Starting phenix.real_space_refine on Sun Feb 8 05:35:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9crx_45885/02_2026/9crx_45885.cif Found real_map, /net/cci-nas-00/data/ceres_data/9crx_45885/02_2026/9crx_45885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9crx_45885/02_2026/9crx_45885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9crx_45885/02_2026/9crx_45885.map" model { file = "/net/cci-nas-00/data/ceres_data/9crx_45885/02_2026/9crx_45885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9crx_45885/02_2026/9crx_45885.cif" } resolution = 3.73 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= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2025 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 167 5.16 5 C 24138 2.51 5 N 6678 2.21 5 O 7540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38554 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3994 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 491} Chain breaks: 2 Chain: "B" Number of atoms: 5726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 731, 5715 Classifications: {'peptide': 731} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 731, 5715 Classifications: {'peptide': 731} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5795 Chain: "C" Number of atoms: 5785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5785 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 711} Chain: "D" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5659 Classifications: {'peptide': 725} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 696} Chain breaks: 1 Chain: "E" Number of atoms: 4120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4120 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 509} Chain: "F" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3867 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 475} Chain breaks: 2 Chain: "G" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2306 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "H" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2269 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 284} Chain breaks: 1 Chain: "I" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2306 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "J" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "K" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 698 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "L" Number of atoms: 1023 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 129, 1015 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'TRANS': 128} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 129, 1015 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'TRANS': 128} Chain breaks: 1 bond proxies already assigned to first conformer: 1007 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 396 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG B 396 " occ=0.57 Time building chain proxies: 9.65, per 1000 atoms: 0.25 Number of scatterers: 38554 At special positions: 0 Unit cell: (153.44, 243.312, 154.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 167 16.00 P 31 15.00 O 7540 8.00 N 6678 7.00 C 24138 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: 3.22 Conformation dependent library (CDL) restraints added in 1.8 seconds 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9150 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 25 sheets defined 60.5% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 286 through 298 removed outlier: 3.596A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (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 320 through 326 removed outlier: 3.794A pdb=" N LEU A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 367 through 380 removed outlier: 3.658A pdb=" N ASP A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.706A pdb=" N LEU A 405 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 406 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 446 through 454 Processing helix chain 'A' and resid 460 through 478 Processing helix chain 'A' and resid 498 through 509 removed outlier: 3.696A pdb=" N PHE A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.893A pdb=" N LEU A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 Processing helix chain 'A' and resid 570 through 580 Processing helix chain 'A' and resid 590 through 595 removed outlier: 3.866A pdb=" N LEU A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 612 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 640 through 651 removed outlier: 3.595A pdb=" N LEU A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 677 Processing helix chain 'A' and resid 678 through 682 removed outlier: 3.775A pdb=" N PHE A 682 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 705 Processing helix chain 'A' and resid 708 through 723 Processing helix chain 'A' and resid 729 through 743 removed outlier: 3.522A pdb=" N THR A 733 " --> pdb=" O GLY A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 758 removed outlier: 3.830A pdb=" N VAL A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 43 Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 103 through 109 Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 135 through 147 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.758A pdb=" N ILE B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.595A pdb=" N ALA B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.859A pdb=" N VAL B 354 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 380 removed outlier: 3.521A pdb=" N ASP B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 446 through 454 Processing helix chain 'B' and resid 458 through 478 removed outlier: 3.783A pdb=" N VAL B 478 " --> pdb=" O ILE B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 495 removed outlier: 3.602A pdb=" N ALA B 493 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 506 removed outlier: 3.616A pdb=" N PHE B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 3.529A pdb=" N LEU B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 551 removed outlier: 4.111A pdb=" N ASN B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 580 removed outlier: 4.001A pdb=" N LEU B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 613 Processing helix chain 'B' and resid 614 through 616 No H-bonds generated for 'chain 'B' and resid 614 through 616' Processing helix chain 'B' and resid 640 through 651 removed outlier: 3.885A pdb=" N LEU B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 693 through 705 Processing helix chain 'B' and resid 710 through 723 removed outlier: 3.855A pdb=" N ARG B 721 " --> pdb=" O ASN B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 743 removed outlier: 3.870A pdb=" N HIS B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 758 removed outlier: 4.379A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 42 Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 103 through 109 Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.594A pdb=" N ALA C 129 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 147 Processing helix chain 'C' and resid 245 through 255 Processing helix chain 'C' and resid 262 through 270 Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 327 through 337 Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.583A pdb=" N SER C 353 " --> pdb=" O GLU C 350 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 354 " --> pdb=" O LEU C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 354' Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.556A pdb=" N ASP C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 446 through 454 Processing helix chain 'C' and resid 458 through 476 removed outlier: 3.947A pdb=" N GLU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.638A pdb=" N ILE C 492 " --> pdb=" O ASN C 488 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 493 " --> pdb=" O THR C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 498 through 506 removed outlier: 3.546A pdb=" N PHE C 502 " --> pdb=" O THR C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 524 removed outlier: 4.339A pdb=" N GLU C 518 " --> pdb=" O GLY C 514 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C 519 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 Processing helix chain 'C' and resid 569 through 582 removed outlier: 3.795A pdb=" N LEU C 573 " --> pdb=" O GLY C 569 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY C 582 " --> pdb=" O ALA C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 595 removed outlier: 3.521A pdb=" N SER C 595 " --> pdb=" O ASN C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 613 removed outlier: 3.684A pdb=" N ALA C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 630 removed outlier: 3.562A pdb=" N VAL C 630 " --> pdb=" O LEU C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.510A pdb=" N LEU C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 677 removed outlier: 3.621A pdb=" N ASP C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 705 removed outlier: 3.562A pdb=" N ASN C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 720 Processing helix chain 'C' and resid 729 through 744 removed outlier: 3.560A pdb=" N THR C 735 " --> pdb=" O LYS C 731 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N HIS C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU C 744 " --> pdb=" O ALA C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 758 removed outlier: 4.287A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 43 Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.511A pdb=" N ALA D 129 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 244 through 255 removed outlier: 3.996A pdb=" N PHE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 270 Processing helix chain 'D' and resid 288 through 297 Processing helix chain 'D' and resid 317 through 325 removed outlier: 3.675A pdb=" N GLU D 321 " --> pdb=" O GLY D 317 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 324 " --> pdb=" O GLU D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 338 removed outlier: 3.963A pdb=" N ALA D 336 " --> pdb=" O ALA D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 350 through 354 removed outlier: 4.080A pdb=" N SER D 353 " --> pdb=" O GLU D 350 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 354 " --> pdb=" O LEU D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 350 through 354' Processing helix chain 'D' and resid 366 through 380 removed outlier: 4.194A pdb=" N ASN D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 433 through 438 Processing helix chain 'D' and resid 446 through 454 Processing helix chain 'D' and resid 458 through 479 removed outlier: 3.798A pdb=" N ILE D 462 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU D 463 " --> pdb=" O GLY D 459 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY D 464 " --> pdb=" O ALA D 460 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR D 477 " --> pdb=" O ALA D 473 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL D 478 " --> pdb=" O ILE D 474 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 493 Processing helix chain 'D' and resid 498 through 506 removed outlier: 3.877A pdb=" N PHE D 502 " --> pdb=" O THR D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 524 removed outlier: 3.718A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 552 Processing helix chain 'D' and resid 570 through 581 removed outlier: 3.911A pdb=" N LYS D 580 " --> pdb=" O GLU D 576 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER D 581 " --> pdb=" O ILE D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 595 removed outlier: 3.947A pdb=" N LEU D 594 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 613 Processing helix chain 'D' and resid 625 through 630 Processing helix chain 'D' and resid 640 through 651 removed outlier: 3.736A pdb=" N LEU D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 677 Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.785A pdb=" N CYS D 681 " --> pdb=" O ILE D 678 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE D 682 " --> pdb=" O LEU D 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 678 through 682' Processing helix chain 'D' and resid 693 through 705 removed outlier: 4.127A pdb=" N LEU D 697 " --> pdb=" O ASN D 693 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D 703 " --> pdb=" O ASN D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 722 Processing helix chain 'D' and resid 729 through 744 removed outlier: 4.201A pdb=" N HIS D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP D 743 " --> pdb=" O THR D 739 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU D 744 " --> pdb=" O ALA D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 758 removed outlier: 4.393A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 256 removed outlier: 3.540A pdb=" N PHE E 256 " --> pdb=" O PHE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 262 through 270 removed outlier: 4.398A pdb=" N ILE E 266 " --> pdb=" O PRO