 0.9633 (mm) cc_final: 0.9422 (tp) REVERT: C 708 MET cc_start: 0.9557 (mmm) cc_final: 0.8939 (mmp) REVERT: C 728 MET cc_start: 0.6187 (ptt) cc_final: 0.4649 (mmt) REVERT: D 631 MET cc_start: 0.9307 (tpt) cc_final: 0.8879 (tpt) REVERT: D 708 MET cc_start: 0.9313 (mmm) cc_final: 0.9085 (mmm) REVERT: E 379 MET cc_start: 0.8796 (mpp) cc_final: 0.7846 (mpp) REVERT: E 390 TYR cc_start: 0.8819 (t80) cc_final: 0.8397 (t80) REVERT: E 631 MET cc_start: 0.8836 (tpt) cc_final: 0.8574 (tpt) REVERT: E 732 MET cc_start: 0.9410 (mmm) cc_final: 0.9067 (mmm) REVERT: F 258 LEU cc_start: 0.5084 (OUTLIER) cc_final: 0.4875 (mt) REVERT: F 681 MET cc_start: 0.8996 (pmm) cc_final: 0.8698 (pmm) outliers start: 90 outliers final: 52 residues processed: 281 average time/residue: 0.2316 time to fit residues: 112.6952 Evaluate side-chains 232 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 797 ILE Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 790 CYS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 578 GLN Chi-restraints excluded: chain D residue 583 CYS Chi-restraints excluded: chain D residue 707 GLU Chi-restraints excluded: chain D residue 789 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 367 HIS Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 340 GLU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 900 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 192 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 16 optimal weight: 50.0000 chunk 232 optimal weight: 3.9990 chunk 378 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 494 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN D 491 HIS ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 ASN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 578 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.070484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.048436 restraints weight = 406492.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.048502 restraints weight = 291460.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.048620 restraints weight = 227048.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.048171 restraints weight = 221058.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.047581 restraints weight = 190273.145| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 41959 Z= 0.204 Angle : 0.628 10.648 56953 Z= 0.328 Chirality : 0.041 0.317 6233 Planarity : 0.005 0.061 7232 Dihedral : 5.948 91.446 5586 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.80 % Favored : 94.06 % Rotamer: Outliers : 2.32 % Allowed : 12.93 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.06 (0.12), residues: 5033 helix: 1.05 (0.10), residues: 2439 sheet: -0.83 (0.23), residues: 499 loop : -0.88 (0.14), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 267 TYR 0.025 0.002 TYR D 862 PHE 0.024 0.002 PHE E 477 TRP 0.026 0.001 TRP F 442 HIS 0.009 0.002 HIS D 574 Details of bonding type rmsd covalent geometry : bond 0.00424 (41959) covalent geometry : angle 0.62807 (56953) hydrogen bonds : bond 0.04409 ( 1919) hydrogen bonds : angle 5.30992 ( 5565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 193 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.9045 (tpp) cc_final: 0.8723 (tpp) REVERT: B 379 MET cc_start: 0.8939 (tpp) cc_final: 0.8730 (tpp) REVERT: B 417 MET cc_start: 0.8131 (mmm) cc_final: 0.7900 (tpt) REVERT: B 708 MET cc_start: 0.8413 (mmm) cc_final: 0.8136 (mmm) REVERT: C 452 MET cc_start: 0.8666 (ppp) cc_final: 0.7986 (ppp) REVERT: C 616 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8905 (m-10) REVERT: C 708 MET cc_start: 0.9534 (mmm) cc_final: 0.9019 (mmm) REVERT: C 728 MET cc_start: 0.6272 (ptt) cc_final: 0.4582 (mmt) REVERT: D 340 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8432 (tp30) REVERT: D 379 MET cc_start: 0.9113 (mpp) cc_final: 0.8776 (mpp) REVERT: D 708 MET cc_start: 0.9422 (mmm) cc_final: 0.9148 (mmm) REVERT: E 294 MET cc_start: 0.8633 (tmm) cc_final: 0.8429 (tmm) REVERT: E 340 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.8914 (tp30) REVERT: F 416 TYR cc_start: 0.8370 (t80) cc_final: 0.7882 (t80) REVERT: F 417 MET cc_start: 0.8200 (mpp) cc_final: 0.7839 (mpp) REVERT: F 452 MET cc_start: 0.8673 (ppp) cc_final: 0.8392 (ppp) REVERT: F 681 MET cc_start: 0.9022 (pmm) cc_final: 0.8698 (pmm) outliers start: 100 outliers final: 57 residues processed: 279 average time/residue: 0.2173 time to fit residues: 104.2308 Evaluate side-chains 240 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 180 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 797 ILE Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 616 PHE Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 790 CYS Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 487 HIS Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 578 GLN Chi-restraints excluded: chain D residue 583 CYS Chi-restraints excluded: chain D residue 707 GLU Chi-restraints excluded: chain D residue 789 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 367 HIS Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 742 ILE Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 900 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 209 optimal weight: 4.9990 chunk 473 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 374 optimal weight: 2.9990 chunk 476 optimal weight: 10.0000 chunk 364 optimal weight: 5.9990 chunk 337 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 HIS ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.070117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.048310 restraints weight = 404725.