Starting phenix.real_space_refine on Sat Aug 8 07:03:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uoe_64377/08_2026/9uoe_64377.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uoe_64377/08_2026/9uoe_64377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uoe_64377/08_2026/9uoe_64377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uoe_64377/08_2026/9uoe_64377.map" model { file = "/net/cci-nas-00/data/ceres_data/9uoe_64377/08_2026/9uoe_64377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uoe_64377/08_2026/9uoe_64377.cif" } resolution = 2.63 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 92 5.16 5 C 16408 2.51 5 N 4488 2.21 5 O 4888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25880 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6465 Classifications: {'peptide': 799} Link IDs: {'PTRANS': 26, 'TRANS': 772} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6465 Classifications: {'peptide': 799} Link IDs: {'PTRANS': 26, 'TRANS': 772} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 6465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6465 Classifications: {'peptide': 799} Link IDs: {'PTRANS': 26, 'TRANS': 772} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6465 Classifications: {'peptide': 799} Link IDs: {'PTRANS': 26, 'TRANS': 772} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.39, per 1000 atoms: 0.21 Number of scatterers: 25880 At special positions: 0 Unit cell: (150.23, 155.21, 112.05, 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 92 16.00 P 4 15.00 O 4888 8.00 N 4488 7.00 C 16408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6008 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 20 sheets defined 58.3% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 37 through 67 removed outlier: 3.559A pdb=" N ARG A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 108 through 114 removed outlier: 3.714A pdb=" N ASP A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 removed outlier: 3.790A pdb=" N GLY A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 251 through 257 removed outlier: 4.000A pdb=" N GLU A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.892A pdb=" N VAL A 265 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A 266 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 306 removed outlier: 3.511A pdb=" N SER A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 322 through 325 removed outlier: 3.576A pdb=" N VAL A 325 " --> pdb=" O THR A 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 325' Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.661A pdb=" N GLN A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.636A pdb=" N LEU A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 378 Processing helix chain 'A' and resid 378 through 400 Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 423 through 430 Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 450 through 457 Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.664A pdb=" N TRP A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 490 Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 509 through 536 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 557 through 575 removed outlier: 3.878A pdb=" N ASN A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 614 removed outlier: 3.772A pdb=" N ASN A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 657 through 666 removed outlier: 4.383A pdb=" N MET A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LLP A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 686 Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 709 through 715 removed outlier: 3.947A pdb=" N TYR A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 730 Processing helix chain 'A' and resid 740 through 749 Processing helix chain 'A' and resid 755 through 775 removed outlier: 4.660A pdb=" N ARG A 761 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER A 762 " --> pdb=" O ALA A 758 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 775 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 790 removed outlier: 3.623A pdb=" N ASN A 790 " --> pdb=" O LEU A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 807 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 37 through 66 removed outlier: 3.634A pdb=" N ASN B 43 " --> pdb=" O HIS B 39 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 124 through 141 removed outlier: 3.578A pdb=" N ARG B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 251 through 257 removed outlier: 3.959A pdb=" N GLU B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 267 removed outlier: 3.854A pdb=" N VAL B 265 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER B 266 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 306 removed outlier: 3.586A pdb=" N LEU B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 325 removed outlier: 3.868A pdb=" N VAL B 325 " --> pdb=" O THR B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 322 through 325' Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.737A pdb=" N MET B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 371 through 378 Processing helix chain 'B' and resid 378 through 400 Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.817A pdb=" N ARG B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 419' Processing helix chain 'B' and resid 423 through 430 Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 