E 262 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU E 267 " --> pdb=" O PRO E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 298 removed outlier: 4.587A pdb=" N GLY E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR E 296 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 311 removed outlier: 3.580A pdb=" N GLU E 310 " --> pdb=" O ASN E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 327 through 338 Processing helix chain 'E' and resid 339 through 341 No H-bonds generated for 'chain 'E' and resid 339 through 341' Processing helix chain 'E' and resid 366 through 381 removed outlier: 3.850A pdb=" N VAL E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL E 372 " --> pdb=" O GLY E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 400 removed outlier: 3.610A pdb=" N LEU E 399 " --> pdb=" O ARG E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 405 Processing helix chain 'E' and resid 420 through 438 removed outlier: 5.100A pdb=" N LYS E 434 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N MET E 435 " --> pdb=" O GLN E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 454 Processing helix chain 'E' and resid 458 through 475 removed outlier: 3.564A pdb=" N PHE E 472 " --> pdb=" O SER E 468 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 509 Processing helix chain 'E' and resid 518 through 524 removed outlier: 3.546A pdb=" N VAL E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 552 removed outlier: 4.002A pdb=" N ASN E 536 " --> pdb=" O SER E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 582 removed outlier: 3.701A pdb=" N GLY E 582 " --> pdb=" O ALA E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 595 removed outlier: 3.693A pdb=" N LEU E 594 " --> pdb=" O SER E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 614 Processing helix chain 'E' and resid 625 through 630 Processing helix chain 'E' and resid 640 through 651 removed outlier: 3.570A pdb=" N LEU E 644 " --> pdb=" O SER E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 677 Processing helix chain 'E' and resid 678 through 682 removed outlier: 3.928A pdb=" N CYS E 681 " --> pdb=" O ILE E 678 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE E 682 " --> pdb=" O LEU E 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 678 through 682' Processing helix chain 'E' and resid 693 through 705 removed outlier: 3.589A pdb=" N LEU E 697 " --> pdb=" O ASN E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 708 through 723 removed outlier: 3.604A pdb=" N ILE E 716 " --> pdb=" O ARG E 712 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG E 721 " --> pdb=" O ASN E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 743 Processing helix chain 'E' and resid 746 through 758 removed outlier: 3.852A pdb=" N LEU E 750 " --> pdb=" O PRO E 746 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU E 752 " --> pdb=" O ASN E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 255 Processing helix chain 'F' and resid 257 through 261 Processing helix chain 'F' and resid 262 through 270 removed outlier: 3.606A pdb=" N ILE F 266 " --> pdb=" O PRO F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 298 removed outlier: 4.090A pdb=" N GLY F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR F 296 " --> pdb=" O ARG F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 317 through 327 removed outlier: 3.969A pdb=" N PHE F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 337 Processing helix chain 'F' and resid 350 through 355 removed outlier: 4.270A pdb=" N VAL F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 380 removed outlier: 4.106A pdb=" N VAL F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 438 removed outlier: 5.010A pdb=" N LYS F 434 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N MET F 435 " --> pdb=" O GLN F 431 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 454 removed outlier: 3.711A pdb=" N LEU F 450 " --> pdb=" O ASN F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 478 removed outlier: 3.763A pdb=" N ALA F 473 " --> pdb=" O ALA F 469 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 495 Processing helix chain 'F' and resid 498 through 506 removed outlier: 3.737A pdb=" N PHE F 502 " --> pdb=" O THR F 498 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU F 506 " --> pdb=" O PHE F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 523 removed outlier: 3.620A pdb=" N CYS F 523 " --> pdb=" O ASP F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 552 removed outlier: 3.961A pdb=" N ASN F 536 " --> pdb=" O SER F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 582 removed outlier: 3.924A pdb=" N GLY F 582 " --> pdb=" O ALA F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 595 removed outlier: 3.995A pdb=" N LEU F 594 " --> pdb=" O SER F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 612 removed outlier: 3.502A pdb=" N ALA F 604 " --> pdb=" O SER F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 615 No H-bonds generated for 'chain 'F' and resid 613 through 615' Processing helix chain 'F' and resid 625 through 630 Processing helix chain 'F' and resid 640 through 651 removed outlier: 3.611A pdb=" N LEU F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 677 Processing helix chain 'F' and resid 678 through 682 Processing helix chain 'F' and resid 693 through 704 removed outlier: 3.547A pdb=" N LEU F 697 " --> pdb=" O ASN F 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 708 through 721 removed outlier: 4.235A pdb=" N ILE F 716 " --> pdb=" O ARG F 712 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN F 717 " --> pdb=" O VAL F 713 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG F 721 " --> pdb=" O ASN F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 744 removed outlier: 4.310A pdb=" N HIS F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU F 744 " --> pdb=" O ALA F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 758 removed outlier: 4.250A pdb=" N LEU F 750 " --> pdb=" O PRO F 746 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU F 752 " --> pdb=" O ASN F 748 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 15 Processing helix chain 'G' and resid 21 through 26 removed outlier: 3.980A pdb=" N PHE G 25 " --> pdb=" O PHE G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 50 Processing helix chain 'G' and resid 52 through 71 Processing helix chain 'G' and resid 72 through 91 Processing helix chain 'G' and resid 92 through 110 Processing helix chain 'G' and resid 112 through 130 Processing helix chain 'G' and resid 133 through 151 Processing helix chain 'G' and resid 153 through 171 Processing helix chain 'G' and resid 173 through 189 Processing helix chain 'G' and resid 191 through 193 No H-bonds generated for 'chain 'G' and resid 191 through 193' Processing helix chain 'G' and resid 194 through 212 removed outlier: 3.774A pdb=" N ASP G 200 " --> pdb=" O TRP G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 229 Processing helix chain 'G' and resid 229 through 234 removed outlier: 3.620A pdb=" N ASP G 234 " --> pdb=" O PRO G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 251 Processing helix chain 'G' and resid 252 through 267 removed outlier: 3.566A pdb=" N PHE G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 292 Processing helix chain 'H' and resid 3 through 15 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 29 through 48 Processing helix chain 'H' and resid 54 through 71 Processing helix chain 'H' and resid 72 through 90 Processing helix chain 'H' and resid 92 through 111 Processing helix chain 'H' and resid 112 through 130 Processing helix chain 'H' and resid 133 through 151 Processing helix chain 'H' and resid 153 through 171 Processing helix chain 'H' and resid 173 through 189 Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 194 through 212 removed outlier: 3.531A pdb=" N LYS H 199 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP H 200 " --> pdb=" O TRP H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 229 Processing helix chain 'H' and resid 229 through 234 Processing helix chain 'H' and resid 235 through 251 Processing helix chain 'H' and resid 252 through 267 removed outlier: 3.567A pdb=" N PHE H 266 " --> pdb=" O GLU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 292 Processing helix chain 'I' and resid 3 through 15 Processing helix chain 'I' and resid 19 through 25 removed outlier: 4.215A pdb=" N MET I 22 " --> pdb=" O SER I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 50 Processing helix chain 'I' and resid 52 through 71 removed outlier: 3.667A pdb=" N ALA I 56 " --> pdb=" O GLU I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 91 Processing helix chain 'I' and resid 92 through 110 Processing helix chain 'I' and resid 112 through 130 Processing helix chain 'I' and resid 133 through 151 Processing helix chain 'I' and resid 153 through 171 Processing helix chain 'I' and resid 173 through 189 Processing helix chain 'I' and resid 194 through 212 removed outlier: 3.814A pdb=" N LYS I 199 " --> pdb=" O GLN I 195 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP I 200 " --> pdb=" O TRP I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 229 Processing helix chain 'I' and resid 229 through 234 Processing helix chain 'I' and resid 235 through 251 Processing helix chain 'I' and resid 252 through 267 Processing helix chain 'I' and resid 270 through 292 Processing helix chain 'J' and resid 28 through 86 Processing helix chain 'K' and resid 178 through 257 removed outlier: 4.021A pdb=" N ARG K 182 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG K 183 " --> pdb=" O ASN K 179 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS K 187 " --> pdb=" O ARG K 183 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL K 193 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG K 196 " --> pdb=" O GLU K 192 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU K 226 " --> pdb=" O ILE K 222 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN K 227 " --> pdb=" O GLU K 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 434 through 499 Processing helix chain 'L' and resid 590 through 649 removed outlier: 3.616A pdb=" N GLY L 649 " --> pdb=" O ASN L 645 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 307 removed outlier: 6.003A pdb=" N LYS A 304 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASP A 349 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 306 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS A 344 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE A 391 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 346 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N MET A 393 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE A 348 " --> pdb=" O MET A 393 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 277 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N THR A 394 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 279 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 586 through 589 removed outlier: 6.511A pdb=" N ARG A 587 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 558 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR A 665 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 560 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR A 667 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 562 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 684 " --> pdb=" O SER A 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 47 removed outlier: 7.201A pdb=" N ILE B 79 " --> pdb=" O HIS B 28 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LYS B 30 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 157 through 162 removed outlier: 5.636A pdb=" N LEU B 169 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N SER B 122 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ILE B 171 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP B 120 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN B 173 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER B 116 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE B 177 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU B 114 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N GLN B 203 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY B 115 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ASN B 205 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 117 " --> pdb=" O ASN B 205 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE B 207 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE B 119 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 152 removed outlier: 3.550A pdb=" N PHE B 152 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 196 " --> pdb=" O PHE B 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.871A pdb=" N MET B 393 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 394 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 557 through 558 removed outlier: 6.814A pdb=" N VAL B 558 