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.048248 restraints weight = 288455.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.048085 restraints weight = 207702.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.048085 restraints weight = 204882.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.048085 restraints weight = 204882.438| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 41959 Z= 0.192 Angle : 0.617 9.522 56953 Z= 0.320 Chirality : 0.041 0.305 6233 Planarity : 0.005 0.061 7232 Dihedral : 5.794 90.710 5580 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.00 % Favored : 93.86 % Rotamer: Outliers : 2.44 % Allowed : 15.37 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.06 (0.12), residues: 5033 helix: 1.06 (0.10), residues: 2434 sheet: -0.89 (0.23), residues: 498 loop : -0.89 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 267 TYR 0.024 0.002 TYR D 862 PHE 0.027 0.002 PHE B 84 TRP 0.013 0.001 TRP D 943 HIS 0.009 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00399 (41959) covalent geometry : angle 0.61660 (56953) hydrogen bonds : bond 0.04164 ( 1919) hydrogen bonds : angle 5.23460 ( 5565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 187 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 ASN cc_start: 0.9345 (t0) cc_final: 0.8945 (m110) REVERT: B 379 MET cc_start: 0.9289 (tpp) cc_final: 0.8960 (tpp) REVERT: C 340 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8533 (tp30) REVERT: C 417 MET cc_start: 0.8785 (ptp) cc_final: 0.8366 (ptp) REVERT: C 616 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.9005 (m-10) REVERT: C 708 MET cc_start: 0.9503 (mmm) cc_final: 0.8991 (mmm) REVERT: C 728 MET cc_start: 0.6685 (ptt) cc_final: 0.4748 (mmt) REVERT: D 340 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8388 (tp30) REVERT: E 82 MET cc_start: 0.5848 (pmm) cc_final: 0.5576 (pmm) REVERT: E 340 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.8906 (tp30) REVERT: E 631 MET cc_start: 0.8524 (tpp) cc_final: 0.8214 (tpp) REVERT: F 416 TYR cc_start: 0.8548 (t80) cc_final: 0.7841 (t80) REVERT: F 417 MET cc_start: 0.8255 (mpp) cc_final: 0.7161 (mpp) REVERT: F 470 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.8713 (t-170) REVERT: F 681 MET cc_start: 0.9015 (pmm) cc_final: 0.8714 (pmm) outliers start: 105 outliers final: 58 residues processed: 282 average time/residue: 0.2269 time to fit residues: 110.1980 Evaluate side-chains 236 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 797 ILE Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 616 PHE Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 790 CYS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 487 HIS Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 583 CYS Chi-restraints excluded: chain D residue 707 GLU Chi-restraints excluded: chain D residue 789 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 367 HIS Chi-restraints excluded: chain E residue 405 TYR Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 742 ILE Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 499 ASN Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 900 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 490 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 168 optimal weight: 30.0000 chunk 38 optimal weight: 0.9990 chunk 398 optimal weight: 8.9990 chunk 413 optimal weight: 0.0020 chunk 208 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 473 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 364 optimal weight: 30.0000 overall best weight: 2.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.070648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.049007 restraints weight = 392375.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.048606 restraints weight = 283955.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.048274 restraints weight = 218652.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.048362 restraints weight = 179219.