450 through 457 Processing helix chain 'B' and resid 469 through 474 removed outlier: 3.547A pdb=" N TRP B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.510A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 509 through 535 removed outlier: 3.635A pdb=" N ASN B 513 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 Processing helix chain 'B' and resid 557 through 575 removed outlier: 3.871A pdb=" N ASN B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 614 removed outlier: 3.778A pdb=" N ASN B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 657 through 665 removed outlier: 4.031A pdb=" N MET B 661 " --> pdb=" O GLY B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 686 removed outlier: 4.425A pdb=" N GLU B 680 " --> pdb=" O GLY B 676 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP B 683 " --> pdb=" O VAL B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 Processing helix chain 'B' and resid 709 through 715 removed outlier: 4.007A pdb=" N TYR B 713 " --> pdb=" O LYS B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 730 Processing helix chain 'B' and resid 740 through 749 removed outlier: 3.515A pdb=" N LEU B 747 " --> pdb=" O LEU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 775 Processing helix chain 'B' and resid 776 through 790 Processing helix chain 'B' and resid 791 through 794 Processing helix chain 'B' and resid 795 through 807 removed outlier: 3.523A pdb=" N THR B 799 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 27 Processing helix chain 'C' and resid 37 through 67 removed outlier: 3.559A pdb=" N ARG C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 108 through 114 removed outlier: 3.714A pdb=" N ASP C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 140 removed outlier: 3.791A pdb=" N GLY C 127 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 251 through 257 removed outlier: 4.000A pdb=" N GLU C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 267 removed outlier: 3.892A pdb=" N VAL C 265 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER C 266 " --> pdb=" O GLU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 306 removed outlier: 3.511A pdb=" N SER C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 314 Processing helix chain 'C' and resid 322 through 325 removed outlier: 3.577A pdb=" N VAL C 325 " --> pdb=" O THR C 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 322 through 325' Processing helix chain 'C' and resid 326 through 340 removed outlier: 3.662A pdb=" N GLN C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.636A pdb=" N LEU C 366 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 378 Processing helix chain 'C' and resid 378 through 400 Processing helix chain 'C' and resid 405 through 411 Processing helix chain 'C' and resid 423 through 430 Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'C' and resid 450 through 457 Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.664A pdb=" N TRP C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 490 Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 509 through 536 Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 557 through 575 removed outlier: 3.879A pdb=" N ASN C 561 " --> pdb=" O ARG C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 614 removed outlier: 3.773A pdb=" N ASN C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 639 Processing helix chain 'C' and resid 640 through 642 No H-bonds generated for 'chain 'C' and resid 640 through 642' Processing helix chain 'C' and resid 657 through 666 removed outlier: 4.383A pdb=" N MET C 661 " --> pdb=" O GLY C 657 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LLP C 662 " --> pdb=" O THR C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 686 Processing helix chain 'C' and resid 696 through 707 Processing helix chain 'C' and resid 709 through 715 removed outlier: 3.947A pdb=" N TYR C 713 " --> pdb=" O LYS C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 730 Processing helix chain 'C' and resid 740 through 749 Processing helix chain 'C' and resid 755 through 775 removed outlier: 4.660A pdb=" N ARG C 761 " --> pdb=" O LEU C 757 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER C 762 " --> pdb=" O ALA C 758 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C 775 " --> pdb=" O ASP C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 790 removed outlier: 3.624A pdb=" N ASN C 790 " --> pdb=" O LEU C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 807 Processing helix chain 'D' and resid 16 through 27 Processing helix chain 'D' and resid 37 through 66 removed outlier: 3.635A pdb=" N ASN D 43 " --> pdb=" O HIS D 39 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 108 through 116 Processing helix chain 'D' and resid 124 through 141 removed outlier: 3.578A pdb=" N ARG D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 246 Processing helix chain 'D' and resid 251 through 257 removed outlier: 3.958A pdb=" N GLU D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 267 removed outlier: 3.854A pdb=" N VAL D 265 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER D 266 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 306 removed outlier: 3.586A pdb=" N LEU D 289 " --> pdb=" O GLN D 285 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 325 removed outlier: 3.867A pdb=" N VAL D 325 " --> pdb=" O THR D 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 