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N THR B 665 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE B 585 " --> pdb=" O LEU B 618 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 557 through 558 removed outlier: 6.814A pdb=" N VAL B 558 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N THR B 665 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AB1, first strand: chain 'C' and resid 64 through 67 removed outlier: 7.245A pdb=" N ILE C 79 " --> pdb=" O HIS C 28 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS C 30 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 157 through 162 removed outlier: 5.752A pdb=" N LEU C 169 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N SER C 122 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE C 171 " --> pdb=" O ASP C 120 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP C 120 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN C 173 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 116 " --> pdb=" O GLN C 175 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE C 177 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU C 114 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 9.545A pdb=" N GLN C 203 " --> pdb=" O TYR C 113 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY C 115 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ASN C 205 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 117 " --> pdb=" O ASN C 205 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE C 207 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE C 119 " --> pdb=" O PHE C 207 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 134 through 135 removed outlier: 5.664A pdb=" N PHE C 134 " --> pdb=" O LYS C 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 151 through 152 removed outlier: 3.532A pdb=" N PHE C 152 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 196 " --> pdb=" O PHE C 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 344 through 348 removed outlier: 3.690A pdb=" N MET C 393 " --> pdb=" O PHE C 348 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 586 through 589 removed outlier: 6.633A pdb=" N LEU C 621 " --> pdb=" O MET C 664 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR C 666 " --> pdb=" O LEU C 621 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE C 623 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN C 684 " --> pdb=" O SER C 559 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 45 through 47 removed outlier: 7.217A pdb=" N ILE D 79 " --> pdb=" O HIS D 28 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS D 30 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 157 through 162 removed outlier: 5.563A pdb=" N LEU D 169 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER D 122 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE D 171 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASP D 120 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN D 173 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER D 116 " --> pdb=" O GLN D 175 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE D 177 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU D 114 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 151 through 152 removed outlier: 3.586A pdb=" N PHE D 152 " --> pdb=" O GLY D 196 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY D 196 " --> pdb=" O PHE D 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 304 through 306 removed outlier: 3.687A pdb=" N MET D 393 " --> pdb=" O PHE D 348 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 277 " --> pdb=" O VAL D 390 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 585 through 589 removed outlier: 3.729A pdb=" N PHE D 585 " --> pdb=" O LEU D 618 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 558 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N THR D 665 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU D 560 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN D 684 " --> pdb=" O SER D 559 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 304 through 306 removed outlier: 6.072A pdb=" N LYS E 304 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP E 349 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL E 306 " --> pdb=" O ASP E 349 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU E 389 " --> pdb=" O HIS E 344 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE E 346 " --> pdb=" O LEU E 389 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY E 276 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL E 414 " --> pdb=" O GLY E 276 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU E 278 " --> pdb=" O VAL E 414 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 585 through 589 removed outlier: 3.530A pdb=" N ARG E 587 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL E 558 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR E 665 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU E 560 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR E 667 " --> pdb=" O LEU E 560 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE E 562 " --> pdb=" O THR E 667 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN E 684 " --> pdb=" O SER E 559 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 304 through 307 removed outlier: 6.240A pdb=" N LYS F 304 " --> pdb=" O ILE F 347 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP F 349 " --> pdb=" O LYS F 304 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL F 306 " --> pdb=" O ASP F 349 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS F 344 " --> pdb=" O LEU F 389 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE F 391 " --> pdb=" O HIS F 344 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE F 346 " --> pdb=" O ILE F 391 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N MET F 393 " --> pdb=" O ILE F 346 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE F 348 " --> pdb=" O MET F 393 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 277 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR F 394 " --> pdb=" O LEU F 279 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY F 276 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL F 414 " --> pdb=" O GLY F 276 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU F 278 " --> pdb=" O VAL F 414 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 585 through 589 removed outlier: 3.910A pdb=" N PHE F 585 " --> pdb=" O LEU F 618 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL F 558 " --> pdb=" O ILE F 663 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N THR F 665 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU F 560 " --> pdb=" O THR F 665 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR F 667 " --> pdb=" O LEU F 560 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE F 562 " --> pdb=" O THR F 667 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN F 684 " --> pdb=" O SER F 559 " (cutoff:3.500A) 2085 hydrogen bonds defined for protein. 6065 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: 7.69 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6744 1.29 - 1.43: 9108 1.43 - 1.56: 22932 1.56 - 1.69: 61 1.69 - 1.82: 289 Bond restraints: 39134 Sorted by residual: bond pdb=" CA PRO C 262 " pdb=" C PRO C 262 " ideal model delta sigma weight residual 1.514 1.452 0.062 5.50e-03 3.31e+04 1.28e+02 bond pdb=" C VAL A 546 " pdb=" N ARG A 547 " ideal model delta sigma weight residual 1.335 1.213 0.122 1.31e-02 5.83e+03 8.71e+01 bond pdb=" C ARG A 556 " pdb=" N LEU A 557 " ideal model delta sigma weight residual 1.332 1.224 0.108 1.25e-02 6.40e+03 7.40e+01 bond pdb=" C GLN C 150 " pdb=" N ILE C 151 " ideal model delta sigma weight residual 1.330 1.225 0.105 1.48e-02 4.57e+03 5.05e+01 bond pdb=" C GLN L 471 " pdb=" N LEU L 472 " ideal model delta sigma weight residual 1.335 1.245 0.091 1.34e-02 5.57e+03 4.57e+01 ... (remaining 39129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 52538 4.45 - 8.90: 262 8.90 - 13.34: 3 13.34 - 17.79: 8 17.79 - 22.24: 4 Bond angle restraints: 52815 Sorted by residual: angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 117.63 22.24 1.00e+00 1.00e+00 4.95e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 114.68 22.15 1.00e+00 1.00e+00 4.91e+02 angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 121.11 18.76 1.00e+00 1.00e+00 3.52e+02 angle pdb=" PB ATP A 802 " pdb=" O3B ATP A 802 " pdb=" PG ATP A 802 " ideal model delta sigma weight residual 139.87 121.25 18.62 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP D 802 " pdb=" O3B ATP D 802 " pdb=" PG ATP D 802 " ideal model delta sigma weight residual 139.87 122.09 17.78 1.00e+00 1.00e+00 3.16e+02 ... (remaining 52810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.08: 23279 28.08 - 56.15: 843 56.15 - 84.23: 89 84.23 - 112.31: 11 112.31 - 140.39: 1 Dihedral angle restraints: 24223 sinusoidal: 10103 harmonic: 14120 Sorted by residual: dihedral pdb=" C2' ADP E 801 " pdb=" C1' ADP E 801 " pdb=" N9 ADP E 801 " pdb=" C4 ADP E 801 " ideal model delta sinusoidal sigma weight residual 91.55 -128.07 -140.39 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" CA GLU I 52 " pdb=" C GLU I 52 " pdb=" N LEU I 53 " pdb=" CA LEU I 53 " ideal model delta harmonic sigma weight residual -180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA GLY B 636 " pdb=" C GLY B 636 " pdb=" N PRO B 637 " pdb=" CA PRO B 637 " ideal model delta harmonic sigma weight residual 0.00 -24.64 24.64 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 24220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5069 0.068 - 0.135: 822 0.135 - 0.203: 72 0.203 - 0.270: 11 0.270 - 0.338: 2 Chirality restraints: 5976 Sorted by residual: chirality pdb=" CB ILE L 601 " pdb=" CA ILE L 601 " pdb=" CG1 ILE L 601 " pdb=" CG2 ILE L 601 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CB ILE A 620 " pdb=" CA ILE A 620 " pdb=" CG1 ILE A 620 " pdb=" CG2 ILE A 620 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB ILE A 603 " pdb=" CA ILE A 603 " pdb=" CG1 ILE A 603 " pdb=" CG2 ILE A 603 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 5973 not shown) Planarity restraints: 6856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 174 " 0.091 2.00e-02 2.50e+03 6.13e-02 7.51e+01 pdb=" CG TYR H 174 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR H 174 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR H 174 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR H 174 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR H 174 " -0.045 2.00e-02 2.50e+03 pdb=" CZ TYR H 174 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR H 174 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN K 170 " -0.032 2.00e-02 2.50e+03 6.33e-02 4.01e+01 pdb=" CD GLN K 170 " 0.110 2.00e-02 2.50e+03 pdb=" OE1 GLN K 170 " -0.041 2.00e-02 2.50e+03 pdb=" NE2 GLN K 170 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN L 606 " 0.025 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" CG ASN L 606 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN L 606 " 0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN L 606 " 0.028 2.00e-02 2.50e+03 ... (remaining 6853 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4490 2.75 - 3.29: 41025 3.29 - 3.82: 61505 3.82 - 4.36: 72453 4.36 - 4.90: 122693 Nonbonded interactions: 302166 Sorted by model distance: nonbonded pdb=" CE2 TRP G 196 " pdb=" ND2 ASN K 215 " model vdw 2.209 3.340 nonbonded pdb=" CB SER C 218 " pdb=" CD2 LEU C 222 " model vdw 2.228 3.860 nonbonded pdb=" NE1 TRP G 196 " pdb=" ND2 ASN K 215 " model vdw 2.324 3.200 nonbonded pdb=" OG SER G 153 " pdb=" OE1 GLU K 226 " model vdw 2.339 3.040 nonbonded pdb=" O LEU C 707 " pdb=" NH1 ARG C 712 " model vdw 2.351 3.120 ... (remaining 302161 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 245 through 357 or resid 366 through 758)) selection = (chain 'E' and (resid 245 through 357 or resid 366 through 478 or resid 491 thro \ ugh 758)) selection = (chain 'F' and (resid 245 through 478 or resid 491 through 758)) } ncs_group { reference = (chain 'B' and (resid 18 through 209 or resid 226 through 395 or resid 397 throu \ gh 802)) selection = (chain 'C' and (resid 18 through 209 or resid 226 through 395 or resid 397 throu \ gh 478 or resid 489 through 802)) selection = (chain 'D' and (resid 18 through 395 or resid 397 through 478 or resid 489 throu \ gh 802)) } ncs_group { reference = (chain 'G' and (resid 1 through 49 or resid 54 through 292)) selection = chain 'H' selection = (chain 'I' and (resid 1 through 49 or resid 54 through 292)) } 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=0.43 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 35.360 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.007 0.122 39134 Z= 0.371 Angle : 0.961 22.240 52815 Z= 0.605 Chirality : 0.049 0.338 5976 Planarity : 0.006 0.112 6856 Dihedral : 14.197 140.386 15073 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.21 % Favored : 95.52 % Rotamer: Outliers : 0.12 % Allowed : 1.59 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 are not related in a simple way. whole: 0.24 (0.12), residues: 4851 helix: 1.05 (0.10), residues: 2548 sheet: -0.02 (0.20), residues: 587 loop : -1.07 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.002 ARG I 50 TYR 0.114 0.003 TYR H 174 PHE 0.063 0.003 PHE A 261 TRP 0.029 0.003 TRP C 88 HIS 0.020 0.002 HIS G 109 Details of bonding type rmsd covalent geometry : bond 0.00696 (39134) covalent geometry : angle 0.96071 (52815) hydrogen bonds : bond 0.15541 ( 2085) hydrogen bonds : angle 5.88863 ( 6065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 682 time to evaluate : 1.546 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: 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: 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 311 ILE cc_start: 0.9692 (mm) cc_final: 0.9296 (tp) REVERT: A 331 GLU cc_start: 0.9626 (pt0) cc_final: 0.9330 (pt0) REVERT: A 369 ASP cc_start: 0.9160 (m-30) cc_final: 0.8950 (m-30) REVERT: A 440 MET cc_start: 0.8619 (mpp) cc_final: 0.8093 (mpp) REVERT: A 661 LEU cc_start: 0.9264 (tp) cc_final: 0.9056 (tp) REVERT: A 662 LEU cc_start: 0.9494 (tp) cc_final: 0.9183 (tp) REVERT: A 691 MET cc_start: 0.9368 (mtm) cc_final: 0.9023 (mpp) REVERT: B 160 MET cc_start: 0.3961 (tpt) cc_final: 0.3747 (tmm) REVERT: B 320 GLU cc_start: 0.8558 (pm20) cc_final: 0.8091 (pm20) REVERT: B 327 PHE cc_start: 0.9359 (m-80) cc_final: 0.8829 (m-80) REVERT: B 608 ASN cc_start: 0.9359 (m110) cc_final: 0.9034 (m110) REVERT: B 648 LYS cc_start: 0.9585 (ttpt) cc_final: 0.9373 (ptmm) REVERT: C 19 MET cc_start: 0.0488 (mtp) cc_final: -0.2083 (tpt) REVERT: C 157 TYR cc_start: 0.9610 (m-80) cc_final: 0.9069 (m-10) REVERT: C 313 SER cc_start: 0.9308 (t) cc_final: 0.8850 (p) REVERT: C 380 ASP cc_start: 0.8371 (t0) cc_final: 0.8160 (t0) REVERT: C 439 ASN cc_start: 0.9403 (m-40) cc_final: 0.9188 (t0) REVERT: C 523 CYS cc_start: 0.9285 (m) cc_final: 0.8929 (m) REVERT: C 646 MET cc_start: 0.8426 (tmm) cc_final: 0.8134 (tmm) REVERT: C 647 LEU cc_start: 0.9816 (mt) cc_final: 0.9395 (mt) REVERT: C 648 LYS cc_start: 0.9682 (ttpt) cc_final: 0.9292 (tppt) REVERT: D 19 MET cc_start: 0.2970 (mmm) cc_final: -0.1799 (ttm) REVERT: D 22 MET cc_start: 0.1056 (ptm) cc_final: -0.1580 (ptm) REVERT: D 269 LEU cc_start: 0.9707 (mm) cc_final: 0.9455 (mt) REVERT: D 297 MET cc_start: 0.9126 (mmp) cc_final: 0.8647 (mmp) REVERT: D 376 LEU cc_start: 0.9439 (mt) cc_final: 0.9103 (mt) REVERT: D 608 ASN cc_start: 0.9249 (m-40) cc_final: 0.8919 (m-40) REVERT: D 663 ILE cc_start: 0.9485 (mp) cc_final: 0.9184 (mp) REVERT: E 278 LEU cc_start: 0.9488 (tp) cc_final: 0.9104 (tp) REVERT: E 379 MET cc_start: 0.9187 (ttt) cc_final: 0.8752 (tmm) REVERT: E 380 ASP cc_start: 0.9068 (t0) cc_final: 0.8853 (t0) REVERT: E 495 LEU cc_start: 0.8634 (mt) cc_final: 0.8384 (mt) REVERT: E 597 MET cc_start: 0.8333 (mtp) cc_final: 0.8120 (mtp) REVERT: E 611 ARG cc_start: 0.8858 (mmp80) cc_final: 0.8650 (mmm160) REVERT: E 614 TYR cc_start: 0.8371 (m-80) cc_final: 0.7401 (m-80) REVERT: E 646 MET cc_start: 0.9072 (tmm) cc_final: 0.8599 (tmm) REVERT: E 647 LEU cc_start: 0.9796 (mt) cc_final: 0.9518 (mt) REVERT: E 661 LEU cc_start: 0.9430 (tp) cc_final: 0.9149 (mt) REVERT: E 732 LYS cc_start: 0.9825 (tppt) cc_final: 0.9485 (tppt) REVERT: F 280 TYR cc_start: 0.8782 (p90) cc_final: 0.8319 (p90) REVERT: F 518 GLU cc_start: 0.8606 (tm-30) cc_final: 0.7943 (pm20) REVERT: F 594 LEU cc_start: 0.9575 (mm) cc_final: 0.9290 (mm) REVERT: F 605 TYR cc_start: 0.9264 (t80) cc_final: 0.9020 (t80) REVERT: G 1 MET cc_start: 0.6174 (ttm) cc_final: 0.5888 (ttt) REVERT: H 1 MET cc_start: 0.1133 (mmt) cc_final: -0.2078 (ptt) REVERT: H 31 TYR cc_start: 0.6667 (t80) cc_final: 0.6062 (m-80) REVERT: I 1 MET cc_start: 0.4602 (ptm) cc_final: 0.4394 (ttp) REVERT: I 84 TYR cc_start: 0.7744 (t80) cc_final: 0.7288 (t80) REVERT: I 136 LYS cc_start: 0.4717 (tmtt) cc_final: 0.4477 (tptp) REVERT: I 173 GLN cc_start: 0.6560 (mt0) cc_final: 0.6358 (mt0) REVERT: I 285 GLN cc_start: 0.8887 (tp40) cc_final: 0.8627 (mm-40) outliers start: 4 outliers final: 1 residues processed: 685 average time/residue: 0.2469 time to fit residues: 267.8889 Evaluate side-chains 486 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 485 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 416 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 40.0000 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 40.0000 chunk 470 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 HIS C 536 ASN C 717 ASN D 165 HIS D 690 ASN ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 ASN F 413 GLN F 439 ASN G 112 GLN G 118 ASN ** I 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 215 ASN L 606 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.101163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.066825 restraints weight = 414875.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.069300 restraints weight = 177564.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.069569 restraints weight = 125061.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.069697 restraints weight = 80894.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.069697 restraints weight = 77638.116| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 39134 Z= 0.186 Angle : 0.708 11.658 52815 Z= 0.368 Chirality : 0.044 0.234 5976 Planarity : 0.005 0.090 6856 Dihedral : 9.157 127.586 5552 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 1.61 % Allowed : 9.18 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 are not related in a simple way. whole: 0.83 (0.12), residues: 4851 helix: 1.56 (0.10), residues: 2625 sheet: 0.21 (0.20), residues: 590 loop : -0.95 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 534 TYR 0.037 0.002 TYR G 47 PHE 0.031 0.002 PHE A 261 TRP 0.017 0.001 TRP B 91 HIS 0.011 0.001 HIS G 109 Details of bonding type rmsd covalent geometry : bond 0.00396 (39134) covalent geometry : angle 0.70752 (52815) hydrogen bonds : bond 0.04769 ( 2085) hydrogen bonds : angle 4.70931 ( 6065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 522 time to evaluate : 1.522 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ILE cc_start: 0.9727 (mm) cc_final: 0.9375 (tp) REVERT: A 369 ASP cc_start: 0.9392 (m-30) cc_final: 0.9181 (m-30) REVERT: A 401 ASP cc_start: 0.9338 (t0) cc_final: 0.9038 (t0) REVERT: A 597 MET cc_start: 0.8809 (mtp) cc_final: 0.8547 (mpp) REVERT: A 648 LYS cc_start: 0.9537 (tptt) cc_final: 0.9320 (tptt) REVERT: A 691 MET cc_start: 0.8963 (mtm) cc_final: 0.8707 (mtm) REVERT: B 139 LEU cc_start: 0.9423 (mt) cc_final: 0.9027 (mt) REVERT: B 160 MET cc_start: 0.4940 (tpt) cc_final: 0.4054 (tmm) REVERT: B 320 GLU cc_start: 0.8779 (pm20) cc_final: 0.8304 (pm20) REVERT: B 376 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9100 (mm) REVERT: B 379 MET cc_start: 0.9324 (mmm) cc_final: 0.8805 (tpp) REVERT: B 597 MET cc_start: 0.9347 (mtp) cc_final: 0.8911 (mpp) REVERT: B 608 ASN cc_start: 0.9447 (m110) cc_final: 0.9126 (m110) REVERT: B 648 LYS cc_start: 0.9770 (ttpt) cc_final: 0.9490 (ptpp) REVERT: C 19 MET cc_start: 0.6470 (mtp) cc_final: 0.4216 (tpt) REVERT: C 157 TYR cc_start: 0.9656 (m-80) cc_final: 0.9256 (m-10) REVERT: C 248 PHE cc_start: 0.9352 (m-80) cc_final: 0.9090 (m-80) REVERT: C 357 GLN cc_start: 0.9617 (tp40) cc_final: 0.9371 (tp40) REVERT: C 380 ASP cc_start: 0.8559 (t0) cc_final: 0.8201 (t0) REVERT: C 410 PHE cc_start: 0.9578 (m-80) cc_final: 0.9336 (m-80) REVERT: C 439 ASN cc_start: 0.9538 (m-40) cc_final: 0.9253 (t0) REVERT: C 529 MET cc_start: 0.8941 (mpp) cc_final: 0.8552 (tmm) REVERT: C 646 MET cc_start: 0.9067 (tmm) cc_final: 0.8707 (tmm) REVERT: C 648 LYS cc_start: 0.9818 (ttpt) cc_final: 0.9372 (tppt) REVERT: D 19 MET cc_start: 0.8640 (mmm) cc_final: 0.7911 (ttp) REVERT: D 160 MET cc_start: -0.2717 (mmt) cc_final: -0.3062 (mmp) REVERT: D 297 MET cc_start: 0.9254 (mmp) cc_final: 0.8990 (mmm) REVERT: D 376 LEU cc_start: 0.9519 (mt) cc_final: 0.9190 (mt) REVERT: D 396 ARG cc_start: 0.9110 (ttp-110) cc_final: 0.8892 (mtm110) REVERT: D 518 GLU cc_start: 0.9462 (mp0) cc_final: 0.9235 (pm20) REVERT: D 520 LEU cc_start: 0.9465 (pp) cc_final: 0.9208 (mp) REVERT: D 528 MET cc_start: 0.8945 (mmm) cc_final: 0.8619 (tpp) REVERT: D 529 MET cc_start: 0.8922 (mpp) cc_final: 0.8643 (mpp) REVERT: D 608 ASN cc_start: 0.9407 (m-40) cc_final: 0.9185 (m110) REVERT: D 621 LEU cc_start: 0.9533 (mm) cc_final: 0.9280 (mm) REVERT: E 349 ASP cc_start: 0.9432 (OUTLIER) cc_final: 0.8919 (p0) REVERT: E 379 MET cc_start: 0.9266 (ttt) cc_final: 0.8819 (tmm) REVERT: E 495 LEU cc_start: 0.8849 (mt) cc_final: 0.8296 (mt) REVERT: E 610 PHE cc_start: 0.9844 (m-80) cc_final: 0.9413 (m-80) REVERT: E 611 ARG cc_start: 0.9284 (mmp80) cc_final: 0.8969 (mmm160) REVERT: E 614 TYR cc_start: 0.8802 (m-80) cc_final: 0.7522 (m-80) REVERT: E 646 MET cc_start: 0.9330 (tmm) cc_final: 0.8946 (tmm) REVERT: E 661 LEU cc_start: 0.9513 (tp) cc_final: 0.9192 (mt) REVERT: E 678 ILE cc_start: 0.9764 (pt) cc_final: 0.9391 (mm) REVERT: E 691 MET cc_start: 0.7085 (ppp) cc_final: 0.6559 (ppp) REVERT: E 732 LYS cc_start: 0.9789 (tppt) cc_final: 0.9377 (tppt) REVERT: F 518 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8141 (pm20) REVERT: F 520 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8559 (mt) REVERT: F 605 TYR cc_start: 0.9463 (t80) cc_final: 0.9073 (t80) REVERT: F 631 ASP cc_start: 0.9340 (m-30) cc_final: 0.8913 (t70) REVERT: H 1 MET cc_start: 0.2377 (mmt) cc_final: -0.0560 (ptt) REVERT: I 1 MET cc_start: 0.5572 (ptm) cc_final: 0.4870 (tmm) REVERT: I 84 TYR cc_start: 0.7601 (t80) cc_final: 0.7294 (t80) REVERT: I 285 GLN cc_start: 0.8781 (tp40) cc_final: 0.8504 (mm-40) REVERT: K 172 ILE cc_start: 0.9153 (mt) cc_final: 0.8944 (mt) outliers start: 67 outliers final: 35 residues processed: 563 average time/residue: 0.2243 time to fit residues: 205.2363 Evaluate side-chains 482 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 444 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 677 ASP Chi-restraints excluded: chain E residue 349 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 523 CYS Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain F residue 259 ARG Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 614 TYR Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain G residue 31 TYR Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 269 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 327 optimal weight: 8.9990 chunk 302 optimal weight: 0.8980 chunk 423 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 129 optimal weight: 30.0000 chunk 214 optimal weight: 0.0980 chunk 390 optimal weight: 8.9990 chunk 396 optimal weight: 7.9990 chunk 473 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN B 475 ASN C 748 ASN D 344 HIS ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 563 HIS H 239 ASN I 42 GLN I 195 GLN I 223 GLN ** I 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 GLN ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 438 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.100469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.066899 restraints weight = 324368.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.068345 restraints weight = 168150.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.069386 restraints weight = 103715.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.069855 restraints weight = 73421.