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.048378 restraints weight = 168432.293| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41959 Z= 0.133 Angle : 0.589 11.281 56953 Z= 0.300 Chirality : 0.041 0.315 6233 Planarity : 0.004 0.063 7232 Dihedral : 5.532 95.673 5569 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.46 % Favored : 94.40 % Rotamer: Outliers : 2.09 % Allowed : 16.48 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 (0.12), residues: 5033 helix: 1.15 (0.11), residues: 2451 sheet: -0.86 (0.23), residues: 524 loop : -0.87 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 117 TYR 0.024 0.001 TYR C 83 PHE 0.026 0.001 PHE E 477 TRP 0.011 0.001 TRP F 442 HIS 0.012 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00285 (41959) covalent geometry : angle 0.58940 (56953) hydrogen bonds : bond 0.03844 ( 1919) hydrogen bonds : angle 5.02737 ( 5565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 188 time to evaluate : 1.685 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 499 ASN cc_start: 0.9245 (t0) cc_final: 0.8876 (m110) REVERT: A 631 MET cc_start: 0.9012 (tpp) cc_final: 0.8493 (tpp) REVERT: A 646 MET cc_start: 0.9087 (tpp) cc_final: 0.8880 (tpp) REVERT: B 379 MET cc_start: 0.9242 (tpp) cc_final: 0.8909 (tpp) REVERT: C 83 TYR cc_start: 0.3189 (OUTLIER) cc_final: 0.2783 (t80) REVERT: C 340 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8673 (tp30) REVERT: C 417 MET cc_start: 0.8711 (ptp) cc_final: 0.8287 (ptp) REVERT: C 708 MET cc_start: 0.9538 (mmm) cc_final: 0.9076 (mmm) REVERT: C 728 MET cc_start: 0.6570 (ptt) cc_final: 0.4865 (mmt) REVERT: D 340 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8622 (mm-30) REVERT: D 379 MET cc_start: 0.9158 (mpp) cc_final: 0.8841 (mpp) REVERT: D 708 MET cc_start: 0.9173 (mmm) cc_final: 0.8922 (mmm) REVERT: E 82 MET cc_start: 0.6261 (pmm) cc_final: 0.5917 (pmm) REVERT: E 340 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8890 (tp30) REVERT: E 631 MET cc_start: 0.8529 (tpp) cc_final: 0.8314 (tpp) REVERT: F 416 TYR cc_start: 0.8380 (t80) cc_final: 0.7855 (t80) REVERT: F 482 ASP cc_start: 0.9021 (m-30) cc_final: 0.8793 (p0) REVERT: F 491 HIS cc_start: 0.8343 (OUTLIER) cc_final: 0.7760 (t70) REVERT: F 681 MET cc_start: 0.9026 (pmm) cc_final: 0.8745 (pmm) outliers start: 90 outliers final: 53 residues processed: 271 average time/residue: 0.2245 time to fit residues: 106.4079 Evaluate side-chains 235 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 177 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 797 ILE Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 790 CYS Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 583 CYS Chi-restraints excluded: chain D residue 707 GLU Chi-restraints excluded: chain D residue 789 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 367 HIS Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain F residue 499 ASN Chi-restraints excluded: chain F residue 755 HIS Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 900 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 99 optimal weight: 50.0000 chunk 409 optimal weight: 0.0670 chunk 451 optimal weight: 7.9990 chunk 439 optimal weight: 8.9990 chunk 217 optimal weight: 6.9990 chunk 434 optimal weight: 50.0000 chunk 426 optimal weight: 20.0000 chunk 506 optimal weight: 20.0000 chunk 491 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 422 optimal weight: 40.0000 overall best weight: 4.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 HIS ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 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 = 0.3696 r_free = 0.3696 target = 0.069561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.048216 restraints weight = 398283.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.048736 restraints weight = 287927.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.048524 restraints weight = 220862.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.048306 restraints weight = 209131.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.048370 restraints weight = 185303.029| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 41959 Z= 0.197 Angle : 0.634 10.718 56953 Z= 0.325 Chirality : 0.041 0.366 6233 Planarity : 0.004 0.059 7232 Dihedral : 5.439 94.219 5563 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.64 % Rotamer: Outliers : 2.37 % Allowed : 17.48 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.04 (0.12), residues: 5033 helix: 1.09 (0.11), residues: 2434 sheet: -0.95 (0.23), residues: 509 loop : -0.95 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 267 TYR 0.032 0.002 TYR A 302 PHE 0.018 0.002 PHE A 801 TRP 0.013 0.001 TRP D 943 HIS 0.015 0.001 HIS F 491 Details of bonding type rmsd covalent geometry : bond 0.00406 (41959) covalent geometry : angle 0.63448 (56953) hydrogen bonds : bond 0.04029 ( 1919) hydrogen bonds : angle 5.14456 ( 5565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 183 time to evaluate : 2.131 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 631 MET cc_start: 0.9206 (tpp) cc_final: 0.8806 (tpp) REVERT: A 646 