322 through 325' Processing helix chain 'D' and resid 326 through 340 removed outlier: 3.736A pdb=" N MET D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 371 through 378 Processing helix chain 'D' and resid 378 through 400 Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 415 through 419 removed outlier: 3.817A pdb=" N ARG D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 419' Processing helix chain 'D' and resid 423 through 430 Processing helix chain 'D' and resid 438 through 448 Processing helix chain 'D' and resid 450 through 457 Processing helix chain 'D' and resid 469 through 474 removed outlier: 3.548A pdb=" N TRP D 473 " --> pdb=" O THR D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 490 removed outlier: 3.510A pdb=" N VAL D 484 " --> pdb=" O SER D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 509 through 535 removed outlier: 3.636A pdb=" N ASN D 513 " --> pdb=" O PHE D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 556 Processing helix chain 'D' and resid 557 through 575 removed outlier: 3.871A pdb=" N ASN D 561 " --> pdb=" O ARG D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 614 removed outlier: 3.777A pdb=" N ASN D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 639 Processing helix chain 'D' and resid 640 through 642 No H-bonds generated for 'chain 'D' and resid 640 through 642' Processing helix chain 'D' and resid 657 through 665 removed outlier: 4.030A pdb=" N MET D 661 " --> pdb=" O GLY D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 686 removed outlier: 4.425A pdb=" N GLU D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP D 683 " --> pdb=" O VAL D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 706 Processing helix chain 'D' and resid 709 through 715 removed outlier: 4.006A pdb=" N TYR D 713 " --> pdb=" O LYS D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 730 Processing helix chain 'D' and resid 740 through 749 removed outlier: 3.515A pdb=" N LEU D 747 " --> pdb=" O LEU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 775 Processing helix chain 'D' and resid 776 through 790 Processing helix chain 'D' and resid 791 through 794 Processing helix chain 'D' and resid 795 through 807 removed outlier: 3.522A pdb=" N THR D 799 " --> pdb=" O SER D 795 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 180 through 192 removed outlier: 14.690A pdb=" N GLU A 180 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 12.706A pdb=" N LYS A 182 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 12.148A pdb=" N ILE A 219 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N HIS A 184 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 11.452A pdb=" N ASP A 217 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR A 186 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLY A 144 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ARG A 232 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY A 146 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N TRP A 234 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLY A 148 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ALA A 236 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 72 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N TYR A 147 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR A 74 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ILE A 149 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N SER A 355 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 317 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR A 357 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 319 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS A 433 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 434 " --> pdb=" O THR A 462 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 157 through 161 Processing sheet with id=3, first strand: chain 'A' and resid 195 through 198 Processing sheet with id=4, first strand: chain 'A' and resid 368 through 370 Processing sheet with id=5, first strand: chain 'A' and resid 622 through 627 removed outlier: 6.238A pdb=" N LEU A 544 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 586 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP A 546 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY A 588 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN A 548 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A 545 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLU A 646 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 547 " --> pdb=" O GLU A 646 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER A 645 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR A 670 " --> pdb=" O PHE A 691 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 181 through 192 removed outlier: 12.771A pdb=" N LYS B 182 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 12.367A pdb=" N ILE B 219 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N HIS B 184 " --> pdb=" O ASP B 217 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N ASP B 217 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR B 186 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLY B 144 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ARG B 232 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLY B 146 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TRP B 234 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY B 148 " --> pdb=" O TRP B 234 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ALA B 236 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 72 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N TYR B 147 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR B 74 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N ILE B 149 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS B 433 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 434 " --> pdb=" O THR B 462 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 157 through 161 Processing sheet with id=8, first strand: chain 'B' and resid 195 through 198 Processing sheet with id=9, first strand: chain 'B' and resid 368 through 370 Processing sheet with id=10, first strand: chain 'B' and resid 622 through 627 removed outlier: 3.970A pdb=" N GLY B 588 " --> pdb=" O GLN B 548 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 549 " --> pdb=" O GLU B 646 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER B 645 " --> pdb=" O ILE B 671 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 180 through 192 removed outlier: 14.689A pdb=" N GLU C 180 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 12.706A pdb=" N LYS C 182 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 12.148A pdb=" N ILE C 219 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N HIS C 184 " --> pdb=" O ASP C 217 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N ASP C 217 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR C 186 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY C 144 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ARG C 232 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY C 146 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N TRP C 234 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLY C 148 " --> pdb=" O TRP C 234 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ALA C 236 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 72 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N TYR C 147 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR C 74 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N ILE C 149 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER C 355 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE C 317 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N THR C 357 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU C 319 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS C 433 " --> pdb=" O PHE C 354 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 434 " --> pdb=" O THR C 462 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 157 through 161 Processing sheet with id=13, first strand: chain 'C' and resid 195 through 198 Processing sheet with id=14, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=15, first strand: chain 'C' and resid 622 through 627 removed outlier: 6.238A pdb=" N LEU C 544 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE C 586 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP C 546 " --> pdb=" O ILE C 586 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY C 588 " --> pdb=" O ASP C 546 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN C 548 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE C 545 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLU C 646 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL C 547 " --> pdb=" O GLU C 646 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER C 645 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR C 670 " --> pdb=" O PHE C 691 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 181 through 192 removed outlier: 12.772A pdb=" N LYS D 182 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 12.366A pdb=" N ILE D 219 " --> pdb=" O LYS D 182 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N HIS D 184 " --> pdb=" O ASP D 217 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N ASP D 217 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR D 186 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLY D 144 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ARG D 232 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLY D 146 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TRP D 234 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY D 148 " --> pdb=" O TRP D 234 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ALA D 236 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL D 72 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N TYR D 147 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR D 74 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N ILE D 149 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS D 433 " --> pdb=" O PHE D 354 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL D 434 " --> pdb=" O THR D 462 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 157 through 161 Processing sheet with id=18, first strand: chain 'D' and resid 195 through 198 Processing sheet with id=19, first strand: chain 'D' and resid 368 through 370 Processing sheet with id=20, first strand: chain 'D' and resid 622 through 627 removed outlier: 3.971A pdb=" N GLY D 588 " --> pdb=" O GLN D 548 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE D 549 " --> pdb=" O GLU D 646 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER D 645 " --> pdb=" O ILE D 671 " (cutoff:3.500A) 1358 hydrogen bonds defined for protein. 