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.070370 restraints weight = 59621.837| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39134 Z= 0.151 Angle : 0.644 10.929 52815 Z= 0.333 Chirality : 0.042 0.184 5976 Planarity : 0.004 0.082 6856 Dihedral : 8.718 114.686 5550 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 1.78 % Allowed : 11.17 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.08 (0.12), residues: 4851 helix: 1.75 (0.10), residues: 2630 sheet: 0.38 (0.20), residues: 589 loop : -0.84 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 712 TYR 0.024 0.001 TYR F 614 PHE 0.025 0.001 PHE F 355 TRP 0.013 0.001 TRP B 91 HIS 0.013 0.001 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00321 (39134) covalent geometry : angle 0.64435 (52815) hydrogen bonds : bond 0.04194 ( 2085) hydrogen bonds : angle 4.36370 ( 6065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 471 time to evaluate : 1.518 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8391 (p0) REVERT: A 311 ILE cc_start: 0.9730 (mm) cc_final: 0.9471 (tp) REVERT: A 369 ASP cc_start: 0.9370 (m-30) cc_final: 0.9140 (m-30) REVERT: A 376 LEU cc_start: 0.9404 (mt) cc_final: 0.9091 (mt) REVERT: A 401 ASP cc_start: 0.9355 (t0) cc_final: 0.8989 (t0) REVERT: A 648 LYS cc_start: 0.9508 (tptt) cc_final: 0.9121 (tptt) REVERT: A 678 ILE cc_start: 0.9591 (pt) cc_final: 0.9062 (mm) REVERT: B 139 LEU cc_start: 0.9389 (mt) cc_final: 0.9064 (mt) REVERT: B 160 MET cc_start: 0.4211 (tpt) cc_final: 0.3801 (tmm) REVERT: B 331 GLU cc_start: 0.9580 (pm20) cc_final: 0.9190 (pm20) REVERT: B 376 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9161 (mm) REVERT: B 379 MET cc_start: 0.9318 (mmm) cc_final: 0.8830 (ttm) REVERT: B 441 MET cc_start: 0.8563 (ptp) cc_final: 0.8300 (pmm) REVERT: B 597 MET cc_start: 0.9290 (mtp) cc_final: 0.9057 (mpp) REVERT: B 608 ASN cc_start: 0.9409 (m110) cc_final: 0.9089 (m110) REVERT: B 648 LYS cc_start: 0.9736 (ttpt) cc_final: 0.9445 (ptpp) REVERT: C 19 MET cc_start: 0.0663 (mtp) cc_final: -0.1655 (tpt) REVERT: C 157 TYR cc_start: 0.9552 (m-80) cc_final: 0.9153 (m-10) REVERT: C 160 MET cc_start: 0.7501 (tpt) cc_final: 0.6312 (mmm) REVERT: C 248 PHE cc_start: 0.9343 (m-80) cc_final: 0.9019 (m-80) REVERT: C 321 GLU cc_start: 0.9338 (tm-30) cc_final: 0.9047 (tm-30) REVERT: C 322 ASN cc_start: 0.9484 (m110) cc_final: 0.9074 (m110) REVERT: C 357 GLN cc_start: 0.9563 (tp40) cc_final: 0.9240 (tp-100) REVERT: C 410 PHE cc_start: 0.9570 (m-80) cc_final: 0.9355 (m-80) REVERT: C 646 MET cc_start: 0.9104 (tmm) cc_final: 0.8485 (tmm) REVERT: C 647 LEU cc_start: 0.9900 (mt) cc_final: 0.9497 (mt) REVERT: D 19 MET cc_start: 0.7306 (mmm) cc_final: 0.5707 (ttp) REVERT: D 396 ARG cc_start: 0.9162 (ttp-110) cc_final: 0.8955 (ttp80) REVERT: D 528 MET cc_start: 0.9057 (mmm) cc_final: 0.8755 (tpp) REVERT: D 529 MET cc_start: 0.9038 (mpp) cc_final: 0.8778 (mpp) REVERT: D 608 ASN cc_start: 0.9433 (m-40) cc_final: 0.9177 (m110) REVERT: D 631 ASP cc_start: 0.9346 (OUTLIER) cc_final: 0.8888 (t0) REVERT: E 349 ASP cc_start: 0.9449 (OUTLIER) cc_final: 0.8942 (p0) REVERT: E 379 MET cc_start: 0.9257 (ttt) cc_final: 0.8924 (tpp) REVERT: E 440 MET cc_start: 0.8064 (mtm) cc_final: 0.7841 (ptt) REVERT: E 495 LEU cc_start: 0.8632 (mt) cc_final: 0.8400 (mt) REVERT: E 597 MET cc_start: 0.9197 (mtp) cc_final: 0.8959 (mpp) REVERT: E 678 ILE cc_start: 0.9750 (pt) cc_final: 0.9407 (mm) REVERT: E 691 MET cc_start: 0.7459 (ppp) cc_final: 0.7149 (ppp) REVERT: F 518 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8086 (pm20) REVERT: F 520 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8640 (mt) REVERT: F 528 MET cc_start: 0.9150 (mmm) cc_final: 0.8842 (mmm) REVERT: F 605 TYR cc_start: 0.9465 (t80) cc_final: 0.9095 (t80) REVERT: F 631 ASP cc_start: 0.9397 (OUTLIER) cc_final: 0.8973 (t70) REVERT: G 1 MET cc_start: 0.7273 (ttt) cc_final: 0.6377 (tmm) REVERT: G 13 LYS cc_start: 0.6490 (tmmt) cc_final: 0.6189 (pttt) REVERT: H 1 MET cc_start: 0.1329 (mmt) cc_final: -0.1851 (ptt) REVERT: I 1 MET cc_start: 0.4905 (ptm) cc_final: 0.4260 (tmm) REVERT: I 285 GLN cc_start: 0.8811 (tp40) cc_final: 0.8524 (mm-40) REVERT: J 43 MET cc_start: -0.3959 (tpp) cc_final: -0.4588 (tpp) REVERT: K 172 ILE cc_start: 0.9277 (mt) cc_final: 0.9046 (mt) REVERT: K 177 LEU cc_start: 0.9123 (pp) cc_final: 0.8734 (tt) REVERT: K 217 MET cc_start: -0.7980 (tpp) cc_final: -0.8372 (tpt) REVERT: L 459 MET cc_start: 0.2198 (mtt) cc_final: 0.1730 (mtt) outliers start: 74 outliers final: 38 residues processed: 516 average time/residue: 0.2213 time to fit residues: 185.9224 Evaluate side-chains 470 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 426 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 631 ASP Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 349 ASP Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 523 CYS Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 614 TYR Chi-restraints excluded: chain F residue 631 ASP Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain G residue 31 TYR Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain L residue 464 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 290 optimal weight: 8.9990 chunk 294 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 272 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 476 optimal weight: 50.0000 chunk 450 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS C 325 ASN C 446 ASN D 33 ASN D 84 ASN D 273 HIS D 742 HIS E 504 ASN ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 438 ASN ** I 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 627 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.097325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064964 restraints weight = 465192.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066120 restraints weight = 208879.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.067176 restraints weight = 124404.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.067792 restraints weight = 86162.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.068024 restraints weight = 67700.156| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 39134 Z= 0.216 Angle : 0.674 11.869 52815 Z= 0.351 Chirality : 0.042 0.207 5976 Planarity : 0.005 0.080 6856 Dihedral : 8.627 105.295 5550 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.21 % Favored : 95.77 % Rotamer: Outliers : 2.25 % Allowed : 13.04 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 0.99 (0.12), residues: 4851 helix: 1.65 (0.10), residues: 2644 sheet: 0.34 (0.20), residues: 586 loop : -0.85 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 145 TYR 0.024 0.002 TYR G 47 PHE 0.021 0.002 PHE B 682 TRP 0.014 0.002 TRP C 632 HIS 0.008 0.001 HIS E 563 Details of bonding type rmsd covalent geometry : bond 0.00442 (39134) covalent geometry : angle 0.67409 (52815) hydrogen bonds : bond 0.03970 ( 2085) hydrogen bonds : angle 4.43340 ( 6065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 428 time to evaluate : 1.438 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: 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: symmetry clash REVERT: A 307 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8336 (p0) REVERT: A 311 ILE cc_start: 0.9722 (mm) cc_final: 0.9490 (tp) REVERT: A 331 GLU cc_start: 0.9738 (pt0) cc_final: 0.9475 (pp20) REVERT: A 401 ASP cc_start: 0.9354 (t0) cc_final: 0.9026 (t0) REVERT: A 648 LYS cc_start: 0.9517 (tptt) cc_final: 0.9225 (tptt) REVERT: A 691 MET cc_start: 0.8980 (mtm) cc_final: 0.8720 (ttm) REVERT: A 701 MET cc_start: 0.8806 (ptt) cc_final: 0.8585 (ptt) REVERT: B 139 LEU cc_start: 0.9359 (mt) cc_final: 0.9019 (mt) REVERT: B 160 MET cc_start: 0.4850 (tpt) cc_final: 0.4508 (tmm) REVERT: B 376 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9042 (mm) REVERT: B 379 MET cc_start: 0.9401 (mmm) cc_final: 0.8864 (tpp) REVERT: B 519 ASP cc_start: 0.9367 (OUTLIER) cc_final: 0.8794 (p0) REVERT: B 608 ASN cc_start: 0.9435 (m110) cc_final: 0.9098 (m110) REVERT: B 648 LYS cc_start: 0.9717 (ttpt) cc_final: 0.9433 (ptpp) REVERT: B 653 ARG cc_start: 0.9240 (tpp80) cc_final: 0.8873 (tpp-160) REVERT: C 19 MET cc_start: 0.1061 (mtp) cc_final: -0.1403 (tpt) REVERT: C 157 TYR cc_start: 0.9554 (m-80) cc_final: 0.9072 (m-10) REVERT: C 160 MET cc_start: 0.7906 (tpt) cc_final: 0.6792 (mmm) REVERT: C 248 PHE cc_start: 0.9417 (m-80) cc_final: 0.9091 (m-80) REVERT: C 321 GLU cc_start: 0.9311 (tm-30) cc_final: 0.9102 (tm-30) REVERT: C 322 ASN cc_start: 0.9419 (m110) cc_final: 0.9059 (m110) REVERT: C 357 GLN cc_start: 0.9579 (tp40) cc_final: 0.8825 (tp-100) REVERT: C 529 MET cc_start: 0.8921 (mpp) cc_final: 0.8410 (tmm) REVERT: C 624 ASP cc_start: 0.9145 (t70) cc_final: 0.8484 (p0) REVERT: C 646 MET cc_start: 0.9182 (tmm) cc_final: 0.8616 (tmm) REVERT: C 647 LEU cc_start: 0.9895 (mt) cc_final: 0.9487 (mt) REVERT: C 648 LYS cc_start: 0.9865 (ttpt) cc_final: 0.9570 (ttpp) REVERT: C 661 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9348 (tp) REVERT: D 19 MET cc_start: 0.7229 (mmm) cc_final: 0.5634 (ttp) REVERT: D 22 MET cc_start: 0.6828 (ptm) cc_final: 0.6535 (mtp) REVERT: D 396 ARG cc_start: 0.9096 (ttp-110) cc_final: 0.8854 (ttp80) REVERT: D 528 MET cc_start: 0.9123 (mmm) cc_final: 0.8875 (tpp) REVERT: D 608 ASN cc_start: 0.9424 (m-40) cc_final: 0.9157 (m110) REVERT: D 631 ASP cc_start: 0.9193 (OUTLIER) cc_final: 0.8807 (t0) REVERT: D 648 LYS cc_start: 0.9602 (tppt) cc_final: 0.9260 (tppt) REVERT: E 349 ASP cc_start: 0.9512 (OUTLIER) cc_final: 0.9291 (p0) REVERT: E 355 PHE cc_start: 0.9195 (m-80) cc_final: 0.8832 (m-80) REVERT: E 379 MET cc_start: 0.9347 (ttt) cc_final: 0.8977 (tpp) REVERT: E 440 MET cc_start: 0.8097 (mtm) cc_final: 0.7770 (mmm) REVERT: E 678 ILE cc_start: 0.9778 (pt) cc_final: 0.9456 (mm) REVERT: F 520 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8595 (mt) REVERT: F 605 TYR cc_start: 0.9489 (t80) cc_final: 0.9171 (t80) REVERT: F 607 ASP cc_start: 0.9325 (t0) cc_final: 0.9028 (t0) REVERT: F 646 MET cc_start: 0.9258 (tpp) cc_final: 0.9021 (tpp) REVERT: G 1 MET cc_start: 0.7592 (ttt) cc_final: 0.6979 (tmm) REVERT: H 1 MET cc_start: 0.1280 (mmt) cc_final: -0.1536 (ttt) REVERT: I 1 MET cc_start: 0.4663 (ptm) cc_final: 0.4074 (tmm) REVERT: I 285 GLN cc_start: 0.8726 (tp40) cc_final: 0.8456 (mm-40) REVERT: J 43 MET cc_start: -0.3480 (tpp) cc_final: -0.3982 (tpp) REVERT: K 172 ILE cc_start: 0.9391 (mt) cc_final: 0.9100 (mp) REVERT: K 177 LEU cc_start: 0.9110 (pp) cc_final: 0.8695 (tt) REVERT: K 183 ARG cc_start: 0.8748 (tpp-160) cc_final: 0.8496 (tpp-160) REVERT: K 196 ARG cc_start: 0.6428 (OUTLIER) cc_final: 0.5393 (ptt90) REVERT: K 217 MET cc_start: -0.7942 (tpp) cc_final: -0.8271 (tpt) REVERT: L 482 MET cc_start: 0.5141 (ptp) cc_final: 0.4801 (ptp) outliers start: 94 outliers final: 56 residues processed: 494 average time/residue: 0.2228 time to fit residues: 180.8764 Evaluate side-chains 459 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 395 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 657 GLN Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 631 ASP Chi-restraints excluded: chain D residue 677 ASP Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 349 ASP Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 523 CYS Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 733 THR Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 614 TYR Chi-restraints excluded: chain F residue 631 ASP Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain G residue 31 TYR Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain K residue 196 ARG Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain L residue 464 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 235 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 133 optimal weight: 40.0000 chunk 255 optimal weight: 1.9990 chunk 438 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 352 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 449 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 257 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 GLN C 325 ASN C 446 ASN D 165 HIS ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.099257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.066457 restraints weight = 319107.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.066415 restraints weight = 206853.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.067560 restraints weight = 140576.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.067198 restraints weight = 88315.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.067198 restraints weight = 101944.161| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 39134 Z= 0.116 Angle : 0.637 11.295 52815 Z= 0.319 Chirality : 0.041 0.187 5976 Planarity : 0.004 0.067 6856 Dihedral : 8.179 102.070 5550 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.18 % Rotamer: Outliers : 1.97 % Allowed : 14.37 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.35 (0.12), residues: 4851 helix: 1.94 (0.10), residues: 2643 sheet: 0.58 (0.20), residues: 583 loop : -0.73 (0.16), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 335 TYR 0.020 0.001 TYR F 614 PHE 0.020 0.001 PHE A 261 TRP 0.016 0.001 TRP B 91 HIS 0.005 0.001 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00247 (39134) covalent geometry : angle 0.63732 (52815) hydrogen bonds : bond 0.03662 ( 2085) hydrogen bonds : angle 4.10718 ( 6065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 445 time to evaluate : 1.504 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: 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: 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 307 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8301 (p0) REVERT: A 311 ILE cc_start: 0.9746 (mm) cc_final: 0.9542 (tp) REVERT: A 331 GLU cc_start: 0.9760 (pt0) cc_final: 0.9526 (pp20) REVERT: A 358 ARG cc_start: 0.9640 (ptt90) cc_final: 0.9176 (ptm-80) REVERT: A 369 ASP cc_start: 0.9418 (m-30) cc_final: 0.9192 (m-30) REVERT: A 401 ASP cc_start: 0.9461 (t0) cc_final: 0.9070 (t0) REVERT: A 648 LYS cc_start: 0.9599 (tptt) cc_final: 0.9259 (tppt) REVERT: A 691 MET cc_start: 0.9069 (mtm) cc_final: 0.8753 (ttt) REVERT: A 701 MET cc_start: 0.8821 (ptt) cc_final: 0.8586 (ptt) REVERT: B 139 LEU cc_start: 0.9426 (mt) cc_final: 0.8988 (mt) REVERT: B 160 MET cc_start: 0.5332 (tpt) cc_final: 0.4677 (tmm) REVERT: B 320 GLU cc_start: 0.9118 (pm20) cc_final: 0.8887 (pm20) REVERT: B 376 LEU cc_start: 0.9510 (mm) cc_final: 0.8998 (mm) REVERT: B 379 MET cc_start: 0.9340 (mmm) cc_final: 0.8852 (ttm) REVERT: B 597 MET cc_start: 0.9275 (mtp) cc_final: 0.9065 (ptp) REVERT: B 607 ASP