MET cc_start: 0.9063 (tpp) cc_final: 0.8858 (tpp) REVERT: A 791 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8763 (mp10) REVERT: B 379 MET cc_start: 0.9156 (tpp) cc_final: 0.8860 (tpp) REVERT: B 615 MET cc_start: 0.9383 (ppp) cc_final: 0.8734 (ppp) REVERT: C 340 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8528 (tp30) REVERT: C 417 MET cc_start: 0.8812 (ptp) cc_final: 0.8390 (ptp) REVERT: C 616 PHE cc_start: 0.9296 (OUTLIER) cc_final: 0.8955 (m-10) REVERT: C 653 LEU cc_start: 0.9621 (mm) cc_final: 0.9373 (tp) REVERT: C 708 MET cc_start: 0.9486 (mmm) cc_final: 0.9108 (mmm) REVERT: C 728 MET cc_start: 0.6551 (ptt) cc_final: 0.4674 (mmt) REVERT: C 791 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.9253 (pm20) REVERT: D 340 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8511 (tp30) REVERT: D 379 MET cc_start: 0.9213 (mpp) cc_final: 0.8939 (mpp) REVERT: D 632 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8949 (mm) REVERT: D 708 MET cc_start: 0.9364 (mmm) cc_final: 0.9083 (mmm) REVERT: E 340 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8850 (tp30) REVERT: E 417 MET cc_start: 0.8939 (mpp) cc_final: 0.8334 (mpp) REVERT: F 616 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.8743 (m-80) REVERT: F 681 MET cc_start: 0.9044 (pmm) cc_final: 0.8778 (pmm) REVERT: F 728 MET cc_start: 0.6452 (pmm) cc_final: 0.5855 (pmm) outliers start: 102 outliers final: 64 residues processed: 276 average time/residue: 0.2358 time to fit residues: 112.6052 Evaluate side-chains 248 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 176 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 797 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 616 PHE Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 790 CYS Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 487 HIS Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 583 CYS Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 707 GLU Chi-restraints excluded: chain D residue 789 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 154 TYR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 367 HIS Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 472 TYR Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 485 THR Chi-restraints excluded: chain F residue 499 ASN Chi-restraints excluded: chain F residue 616 PHE Chi-restraints excluded: chain F residue 755 HIS Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 900 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 282 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 409 optimal weight: 10.0000 chunk 345 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 417 optimal weight: 0.0040 chunk 215 optimal weight: 10.0000 chunk 404 optimal weight: 20.0000 chunk 500 optimal weight: 9.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** D 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN E 530 GLN F 51 ASN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.071064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.049652 restraints weight = 390399.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.049278 restraints weight = 289163.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.049407 restraints weight = 224301.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.049261 restraints weight = 182128.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.049260 restraints weight = 164773.601| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 41959 Z= 0.108 Angle : 0.613 12.596 56953 Z= 0.304 Chirality : 0.041 0.303 6233 Planarity : 0.004 0.056 7232 Dihedral : 5.138 93.121 5562 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.97 % Favored : 94.93 % Rotamer: Outliers : 1.76 % Allowed : 18.55 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.18 (0.12), residues: 5033 helix: 1.20 (0.11), residues: 2447 sheet: -0.86 (0.23), residues: 518 loop : -0.90 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 757 TYR 0.029 0.001 TYR A 302 PHE 0.039 0.001 PHE B 84 TRP 0.013 0.001 TRP F 442 HIS 0.015 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00231 (41959) covalent geometry : angle 0.61333 (56953) hydrogen bonds : bond 0.03605 ( 1919) hydrogen bonds : angle 4.84900 ( 5565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 193 time to evaluate : 1.905 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 209 LEU cc_start: 0.4276 (OUTLIER) cc_final: 0.4038 (pp) REVERT: A 631 MET cc_start: 0.9150 (tpp) cc_final: 0.8687 (tpp) REVERT: A 646 MET cc_start: 0.9097 (tpp) cc_final: 0.8891 (tpp) REVERT: A 791 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: B 379 MET cc_start: 0.9246 (tpp) cc_final: 0.8948 (tpp) REVERT: B 615 MET cc_start: 0.9387 (ppp) cc_final: 0.8819 (ppp) REVERT: C 340 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8656 (mm-30) REVERT: C 412 MET cc_start: 0.8715 (mmm) cc_final: 0.7907 (mpp) REVERT: C 417 MET cc_start: 