cc_start: 0.9551 (t0) cc_final: 0.9176 (t0) REVERT: B 608 ASN cc_start: 0.9461 (m110) cc_final: 0.9210 (m110) REVERT: B 646 MET cc_start: 0.9065 (tpp) cc_final: 0.8815 (tpp) REVERT: C 19 MET cc_start: 0.6486 (mtp) cc_final: 0.3900 (tpt) REVERT: C 157 TYR cc_start: 0.9642 (m-80) cc_final: 0.9256 (m-10) REVERT: C 160 MET cc_start: 0.7662 (tpt) cc_final: 0.6182 (mmm) REVERT: C 248 PHE cc_start: 0.9404 (m-80) cc_final: 0.9067 (m-80) REVERT: C 321 GLU cc_start: 0.9345 (tm-30) cc_final: 0.9087 (tm-30) REVERT: C 322 ASN cc_start: 0.9415 (m110) cc_final: 0.9029 (m-40) REVERT: C 357 GLN cc_start: 0.9705 (tp40) cc_final: 0.9425 (mm110) REVERT: C 410 PHE cc_start: 0.9632 (m-80) cc_final: 0.9402 (m-80) REVERT: C 529 MET cc_start: 0.8903 (mpp) cc_final: 0.8695 (ppp) REVERT: C 597 MET cc_start: 0.9206 (mtp) cc_final: 0.8907 (ptm) REVERT: C 638 ARG cc_start: 0.8641 (mtt180) cc_final: 0.8425 (mtt90) REVERT: C 646 MET cc_start: 0.9164 (tmm) cc_final: 0.8630 (tmm) REVERT: C 647 LEU cc_start: 0.9869 (mt) cc_final: 0.9419 (mt) REVERT: C 648 LYS cc_start: 0.9844 (ttpt) cc_final: 0.9549 (ttpp) REVERT: C 661 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9433 (tp) REVERT: D 19 MET cc_start: 0.8729 (mmm) cc_final: 0.8227 (ttp) REVERT: D 160 MET cc_start: -0.1063 (mmp) cc_final: -0.1505 (mmp) REVERT: D 321 GLU cc_start: 0.9233 (tm-30) cc_final: 0.9004 (tm-30) REVERT: D 337 LYS cc_start: 0.9742 (mtpp) cc_final: 0.9522 (ttpt) REVERT: D 393 MET cc_start: 0.9388 (pmm) cc_final: 0.9005 (pmm) REVERT: D 396 ARG cc_start: 0.9106 (ttp-110) cc_final: 0.8825 (ttp80) REVERT: D 631 ASP cc_start: 0.9294 (OUTLIER) cc_final: 0.8845 (t0) REVERT: D 648 LYS cc_start: 0.9599 (tppt) cc_final: 0.9230 (tppt) REVERT: E 349 ASP cc_start: 0.9533 (OUTLIER) cc_final: 0.9295 (p0) REVERT: E 440 MET cc_start: 0.8062 (mtm) cc_final: 0.7806 (mmm) REVERT: E 517 GLU cc_start: 0.7422 (mp0) cc_final: 0.7120 (mp0) REVERT: E 644 LEU cc_start: 0.9875 (tp) cc_final: 0.9665 (pp) REVERT: E 661 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9022 (mm) REVERT: E 678 ILE cc_start: 0.9803 (pt) cc_final: 0.9553 (mm) REVERT: E 691 MET cc_start: 0.7561 (ppp) cc_final: 0.7106 (ppp) REVERT: E 753 LEU cc_start: 0.9740 (mm) cc_final: 0.9526 (mt) REVERT: F 518 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8601 (pp20) REVERT: F 520 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8679 (mt) REVERT: F 529 MET cc_start: 0.8847 (mmt) cc_final: 0.7604 (tpt) REVERT: F 605 TYR cc_start: 0.9476 (t80) cc_final: 0.9174 (t80) REVERT: F 607 ASP cc_start: 0.9332 (t0) cc_final: 0.9012 (t0) REVERT: F 646 MET cc_start: 0.9181 (tpp) cc_final: 0.8872 (tpp) REVERT: F 648 LYS cc_start: 0.9567 (tptt) cc_final: 0.9233 (tppt) REVERT: G 1 MET cc_start: 0.7479 (ttt) cc_final: 0.6746 (tmm) REVERT: H 1 MET cc_start: 0.1913 (mmt) cc_final: -0.0708 (ttt) REVERT: I 1 MET cc_start: 0.5046 (ptm) cc_final: 0.4426 (tmm) REVERT: I 285 GLN cc_start: 0.8708 (tp40) cc_final: 0.8454 (mm-40) REVERT: K 172 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.9266 (mt) REVERT: K 177 LEU cc_start: 0.9087 (pp) cc_final: 0.8709 (tt) REVERT: K 196 ARG cc_start: 0.6084 (OUTLIER) cc_final: 0.5312 (ptt90) outliers start: 82 outliers final: 47 residues processed: 499 average time/residue: 0.2228 time to fit residues: 182.4657 Evaluate side-chains 472 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 417 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain B residue 397 LYS Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 597 MET Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 631 ASP Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 349 ASP Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 679 LEU Chi-restraints excluded: chain E residue 733 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 614 TYR Chi-restraints excluded: chain F residue 633 VAL Chi-restraints excluded: chain G residue 31 TYR Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 196 ARG Chi-restraints excluded: chain K residue 205 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 184 optimal weight: 7.9990 chunk 460 optimal weight: 30.0000 chunk 132 optimal weight: 7.9990 chunk 367 optimal weight: 9.9990 chunk 385 optimal weight: 50.0000 chunk 80 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 438 optimal weight: 50.0000 chunk 336 optimal weight: 0.0770 chunk 50 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 overall best weight: 3.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 373 ASN D 165 HIS ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 485 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 = 0.3970 r_free = 0.3970 target = 0.097685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.065797 restraints weight = 348860.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.067109 restraints weight = 171277.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.068025 restraints weight = 106164.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.068413 restraints weight = 76509.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.069052 restraints weight = 63338.259| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39134 Z= 0.152 Angle : 0.634 12.264 52815 Z= 0.321 Chirality : 0.041 0.211 5976 Planarity : 0.004 0.067 6856 Dihedral : 8.094 99.736 5550 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.12 % Rotamer: Outliers : 1.80 % Allowed : 15.82 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 are not related in a simple way. whole: 1.33 (0.12), residues: 4851 helix: 1.91 (0.10), residues: 2656 sheet: 0.54 (0.20), residues: 587 loop : -0.72 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 335 TYR 0.017 0.001 TYR F 614 PHE 0.018 0.001 PHE A 261 TRP 0.011 0.001 TRP C 632 HIS 0.005 0.001 HIS E 563 Details of bonding type rmsd covalent geometry : bond 0.00323 (39134) covalent geometry : angle 0.63375 (52815) hydrogen bonds : bond 0.03584 ( 2085) hydrogen bonds : angle 4.19300 ( 6065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 415 time to evaluate : 1.298 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: 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: 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 307 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8283 (p0) REVERT: A 331 GLU cc_start: 0.9743 (pt0) cc_final: 0.9511 (pp20) REVERT: A 358 ARG cc_start: 0.9670 (ptt90) cc_final: 0.9271 (ptm-80) REVERT: A 401 ASP cc_start: 0.9405 (t0) cc_final: 0.9015 (t0) REVERT: A 597 MET cc_start: 0.9025 (ptp) cc_final: 0.8780 (pmm) REVERT: A 648 LYS cc_start: 0.9586 (tptt) cc_final: 0.9269 (tptt) REVERT: A 691 MET cc_start: 0.9038 (mtm) cc_final: 0.8741 (ttt) REVERT: A 701 MET cc_start: 0.8832 (ptt) cc_final: 0.8587 (ptt) REVERT: B 19 MET cc_start: 0.2844 (ttm) cc_final: 0.2272 (tpp) REVERT: B 139 LEU cc_start: 0.9386 (mt) cc_final: 0.9054 (mt) REVERT: B 160 MET cc_start: 0.4797 (tpt) cc_final: 0.4518 (tmm) REVERT: B 379 MET cc_start: 0.9389 (mmm) cc_final: 0.8800 (tpp) REVERT: B 519 ASP cc_start: 0.9350 (m-30) cc_final: 0.8721 (p0) REVERT: B 607 ASP cc_start: 0.9441 (t0) cc_final: 0.8724 (t0) REVERT: B 608 ASN cc_start: 0.9530 (m110) cc_final: 0.9273 (m110) REVERT: B 611 ARG cc_start: 0.9484 (mtp85) cc_final: 0.9031 (ptp-110) REVERT: B 646 MET cc_start: 0.9161 (tpp) cc_final: 0.8892 (tpp) REVERT: C 19 MET cc_start: 0.0145 (mtp) cc_final: -0.2075 (tpt) REVERT: C 157 TYR cc_start: 0.9538 (m-80) cc_final: 0.9136 (m-10) REVERT: C 160 MET cc_start: 0.7798 (tpt) cc_final: 0.6570 (tpt) REVERT: C 248 PHE cc_start: 0.9446 (m-80) cc_final: 0.9136 (m-80) REVERT: C 321 GLU cc_start: 0.9338 (tm-30) cc_final: 0.9102 (tm-30) REVERT: C 322 ASN cc_start: 0.9411 (m110) cc_final: 0.9017 (m110) REVERT: C 357 GLN cc_start: 0.9593 (tp40) cc_final: 0.8924 (tp-100) REVERT: C 638 ARG cc_start: 0.8641 (mtt180) cc_final: 0.8153 (mtt90) REVERT: C 646 MET cc_start: 0.9168 (tmm) cc_final: 0.8711 (tmm) REVERT: C 647 LEU cc_start: 0.9884 (mt) cc_final: 0.9407 (mt) REVERT: C 648 LYS cc_start: 0.9833 (ttpt) cc_final: 0.9535 (ttpp) REVERT: C 701 MET cc_start: 0.8972 (ppp) cc_final: 0.8738 (ppp) REVERT: D 19 MET cc_start: 0.6513 (mmm) cc_final: 0.4284 (ttp) REVERT: D 22 MET cc_start: 0.7119 (mtp) cc_final: 0.6415 (ptt) REVERT: D 160 MET cc_start: -0.1514 (mmp) cc_final: -0.1821 (mmp) REVERT: D 256 PHE cc_start: 0.9434 (m-10) cc_final: 0.9176 (m-80) REVERT: D 321 GLU cc_start: 0.9232 (tm-30) cc_final: 0.9008 (tm-30) REVERT: D 393 MET cc_start: 0.9379 (pmm) cc_final: 0.8991 (pmm) REVERT: D 608 ASN cc_start: 0.9445 (m-40) cc_final: 0.9143 (m110) REVERT: D 631 ASP cc_start: 0.9340 (OUTLIER) cc_final: 0.8901 (t0) REVERT: D 648 LYS cc_start: 0.9620 (tppt) cc_final: 0.9262 (tppt) REVERT: E 355 PHE cc_start: 0.9274 (m-10) cc_final: 0.9051 (m-10) REVERT: E 440 MET cc_start: 0.8013 (mtm) cc_final: 0.7796 (mmm) REVERT: E 661 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9050 (mm) REVERT: E 678 ILE cc_start: 0.9815 (pt) cc_final: 0.9512 (mm) REVERT: E 691 MET cc_start: 0.7662 (ppp) cc_final: 0.7312 (ppp) REVERT: E 753 LEU cc_start: 0.9741 (mm) cc_final: 0.9528 (mt) REVERT: F 379 MET cc_start: 0.8098 (tmm) cc_final: 0.7737 (ppp) REVERT: F 518 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8291 (pm20) REVERT: F 520 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8617 (mt) REVERT: F 529 MET cc_start: 0.8815 (mmt) cc_final: 0.7851 (tpt) REVERT: F 605 TYR cc_start: 0.9489 (t80) cc_final: 0.9210 (t80) REVERT: F 607 ASP cc_start: 0.9254 (t0) cc_final: 0.8865 (t0) REVERT: F 646 MET cc_start: 0.9283 (tpp) cc_final: 0.8966 (tpp) REVERT: F 648 LYS cc_start: 0.9598 (tptt) cc_final: 0.9309 (tppt) REVERT: G 1 MET cc_start: 0.7398 (ttt) cc_final: 0.6599 (tmm) REVERT: G 189 MET cc_start: -0.0701 (mtt) cc_final: -0.2545 (ttp) REVERT: H 1 MET cc_start: 0.0646 (mmt) cc_final: -0.2072 (ttt) REVERT: I 1 MET cc_start: 0.4436 (ptm) cc_final: 0.4203 (ttp) REVERT: I 285 GLN cc_start: 0.8842 (tp40) cc_final: 0.8590 (mm-40) REVERT: K 172 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9198 (mt) REVERT: K 177 LEU cc_start: 0.9206 (pp) cc_final: 0.8901 (tt) outliers start: 75 outliers final: 54 residues processed: 468 average time/residue: 0.2260 time to fit residues: 173.9295 Evaluate side-chains 454 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 395 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 631 ASP Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 523 CYS Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 679 LEU Chi-restraints excluded: chain E residue 733 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 614 TYR Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 196 ARG Chi-restraints excluded: chain K residue 205 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 168 optimal weight: 8.9990 chunk 363 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 40.0000 chunk 373 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 308 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 376 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN C 446 ASN ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 GLN ** I 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 602 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.095464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.064026 restraints weight = 379845.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066074 restraints weight = 209775.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065200 restraints weight = 122377.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065236 restraints weight = 104567.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065275 restraints weight = 103368.744| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 39134 Z= 0.218 Angle : 0.698 11.720 52815 Z= 0.359 Chirality : 0.042 0.240 5976 Planarity : 0.005 0.156 6856 Dihedral : 8.326 101.029 5550 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 2.25 % Allowed : 15.94 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.05 (0.12), residues: 4851 helix: 1.69 (0.10), residues: 2678 sheet: 0.23 (0.20), residues: 594 loop : -0.80 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 324 TYR 0.017 0.002 TYR E 605 PHE 0.023 0.002 PHE I 202 TRP 0.014 0.001 TRP C 632 HIS 0.008 0.001 HIS E 563 Details of bonding type rmsd covalent geometry : bond 0.00453 (39134) covalent geometry : angle 0.69759 (52815) hydrogen bonds : bond 0.03800 ( 2085) hydrogen bonds : angle 4.42877 ( 6065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 408 time to evaluate : 1.454 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8384 (p0) REVERT: A 358 ARG cc_start: 0.9627 (ptt90) cc_final: 0.9298 (ptm-80) REVERT: A 401 ASP cc_start: 0.9416 (t0) cc_final: 0.8980 (t0) REVERT: A 648 LYS cc_start: 0.9572 (tptt) cc_final: 0.9144 (tptt) REVERT: A 678 ILE cc_start: 0.9535 (pt) cc_final: 0.9302 (mp) REVERT: A 691 MET cc_start: 0.9085 (mtm) cc_final: 0.8864 (ttm) REVERT: A 701 MET cc_start: 0.8844 (ptt) cc_final: 0.8602 (ptt) REVERT: A 754 MET cc_start: 0.9378 (mmp) cc_final: 0.9166 (mmm) REVERT: B 139 LEU cc_start: 0.9432 (mt) cc_final: 0.9048 (mt) REVERT: B 160 MET cc_start: 0.5924 (tpt) cc_final: 0.5442 (tmm) REVERT: B 379 MET cc_start: 0.9511 (mmm) cc_final: 0.9002 (tpp) REVERT: B 389 LEU cc_start: 0.9581 (tt) cc_final: 0.9338 (mm) REVERT: B 519 ASP cc_start: 0.9364 (m-30) cc_final: 0.8762 (p0) REVERT: B 607 ASP cc_start: 0.9461 (t0) cc_final: 0.9126 (t0) REVERT: B 608 ASN cc_start: 0.9503 (m110) cc_final: 0.9241 (m110) REVERT: B 611 ARG cc_start: 0.9538 (mtp85) cc_final: 0.9083 (mtp85) REVERT: B 646 MET cc_start: 0.9118 (tpp) cc_final: 0.8872 (tpp) REVERT: C 19 MET cc_start: 0.6167 (mtp) cc_final: 0.3264 (tpt) REVERT: C 157 TYR cc_start: 0.9608 (m-80) cc_final: 0.9268 (m-10) REVERT: C 160 MET cc_start: 0.7957 (tpt) cc_final: 0.6877 (tpt) REVERT: C 248 PHE cc_start: 0.9451 (m-80) cc_final: 0.9162 (m-80) REVERT: C 321 GLU cc_start: 0.9371 (tm-30) cc_final: 0.9151 (tm-30) REVERT: C 322 ASN cc_start: 0.9407 (m110) cc_final: 0.9011 (m-40) REVERT: C 357 GLN cc_start: 0.9650 (tp40) cc_final: 0.9090 (tp-100) REVERT: C 589 ILE cc_start: 0.9635 (mm) cc_final: 0.9045 (mm) REVERT: C 624 ASP cc_start: 0.9313 (OUTLIER) cc_final: 0.8670 (p0) REVERT: C 638 ARG cc_start: 0.8813 (mtt180) cc_final: 0.8298 (mtt90) REVERT: C 646 MET cc_start: 0.8921 (tmm) cc_final: 0.8615 (tmm) REVERT: C 647 LEU cc_start: 0.9848 (mt) cc_final: 0.9443 (mt) REVERT: C 648 LYS cc_start: 0.9826 (ttpt) cc_final: 0.9574 (ttpp) REVERT: C 701 MET cc_start: 0.9229 (ppp) cc_final: 0.8986 (ppp) REVERT: D 19 MET cc_start: 0.8478 (mmm) cc_final: 0.7562 (ttp) REVERT: D 160 MET cc_start: -0.1114 (mmp) cc_final: -0.1376 (mmp) REVERT: D 260 ILE cc_start: 0.9659 (OUTLIER) cc_final: 0.9327 (mm) REVERT: D 269 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9452 (mm) REVERT: D 321 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8981 (tm-30) REVERT: D 393 MET cc_start: 0.9345 (pmm) cc_final: 0.8983 (pmm) REVERT: D 608 ASN cc_start: 0.9452 (m-40) cc_final: 0.9125 (m-40) REVERT: D 631 ASP cc_start: 0.9203 (OUTLIER) cc_final: 0.8865 (t0) REVERT: D 648 LYS cc_start: 0.9606 (tppt) cc_final: 0.9305 (tppt) REVERT: E 355 PHE cc_start: 0.9263 (m-10) cc_final: 0.8952 (m-80) REVERT: E 379 MET cc_start: 0.9451 (ttt) cc_final: 0.9115 (ttt) REVERT: E 393 MET cc_start: 0.8245 (ttt) cc_final: 0.7630 (mmm) REVERT: E 678 ILE cc_start: 0.9729 (pt) cc_final: 0.9366 (mm) REVERT: E 701 MET cc_start: 0.8942 (ptt) cc_final: 0.8735 (ptt) REVERT: E 732 LYS cc_start: 0.9714 (tppt) cc_final: 0.9305 (tppt) REVERT: E 753 LEU cc_start: 0.9730 (mm) cc_final: 0.9528 (mt) REVERT: F 379 MET cc_start: 0.8182 (tmm) cc_final: 0.7734 (ppp) REVERT: F 518 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8577 (pm20) REVERT: F 520 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8816 (mm) REVERT: F 529 MET cc_start: 0.8910 (mmt) cc_final: 0.8356 (tpt) REVERT: F 605 TYR cc_start: 0.9455 (t80) cc_final: 0.9185 (t80) REVERT: F 607 ASP cc_start: 0.9183 (t0) cc_final: 0.8826 (t0) REVERT: F 646 MET cc_start: 0.9249 (tpp) cc_final: 0.9010 (tpp) REVERT: F 648 LYS cc_start: 0.9561 (tptt) cc_final: 0.9283 (tppt) REVERT: G 1 MET cc_start: 0.7415 (ttt) cc_final: 0.6600 (tmm) REVERT: G 189 MET cc_start: 0.0070 (mtt) cc_final: -0.1516 (ttp) REVERT: H 1 MET cc_start: 0.1154 (mmt) cc_final: -0.1218 (ttt) REVERT: I 1 MET cc_start: 0.4836 (ptm) cc_final: 0.4364 (ttp) REVERT: I 285 GLN cc_start: 0.8769 (tp40) cc_final: 0.8526 (mm-40) REVERT: K 172 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9151 (mt) REVERT: K 177 LEU cc_start: 0.9112 (pp) cc_final: 0.8741 (tt) outliers start: 94 outliers final: 61 residues processed: 476 average time/residue: 0.2270 time to fit residues: 177.3502 Evaluate side-chains 447 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 379 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 397 LYS Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 705 ASN Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 631 ASP Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 349 ASP Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 523 CYS Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 679 LEU Chi-restraints excluded: chain E residue 733 THR Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 334 TYR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 614 TYR Chi-restraints excluded: chain F residue 631 ASP Chi-restraints excluded: chain F residue 633 VAL Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 196 ARG Chi-restraints excluded: chain K residue 205 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 29 optimal weight: 5.9990 chunk 408 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 366 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 368 optimal weight: 5.9990 chunk 200 optimal weight: 40.0000 chunk 329 optimal weight: 30.0000 chunk 278 optimal weight: 0.0770 chunk 45 optimal weight: 5.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 278 ASN ** I 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 171 GLN ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 438 GLN ** L 485 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 = 0.3949 r_free = 0.3949 target = 0.096478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.063727 restraints weight = 485135.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.065875 restraints weight = 237270.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.065788 restraints weight = 145745.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.066118 restraints weight = 93739.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.066177 restraints weight = 84636.436| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 39134 Z= 0.136 Angle : 0.675 14.011 52815 Z= 0.336 Chirality : 0.041 0.224 5976 Planarity : 0.004 0.099 6856 Dihedral : 8.116 99.112 5550 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 1.78 % Allowed : 17.05 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 are not related in a simple way. whole: 1.19 (0.12), residues: 4851 helix: 1.80 (0.10), residues: 2679 sheet: 0.24 (0.20), residues: 580 loop : -0.72 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 335 TYR 0.016 0.001 TYR I 201 PHE 0.019 0.001 PHE A 261 TRP 0.011 0.001 TRP C 632 HIS 0.005 0.001 HIS E 563 Details of bonding type rmsd covalent geometry : bond 0.00298 (39134) covalent geometry : angle 0.67480 (52815) hydrogen bonds : bond 0.03524 ( 2085) hydrogen bonds : angle 4.22421 ( 6065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 403 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 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 307 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8318 (p0) REVERT: A 331 GLU cc_start: 0.9737 (pt0) cc_final: 0.9510 (pp20) REVERT: A 358 ARG cc_start: 0.9577 (ptt90) cc_final: 0.9255 (ptm-80) REVERT: A 401 ASP cc_start: 0.9444 (t0) cc_final: 0.9046 (t0) REVERT: A 597 MET cc_start: 0.9071 (ptp) cc_final: 0.8780 (pmm) REVERT: A 678 ILE cc_start: 0.9590 (pt) cc_final: 0.9248 (mp) REVERT: A 691 MET cc_start: 0.9060 (mtm) cc_final: 0.8844 (ttm) REVERT: A 701 MET cc_start: 0.8747 (ptt) cc_final: 0.8531 (ptt) REVERT: B 139 LEU cc_start: 0.9450 (mt) cc_final: 0.9035 (mt) REVERT: B 160 MET cc_start: 0.5969 (tpt) cc_final: 0.5574 (tmm) REVERT: B 435 MET cc_start: 0.8945 (mmm) cc_final: 0.8617 (mmm) REVERT: B 519 ASP cc_start: 0.9325 (m-30) cc_final: 0.8723 (p0) REVERT: B 607 ASP cc_start: 0.9491 (t0) cc_final: 0.9159 (t0) REVERT: B 608 ASN cc_start: 0.9486 (m110) cc_final: 0.9205 (m110) REVERT: B 611 ARG cc_start: 0.9508 (mtp85) cc_final: 0.9099 (mtp85) REVERT: B 646 MET cc_start: 0.9138 (tpp) cc_final: 0.8821 (tpp) REVERT: B 707 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8150 (pp) REVERT: C 19 MET cc_start: 0.6551 (mtp) cc_final: 0.3812 (tpt) REVERT: C 157 TYR cc_start: 0.9625 (m-80) cc_final: 0.9308 (m-10) REVERT: C 160 MET cc_start: 0.8044 (tpt) cc_final: 0.6971 (tpt) REVERT: C 248 PHE cc_start: 0.9395 (m-80) cc_final: 0.9132 (m-80) REVERT: C 321 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9112 (tm-30) REVERT: C 322 ASN cc_start: 0.9415 (m110) cc_final: 0.9053 (m110) REVERT: C 589 ILE cc_start: 0.9585 (mm) cc_final: 0.8913 (mm) REVERT: C 624 ASP cc_start: 0.9212 (t70) cc_final: 0.8514 (p0) REVERT: C 638 ARG cc_start: 0.8737 (mtt180) cc_final: 0.8395 (mtt180) REVERT: C 646 MET cc_start: 0.9096 (tmm) cc_final: 0.8825 (tmm) REVERT: C 647 LEU cc_start: 0.9877 (mt) cc_final: 0.9461 (mt) REVERT: C 648 LYS cc_start: 0.9834 (ttpt) cc_final: 0.9544 (ttpp) REVERT: D 19 MET cc_start: 0.8477 (mmm) cc_final: 0.7731 (ttp) REVERT: D 160 MET cc_start: -0.1002 (mmp) cc_final: -0.1249 (mmp) REVERT: D 260 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9303 (mm) REVERT: D 321 GLU cc_start: 0.9232 (tm-30) cc_final: 0.9011 (tm-30) REVERT: D 393 MET cc_start: 0.9416 (pmm) cc_final: 0.9004 (pmm) REVERT: D 597 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8966 (ptm) REVERT: D 631 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.8841 (t0) REVERT: D 648 LYS cc_start: 0.9631 (tppt) cc_final: 0.9311 (tppt) REVERT: E 355 PHE cc_start: 0.9270 (m-10) cc_final: 0.8920 (m-80) REVERT: E 379 MET cc_start: 0.9439 (ttt) cc_final: 0.9014 (tpp) REVERT: E 440 MET cc_start: 0.9251 (mmm) cc_final: 0.8834 (pmm) REVERT: E 602 LYS cc_start: 0.9802 (mmtp) cc_final: 0.9512 (mptt) REVERT: E 661 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9069 (mm) REVERT: E 678 ILE cc_start: 0.9762 (pt) cc_final: 0.9483 (mm) REVERT: F 379 MET cc_start: 0.8162 (tmm) cc_final: 0.7744 (ppp) REVERT: F 440 MET cc_start: 0.8998 (mmt) cc_final: 0.8785 (mmp) REVERT: F 518 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8530 (pm20) REVERT: F 520 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8698 (mm) REVERT: F 529 MET cc_start: 0.8911 (mmt) cc_final: 0.8294 (tpt) REVERT: F 607 ASP cc_start: 0.9162 (t0) cc_final: 0.8843 (t0) REVERT: F 646 MET cc_start: 0.9255 (tpp) cc_final: 0.8985 (tpp) REVERT: F 648 LYS cc_start: 0.9580 (tptt) cc_final: 0.9277 (tppt) REVERT: G 1 MET cc_start: 0.7592 (ttt) cc_final: 0.6858 (tmm) REVERT: G 189 MET cc_start: -0.0127 (mtt) cc_final: -0.1609 (ttp) REVERT: H 1 MET cc_start: 0.1216 (mmt) cc_final: -0.0989 (ttt) REVERT: I 1 MET cc_start: 0.5155 (ptm) cc_final: 0.4831 (ttp) REVERT: I 285 GLN cc_start: 0.8757 (tp40) cc_final: 0.8520 (mm-40) REVERT: K 172 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9089 (mt) REVERT: K 177 LEU cc_start: 0.9125 (pp) cc_final: 0.8823 (tt) outliers start: 74 outliers final: 47 residues processed: 455 average time/residue: 0.2161 time to fit residues: 163.4791 Evaluate side-chains 440 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 385 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 597 MET Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 631 ASP Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 679 LEU Chi-restraints excluded: chain E residue 733 THR Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 633 VAL Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 196 ARG Chi-restraints excluded: chain K residue 205 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 321 optimal weight: 4.9990 chunk 420 optimal weight: 0.0670 chunk 137 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 171 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 303 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 436 optimal weight: 50.0000 chunk 150 optimal weight: 6.9990 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.097300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.065412 restraints weight = 373245.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.067093 restraints weight = 190099.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.067093 restraints weight = 125162.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.067093 restraints weight = 125162.