0.8743 (ptp) cc_final: 0.8298 (ptp) REVERT: C 653 LEU cc_start: 0.9610 (mm) cc_final: 0.9402 (tp) REVERT: C 708 MET cc_start: 0.9508 (mmm) cc_final: 0.9148 (mmm) REVERT: C 728 MET cc_start: 0.6823 (ptt) cc_final: 0.4807 (mmt) REVERT: D 340 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8632 (mm-30) REVERT: D 708 MET cc_start: 0.9360 (mmm) cc_final: 0.9087 (mmm) REVERT: E 340 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8938 (tp30) REVERT: E 417 MET cc_start: 0.8757 (mpp) cc_final: 0.7847 (mpp) REVERT: F 416 TYR cc_start: 0.8361 (t80) cc_final: 0.7679 (t80) REVERT: F 417 MET cc_start: 0.8116 (mpp) cc_final: 0.7175 (mpp) REVERT: F 491 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.8082 (t70) REVERT: F 681 MET cc_start: 0.8998 (pmm) cc_final: 0.8734 (pmm) outliers start: 76 outliers final: 45 residues processed: 262 average time/residue: 0.2305 time to fit residues: 104.9279 Evaluate side-chains 231 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 797 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 707 GLU Chi-restraints excluded: chain D residue 789 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 154 TYR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 367 HIS Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain F residue 755 HIS Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 900 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 427 optimal weight: 8.9990 chunk 274 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 362 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 494 optimal weight: 4.9990 chunk 379 optimal weight: 0.2980 chunk 133 optimal weight: 0.9980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** D 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.070549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.049300 restraints weight = 389520.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.049842 restraints weight = 287664.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.049989 restraints weight = 215144.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.049277 restraints weight = 189996.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.049258 restraints weight = 171276.099| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41959 Z= 0.123 Angle : 0.621 13.315 56953 Z= 0.309 Chirality : 0.041 0.321 6233 Planarity : 0.004 0.056 7232 Dihedral : 4.967 92.775 5559 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.23 % Favored : 94.68 % Rotamer: Outliers : 1.65 % Allowed : 19.10 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.21 (0.12), residues: 5033 helix: 1.23 (0.11), residues: 2445 sheet: -0.85 (0.23), residues: 520 loop : -0.87 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 757 TYR 0.029 0.001 TYR A 302 PHE 0.025 0.001 PHE E 511 TRP 0.008 0.001 TRP D 442 HIS 0.019 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00265 (41959) covalent geometry : angle 0.62066 (56953) hydrogen bonds : bond 0.03576 ( 1919) hydrogen bonds : angle 4.84975 ( 5565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 187 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.9102 (tpp) cc_final: 0.8679 (tpp) REVERT: A 646 MET cc_start: 0.9095 (tpp) cc_final: 0.8860 (tpp) REVERT: A 791 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8590 (pm20) REVERT: B 379 MET cc_start: 0.9198 (tpp) cc_final: 0.8912 (tpp) REVERT: B 615 MET cc_start: 0.9383 (ppp) cc_final: 0.8803 (ppp) REVERT: C 340 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8663 (tp30) REVERT: C 417 MET cc_start: 0.8702 (ptp) cc_final: 0.8269 (ptp) REVERT: C 452 MET cc_start: 0.8937 (ppp) cc_final: 0.8425 (ppp) REVERT: C 615 MET cc_start: 0.9024 (tmm) cc_final: 0.8634 (tmm) REVERT: C 616 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8912 (m-10) REVERT: C 708 MET cc_start: 0.9504 (mmm) cc_final: 0.9187 (mmm) REVERT: C 728 MET cc_start: 0.6807 (ptt) cc_final: 0.4801 (mmt) REVERT: C 791 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.9266 (pm20) REVERT: D 340 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8633 (mm-30) REVERT: D 708 MET cc_start: 0.9358 (mmm) cc_final: 0.9075 (mmm) REVERT: E 340 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8842 (tp30) REVERT: E 390 TYR cc_start: 0.8858 (t80) cc_final: 0.8421 (t80) REVERT: E 417 MET cc_start: 0.8812 (mpp) cc_final: 0.8052 (mpp) REVERT: F 417 MET cc_start: 0.8168 (mpp) cc_final: 0.7289 (mpp) REVERT: F 616 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: F 646 MET cc_start: 0.8753 (pmm) cc_final: 0.8491 (pmm) REVERT: F 681 MET cc_start: 0.8996 (pmm) cc_final: 0.8717 (pmm) outliers start: 71 outliers final: 49 residues processed: 252 average time/residue: 0.2328 time to fit residues: 102.1776 Evaluate side-chains 235 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 797 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 616 PHE Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 