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.067093 restraints weight = 125162.427| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39134 Z= 0.118 Angle : 0.686 14.836 52815 Z= 0.337 Chirality : 0.042 0.226 5976 Planarity : 0.004 0.078 6856 Dihedral : 7.860 96.351 5550 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.12 % Rotamer: Outliers : 1.42 % Allowed : 17.48 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 are not related in a simple way. whole: 1.32 (0.12), residues: 4851 helix: 1.89 (0.10), residues: 2685 sheet: 0.36 (0.20), residues: 581 loop : -0.66 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 335 TYR 0.016 0.001 TYR I 201 PHE 0.019 0.001 PHE F 348 TRP 0.012 0.001 TRP E 632 HIS 0.005 0.001 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00259 (39134) covalent geometry : angle 0.68612 (52815) hydrogen bonds : bond 0.03441 ( 2085) hydrogen bonds : angle 4.10556 ( 6065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 425 time to evaluate : 1.413 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: 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: symmetry clash REVERT: A 307 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8420 (p0) REVERT: A 331 GLU cc_start: 0.9755 (pt0) cc_final: 0.9502 (pp20) REVERT: A 335 ARG cc_start: 0.9317 (mtm110) cc_final: 0.9025 (mtm-85) REVERT: A 358 ARG cc_start: 0.9557 (ptt90) cc_final: 0.9252 (ptm-80) REVERT: A 401 ASP cc_start: 0.9553 (t0) cc_final: 0.9166 (t0) REVERT: A 587 ARG cc_start: 0.9267 (mmm-85) cc_final: 0.8874 (mmt90) REVERT: A 597 MET cc_start: 0.9125 (ptp) cc_final: 0.8842 (pmm) REVERT: A 678 ILE cc_start: 0.9624 (pt) cc_final: 0.9330 (mp) REVERT: A 691 MET cc_start: 0.9115 (mtm) cc_final: 0.8886 (ttm) REVERT: A 701 MET cc_start: 0.8886 (ptt) cc_final: 0.8675 (ptt) REVERT: B 139 LEU cc_start: 0.9445 (mt) cc_final: 0.9010 (mt) REVERT: B 160 MET cc_start: 0.5674 (tpt) cc_final: 0.5382 (tmm) REVERT: B 356 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8672 (mmtm) REVERT: B 379 MET cc_start: 0.9555 (mmm) cc_final: 0.8958 (ttm) REVERT: B 414 VAL cc_start: 0.9555 (t) cc_final: 0.9315 (m) REVERT: B 441 MET cc_start: 0.9192 (pmm) cc_final: 0.8414 (pmm) REVERT: B 519 ASP cc_start: 0.9356 (m-30) cc_final: 0.8740 (p0) REVERT: B 607 ASP cc_start: 0.9522 (t0) cc_final: 0.9301 (t0) REVERT: B 646 MET cc_start: 0.9252 (tpp) cc_final: 0.8917 (tpp) REVERT: C 19 MET cc_start: 0.6912 (mtp) cc_final: 0.4522 (tpt) REVERT: C 157 TYR cc_start: 0.9646 (m-80) cc_final: 0.9371 (m-10) REVERT: C 160 MET cc_start: 0.8042 (tpt) cc_final: 0.6972 (tpt) REVERT: C 248 PHE cc_start: 0.9420 (m-80) cc_final: 0.9143 (m-80) REVERT: C 321 GLU cc_start: 0.9351 (tm-30) cc_final: 0.9106 (tm-30) REVERT: C 322 ASN cc_start: 0.9362 (m110) cc_final: 0.8972 (m-40) REVERT: C 529 MET cc_start: 0.9128 (mpp) cc_final: 0.8445 (ppp) REVERT: C 589 ILE cc_start: 0.9477 (mm) cc_final: 0.8904 (mm) REVERT: C 597 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8028 (ptp) REVERT: C 624 ASP cc_start: 0.9510 (t70) cc_final: 0.8650 (p0) REVERT: C 638 ARG cc_start: 0.8957 (mtt180) cc_final: 0.8568 (mtt180) REVERT: C 646 MET cc_start: 0.9352 (tmm) cc_final: 0.8963 (tmm) REVERT: C 647 LEU cc_start: 0.9890 (mt) cc_final: 0.9494 (mt) REVERT: C 648 LYS cc_start: 0.9824 (ttpt) cc_final: 0.9521 (ttpp) REVERT: D 19 MET cc_start: 0.8515 (mmm) cc_final: 0.7891 (ttp) REVERT: D 160 MET cc_start: -0.1040 (mmp) cc_final: -0.1264 (mmp) REVERT: D 321 GLU cc_start: 0.9276 (tm-30) cc_final: 0.9042 (tm-30) REVERT: D 393 MET cc_start: 0.9458 (pmm) cc_final: 0.9020 (pmm) REVERT: D 597 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8981 (ptm) REVERT: D 631 ASP cc_start: 0.9482 (OUTLIER) cc_final: 0.8972 (t0) REVERT: D 648 LYS cc_start: 0.9622 (tppt) cc_final: 0.9314 (tppt) REVERT: E 355 PHE cc_start: 0.9368 (m-10) cc_final: 0.9069 (m-10) REVERT: E 379 MET cc_start: 0.9469 (ttt) cc_final: 0.9099 (tpp) REVERT: E 393 MET cc_start: 0.8320 (ttt) cc_final: 0.7995 (mmm) REVERT: E 440 MET cc_start: 0.9387 (mmm) cc_final: 0.8823 (pmm) REVERT: E 661 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9066 (mm) REVERT: E 678 ILE cc_start: 0.9808 (pt) cc_final: 0.9519 (mm) REVERT: F 379 MET cc_start: 0.8105 (tmm) cc_final: 0.7702 (ppp) REVERT: F 518 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8581 (pm20) REVERT: F 520 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8629 (mm) REVERT: F 529 MET cc_start: 0.9015 (mmt) cc_final: 0.8345 (tpt) REVERT: F 607 ASP cc_start: 0.9104 (t0) cc_final: 0.8782 (t0) REVERT: F 646 MET cc_start: 0.9454 (tpp) cc_final: 0.9142 (tpp) REVERT: F 648 LYS cc_start: 0.9650 (tptt) cc_final: 0.9328 (tppt) REVERT: G 1 MET cc_start: 0.7586 (ttt) cc_final: 0.6861 (tmm) REVERT: G 189 MET cc_start: 0.0364 (mtt) cc_final: -0.0843 (ttp) REVERT: H 1 MET cc_start: 0.0912 (mmt) cc_final: -0.1183 (ttt) REVERT: I 1 MET cc_start: 0.4844 (ptm) cc_final: 0.4557 (ttp) REVERT: I 152 GLN cc_start: 0.5549 (tp40) cc_final: 0.5038 (pm20) REVERT: I 201 TYR cc_start: 0.4605 (OUTLIER) cc_final: 0.4156 (t80) REVERT: I 285 GLN cc_start: 0.8754 (tp40) cc_final: 0.8523 (mm-40) REVERT: K 172 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9159 (mt) REVERT: K 177 LEU cc_start: 0.9271 (pp) cc_final: 0.9011 (tt) REVERT: K 196 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.5465 (ptt90) outliers start: 59 outliers final: 39 residues processed: 465 average time/residue: 0.2219 time to fit residues: 170.6600 Evaluate side-chains 445 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 397 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 705 ASN Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 597 MET Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 631 ASP Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 548 GLN Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 679 LEU Chi-restraints excluded: chain E residue 733 THR Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 633 VAL Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 201 TYR Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 196 ARG Chi-restraints excluded: chain K residue 205 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 207 optimal weight: 40.0000 chunk 387 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 204 optimal weight: 50.0000 chunk 108 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 430 optimal weight: 10.0000 chunk 239 optimal weight: 0.5980 chunk 85 optimal weight: 20.0000 chunk 271 optimal weight: 6.9990 overall best weight: 3.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.096195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.064795 restraints weight = 380067.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066220 restraints weight = 208525.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066220 restraints weight = 139325.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066220 restraints weight = 139325.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066220 restraints weight = 139325.632| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 39134 Z= 0.145 Angle : 0.708 16.259 52815 Z= 0.351 Chirality : 0.041 0.203 5976 Planarity : 0.004 0.065 6856 Dihedral : 7.806 95.140 5550 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.23 % Favored : 95.75 % Rotamer: Outliers : 1.35 % Allowed : 18.12 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 are not related in a simple way. whole: 1.30 (0.12), residues: 4851 helix: 1.87 (0.10), residues: 2675 sheet: 0.35 (0.20), residues: 564 loop : -0.65 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 335 TYR 0.021 0.001 TYR F 605 PHE 0.019 0.001 PHE F 348 TRP 0.012 0.001 TRP E 632 HIS 0.004 0.001 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00315 (39134) covalent geometry : angle 0.70787 (52815) hydrogen bonds : bond 0.03468 ( 2085) hydrogen bonds : angle 4.22759 ( 6065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 395 time to evaluate : 1.481 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: 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 307 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8455 (p0) REVERT: A 331 GLU cc_start: 0.9764 (pt0) cc_final: 0.9537 (pp20) REVERT: A 358 ARG cc_start: 0.9568 (ptt90) cc_final: 0.9282 (ptm-80) REVERT: A 401 ASP cc_start: 0.9524 (t0) cc_final: 0.9136 (t0) REVERT: A 587 ARG cc_start: 0.9313 (mmm-85) cc_final: 0.8903 (mmt90) REVERT: A 597 MET cc_start: 0.9124 (ptp) cc_final: 0.8811 (pmm) REVERT: A 678 ILE cc_start: 0.9623 (pt) cc_final: 0.9128 (mm) REVERT: A 691 MET cc_start: 0.9027 (mtm) cc_final: 0.8788 (ttm) REVERT: B 139 LEU cc_start: 0.9501 (mt) cc_final: 0.9068 (mt) REVERT: B 160 MET cc_start: 0.6097 (tpt) cc_final: 0.5615 (tmm) REVERT: B 414 VAL cc_start: 0.9520 (t) cc_final: 0.9288 (m) REVERT: B 519 ASP cc_start: 0.9325 (m-30) cc_final: 0.8734 (p0) REVERT: B 646 MET cc_start: 0.9120 (tpp) cc_final: 0.8854 (tpp) REVERT: C 19 MET cc_start: 0.7695 (mtp) cc_final: 0.6092 (tpt) REVERT: C 157 TYR cc_start: 0.9666 (m-80) cc_final: 0.9408 (m-10) REVERT: C 160 MET cc_start: 0.8093 (tpt) cc_final: 0.7022 (tpt) REVERT: C 248 PHE cc_start: 0.9417 (m-80) cc_final: 0.9151 (m-80) REVERT: C 322 ASN cc_start: 0.9427 (m110) cc_final: 0.9073 (m110) REVERT: C 357 GLN cc_start: 0.9600 (tp40) cc_final: 0.9308 (mm110) REVERT: C 529 MET cc_start: 0.9111 (mpp) cc_final: 0.8438 (ppp) REVERT: C 589 ILE cc_start: 0.9569 (mm) cc_final: 0.8975 (mm) REVERT: C 597 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8236 (ptp) REVERT: C 624 ASP cc_start: 0.9448 (t70) cc_final: 0.8687 (p0) REVERT: C 638 ARG cc_start: 0.8784 (mtt180) cc_final: 0.8437 (mtt180) REVERT: C 646 MET cc_start: 0.9297 (tmm) cc_final: 0.8915 (tmm) REVERT: C 647 LEU cc_start: 0.9888 (mt) cc_final: 0.9520 (mt) REVERT: C 648 LYS cc_start: 0.9810 (ttpt) cc_final: 0.9517 (ttpp) REVERT: D 19 MET cc_start: 0.8628 (mmm) cc_final: 0.8149 (ttm) REVERT: D 160 MET cc_start: -0.0251 (mmp) cc_final: -0.0518 (mmp) REVERT: D 321 GLU cc_start: 0.9237 (tm-30) cc_final: 0.9005 (tm-30) REVERT: D 393 MET cc_start: 0.9478 (pmm) cc_final: 0.9057 (pmm) REVERT: D 631 ASP cc_start: 0.9419 (OUTLIER) cc_final: 0.8951 (t0) REVERT: D 648 LYS cc_start: 0.9629 (tppt) cc_final: 0.9368 (tppt) REVERT: E 355 PHE cc_start: 0.9387 (m-10) cc_final: 0.9040 (m-10) REVERT: E 393 MET cc_start: 0.8436 (ttt) cc_final: 0.8017 (mmm) REVERT: E 661 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9066 (mm) REVERT: E 678 ILE cc_start: 0.9808 (pt) cc_final: 0.9541 (mm) REVERT: F 379 MET cc_start: 0.8219 (tmm) cc_final: 0.7800 (ppp) REVERT: F 518 GLU cc_start: 0.9451 (tm-30) cc_final: 0.8937 (pm20) REVERT: F 520 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8880 (mm) REVERT: F 529 MET cc_start: 0.8935 (mmt) cc_final: 0.8340 (tpt) REVERT: F 605 TYR cc_start: 0.9467 (t80) cc_final: 0.9170 (t80) REVERT: F 607 ASP cc_start: 0.9180 (t0) cc_final: 0.8886 (t0) REVERT: F 646 MET cc_start: 0.9337 (tpp) cc_final: 0.9081 (tpp) REVERT: F 648 LYS cc_start: 0.9606 (tptt) cc_final: 0.9319 (tppt) REVERT: G 1 MET cc_start: 0.7679 (ttt) cc_final: 0.7045 (tmm) REVERT: G 189 MET cc_start: 0.0737 (mtt) cc_final: -0.0374 (ttp) REVERT: H 1 MET cc_start: 0.1513 (mmt) cc_final: -0.0510 (ttt) REVERT: I 1 MET cc_start: 0.5312 (ptm) cc_final: 0.4937 (ttp) REVERT: I 152 GLN cc_start: 0.5775 (tp40) cc_final: 0.5316 (pm20) REVERT: I 201 TYR cc_start: 0.4813 (OUTLIER) cc_final: 0.4476 (t80) REVERT: I 285 GLN cc_start: 0.8822 (tp40) cc_final: 0.8594 (mm-40) REVERT: K 172 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9170 (mt) REVERT: K 177 LEU cc_start: 0.9195 (pp) cc_final: 0.8963 (tt) REVERT: K 196 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5328 (ptt90) REVERT: K 217 MET cc_start: -0.7957 (tpp) cc_final: -0.8268 (tpt) outliers start: 56 outliers final: 44 residues processed: 435 average time/residue: 0.2438 time to fit residues: 175.7577 Evaluate side-chains 440 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 388 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 631 ASP Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 679 LEU Chi-restraints excluded: chain E residue 733 THR Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 633 VAL Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 201 TYR Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 196 ARG Chi-restraints excluded: chain K residue 205 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 191 optimal weight: 0.7980 chunk 246 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 479 optimal weight: 50.0000 chunk 481 optimal weight: 50.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 690 ASN D 374 GLN ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 485 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 = 0.3926 r_free = 0.3926 target = 0.094799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.061582 restraints weight = 432826.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.063196 restraints weight = 227359.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.063963 restraints weight = 145061.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063656 restraints weight = 116061.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063656 restraints weight = 110331.382| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 39134 Z= 0.194 Angle : 0.734 16.044 52815 Z= 0.370 Chirality : 0.042 0.223 5976 Planarity : 0.004 0.063 6856 Dihedral : 8.004 93.485 5550 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.72 % Favored : 95.25 % Rotamer: Outliers : 1.54 % Allowed : 18.09 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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 are not related in a simple way. whole: 1.10 (0.12), residues: 4851 helix: 1.69 (0.10), residues: 2683 sheet: 0.16 (0.20), residues: 570 loop : -0.67 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 335 TYR 0.020 0.001 TYR F 605 PHE 0.018 0.002 PHE F 348 TRP 0.013 0.001 TRP C 632 HIS 0.005 0.001 HIS E 563 Details of bonding type rmsd covalent geometry : bond 0.00412 (39134) covalent geometry : angle 0.73425 (52815) hydrogen bonds : bond 0.03631 ( 2085) hydrogen bonds : angle 4.43707 ( 6065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11980.31 seconds wall clock time: 205 minutes 26.84 seconds (12326.84 seconds total)