790 CYS Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 707 GLU Chi-restraints excluded: chain D residue 789 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 154 TYR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 367 HIS Chi-restraints excluded: chain E residue 472 TYR Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 616 PHE Chi-restraints excluded: chain F residue 755 HIS Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 900 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 141 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 509 optimal weight: 30.0000 chunk 293 optimal weight: 2.9990 chunk 470 optimal weight: 0.0030 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 335 optimal weight: 1.9990 chunk 468 optimal weight: 0.7980 chunk 289 optimal weight: 4.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 HIS ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.071299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.050009 restraints weight = 390018.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.050477 restraints weight = 288974.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.050753 restraints weight = 206407.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.050271 restraints weight = 196499.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.050137 restraints weight = 167481.525| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 41959 Z= 0.105 Angle : 0.636 15.178 56953 Z= 0.310 Chirality : 0.041 0.290 6233 Planarity : 0.004 0.055 7232 Dihedral : 4.829 92.473 5559 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 1.49 % Allowed : 19.36 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.25 (0.12), residues: 5033 helix: 1.24 (0.11), residues: 2452 sheet: -0.74 (0.23), residues: 520 loop : -0.86 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 513 TYR 0.027 0.001 TYR A 302 PHE 0.050 0.001 PHE B 84 TRP 0.013 0.001 TRP F 442 HIS 0.022 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00228 (41959) covalent geometry : angle 0.63562 (56953) hydrogen bonds : bond 0.03430 ( 1919) hydrogen bonds : angle 4.72537 ( 5565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 196 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.9072 (tpp) cc_final: 0.8640 (tpp) REVERT: A 646 MET cc_start: 0.9080 (tpp) cc_final: 0.8857 (tpp) REVERT: A 791 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8541 (pm20) REVERT: B 379 MET cc_start: 0.9179 (tpp) cc_final: 0.8951 (tpp) REVERT: B 615 MET cc_start: 0.9389 (ppp) cc_final: 0.8868 (ppp) REVERT: C 340 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8699 (tp30) REVERT: C 412 MET cc_start: 0.8608 (mmm) cc_final: 0.7809 (mpp) REVERT: C 708 MET cc_start: 0.9501 (mmm) cc_final: 0.9191 (mmm) REVERT: C 728 MET cc_start: 0.6824 (ptt) cc_final: 0.4743 (mmt) REVERT: D 20 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: D 340 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8624 (mm-30) REVERT: D 632 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8953 (mm) REVERT: D 708 MET cc_start: 0.9371 (mmm) cc_final: 0.9079 (mmm) REVERT: E 340 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8886 (tp30) REVERT: F 417 MET cc_start: 0.8187 (mpp) cc_final: 0.7368 (mpp) REVERT: F 491 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.8254 (t70) REVERT: F 616 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8537 (m-80) REVERT: F 681 MET cc_start: 0.8950 (pmm) cc_final: 0.8677 (pmm) outliers start: 64 outliers final: 44 residues processed: 254 average time/residue: 0.2287 time to fit residues: 100.9299 Evaluate side-chains 240 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 797 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain D residue 20 TYR Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 707 GLU Chi-restraints excluded: chain D residue 789 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 154 TYR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 367 HIS Chi-restraints excluded: chain E residue 472 TYR Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 616 PHE Chi-restraints excluded: chain F residue 755 HIS Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 900 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 223 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 136 optimal weight: 20.0000 chunk 379 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 386 optimal weight: 0.9990 chunk 479 optimal weight: 0.2980 chunk 387 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.070594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.049418 restraints weight = 388782.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.050086 restraints weight = 277269.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.050221 restraints weight = 194413.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.049756 restraints weight = 174050.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.049795 restraints weight = 152354.508| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41959 Z= 0.122 Angle : 0.646 16.932 56953 Z= 0.317 Chirality : 0.041 0.293 6233 Planarity : 0.004 0.053 7232 Dihedral : 4.762 92.436 5553 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 1.28 % Allowed : 19.64 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.30 (0.12), residues: 5033 helix: 1.31 (0.11), residues: 2445 sheet: -0.72 (0.23), residues: 513 loop : -0.85 (0.14), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 76 TYR 0.027 0.001 TYR A 302 PHE 0.029 0.001 PHE E 477 TRP 0.048 0.001 TRP B 442 HIS 0.023 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00266 (41959) covalent geometry : angle 0.64593 (56953) hydrogen bonds : bond 0.03484 ( 1919) hydrogen bonds : angle 4.76036 ( 5565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 1.809 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 631 MET cc_start: 0.9018 (tpp) cc_final: 0.8601 (tpp) REVERT: A 791 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8550 (mp10) REVERT: B 379 MET cc_start: 0.9205 (tpp) cc_final: 0.8968 (tpp) REVERT: C 340 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8682 (tp30) REVERT: C 412 MET cc_start: 0.8564 (mmm) cc_final: 0.7932 (mpp) REVERT: C 417 MET cc_start: 0.8605 (ptp) cc_final: 0.8088 (ptp) REVERT: C 708 MET cc_start: 0.9499 (mmm) cc_final: 0.9214 (mmm) REVERT: C 728 MET cc_start: 0.6812 (ptt) cc_final: 0.4779 (mmt) REVERT: D 20 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.6678 (m-80) REVERT: D 340 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8615 (mm-30) REVERT: D 632 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8749 (mm) REVERT: D 708 MET cc_start: 0.9364 (mmm) cc_final: 0.9071 (mmm) REVERT: E 340 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8848 (tp30) REVERT: F 417 MET cc_start: 0.8296 (mpp) cc_final: 0.7495 (mpp) REVERT: F 616 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: F 681 MET cc_start: 0.8969 (pmm) cc_final: 0.8685 (pmm) outliers start: 55 outliers final: 44 residues processed: 238 average time/residue: 0.2279 time to fit residues: 94.8987 Evaluate side-chains 237 residues out of total 4655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 186 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 797 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 790 CYS Chi-restraints excluded: chain C residue 791 GLN Chi-restraints excluded: chain D residue 20 TYR Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 583 CYS Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 707 GLU Chi-restraints excluded: chain D residue 789 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 154 TYR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 367 HIS Chi-restraints excluded: chain E residue 472 TYR Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 499 ASN Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 616 PHE Chi-restraints excluded: chain F residue 755 HIS Chi-restraints excluded: chain F residue 789 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 20 optimal weight: 20.0000 chunk 211 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 167 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 449 optimal weight: 5.9990 chunk 436 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 420 optimal weight: 30.0000 chunk 219 optimal weight: 0.0570 overall best weight: 2.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.070253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.049096 restraints weight = 394314.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.049890 restraints weight = 283804.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.049100 restraints weight = 200867.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.049327 restraints weight = 184594.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.049225 restraints weight = 167627.972| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41959 Z= 0.130 Angle : 0.645 14.760 56953 Z= 0.317 Chirality : 0.041 0.287 6233 Planarity : 0.004 0.053 7232 Dihedral : 4.745 92.034 5552 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.87 % Rotamer: Outliers : 1.46 % Allowed : 19.41 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.29 (0.12), residues: 5033 helix: 1.29 (0.11), residues: 2449 sheet: -0.76 (0.23), residues: 514 loop : -0.84 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 76 TYR 0.027 0.001 TYR A 302 PHE 0.035 0.001 PHE E 141 TRP 0.038 0.001 TRP B 442 HIS 0.022 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00280 (41959) covalent geometry : angle 0.64510 (56953) hydrogen bonds : bond 0.03528 ( 1919) hydrogen bonds : angle 4.77025 ( 5565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9975.83 seconds wall clock time: 173 minutes 29.43 seconds (10409.43 seconds total)