3852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.43 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4810 1.32 - 1.45: 6833 1.45 - 1.57: 14633 1.57 - 1.69: 4 1.69 - 1.81: 164 Bond restraints: 26444 Sorted by residual: bond pdb=" OP4 LLP C 662 " pdb=" P LLP C 662 " ideal model delta sigma weight residual 1.726 1.603 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" OP4 LLP A 662 " pdb=" P LLP A 662 " ideal model delta sigma weight residual 1.726 1.604 0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" OP4 LLP B 662 " pdb=" P LLP B 662 " ideal model delta sigma weight residual 1.726 1.605 0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" OP4 LLP D 662 " pdb=" P LLP D 662 " ideal model delta sigma weight residual 1.726 1.605 0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" CA SER B 659 " pdb=" CB SER B 659 " ideal model delta sigma weight residual 1.528 1.472 0.057 1.66e-02 3.63e+03 1.17e+01 ... (remaining 26439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 35155 1.71 - 3.42: 609 3.42 - 5.12: 78 5.12 - 6.83: 24 6.83 - 8.54: 2 Bond angle restraints: 35868 Sorted by residual: angle pdb=" CA PHE C 663 " pdb=" CB PHE C 663 " pdb=" CG PHE C 663 " ideal model delta sigma weight residual 113.80 118.41 -4.61 1.00e+00 1.00e+00 2.12e+01 angle pdb=" CA PHE A 663 " pdb=" CB PHE A 663 " pdb=" CG PHE A 663 " ideal model delta sigma weight residual 113.80 118.40 -4.60 1.00e+00 1.00e+00 2.12e+01 angle pdb=" N SER D 659 " pdb=" CA SER D 659 " pdb=" C SER D 659 " ideal model delta sigma weight residual 111.82 106.57 5.25 1.16e+00 7.43e-01 2.05e+01 angle pdb=" N SER B 659 " pdb=" CA SER B 659 " pdb=" C SER B 659 " ideal model delta sigma weight residual 111.82 106.60 5.22 1.16e+00 7.43e-01 2.03e+01 angle pdb=" N ASN D 660 " pdb=" CA ASN D 660 " pdb=" C ASN D 660 " ideal model delta sigma weight residual 111.07 106.66 4.41 1.07e+00 8.73e-01 1.70e+01 ... (remaining 35863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 13692 18.10 - 36.19: 1468 36.19 - 54.29: 442 54.29 - 72.38: 108 72.38 - 90.48: 30 Dihedral angle restraints: 15740 sinusoidal: 6392 harmonic: 9348 Sorted by residual: dihedral pdb=" CA ASP D 309 " pdb=" CB ASP D 309 " pdb=" CG ASP D 309 " pdb=" OD1 ASP D 309 " ideal model delta sinusoidal sigma weight residual -30.00 -88.51 58.51 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP B 309 " pdb=" CB ASP B 309 " pdb=" CG ASP B 309 " pdb=" OD1 ASP B 309 " ideal model delta sinusoidal sigma weight residual -30.00 -88.44 58.44 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU A 280 " pdb=" CG GLU A 280 " pdb=" CD GLU A 280 " pdb=" OE1 GLU A 280 " ideal model delta sinusoidal sigma weight residual 0.00 -90.48 90.48 1 3.00e+01 1.11e-03 1.08e+01 ... (remaining 15737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2902 0.043 - 0.086: 783 0.086 - 0.129: 169 0.129 - 0.172: 28 0.172 - 0.215: 6 Chirality restraints: 3888 Sorted by residual: chirality pdb=" CA ILE D 671 " pdb=" N ILE D 671 " pdb=" C ILE D 671 " pdb=" CB ILE D 671 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE B 671 " pdb=" N ILE B 671 " pdb=" C ILE B 671 " pdb=" CB ILE B 671 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA THR B 658 " pdb=" N THR B 658 " pdb=" C THR B 658 " pdb=" CB THR B 658 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 3885 not shown) Planarity restraints: 4672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP C 662 " -0.027 2.00e-02 2.50e+03 2.81e-02 7.87e+00 pdb=" NZ LLP C 662 " 0.024 2.00e-02 2.50e+03 pdb=" C4 LLP C 662 " -0.029 2.00e-02 2.50e+03 pdb=" C4' LLP C 662 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 657 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.73e+00 pdb=" C GLY B 657 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY B 657 " 0.018 2.00e-02 2.50e+03 pdb=" N THR B 658 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP A 662 " 0.027 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" NZ LLP A 662 " -0.024 2.00e-02 2.50e+03 pdb=" C4 LLP A 662 " 0.028 2.00e-02 2.50e+03 pdb=" C4' LLP A 662 " -0.031 2.00e-02 2.50e+03 ... (remaining 4669 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 9350 2.89 - 3.39: 24585 3.39 - 3.89: 45891 3.89 - 4.40: 53968 4.40 - 4.90: 89514 Nonbonded interactions: 223308 Sorted by model distance: nonbonded pdb=" N ASN B 660 " pdb=" OD1 ASN B 660 " model vdw 2.386 3.120 nonbonded pdb=" N ASN D 660 " pdb=" OD1 ASN D 660 " model vdw 2.386 3.120 nonbonded pdb=" OD1 ASP C 403 " pdb=" N LEU C 406 " model vdw 2.435 3.120 nonbonded pdb=" OD1 ASP A 403 " pdb=" N LEU A 406 " model vdw 2.435 3.120 nonbonded pdb=" O ASN C 87 " pdb=" OG SER C 91 " model vdw 2.491 3.040 ... (remaining 223303 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 7.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.360 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 : 0.004 0.123 26444 Z= 0.209 Angle : 0.548 8.542 35868 Z= 0.329 Chirality : 0.041 0.215 3888 Planarity : 0.004 0.065 4672 Dihedral : 17.022 90.475 9732 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 2.67 % Allowed : 17.97 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3176 helix: 0.85 (0.13), residues: 1668 sheet: 0.49 (0.24), residues: 444 loop : -0.83 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.019 0.001 TYR C 188 PHE 0.019 0.001 PHE B 663 TRP 0.012 0.001 TRP B 473 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.21 (26444) covalent geometry : angle 0.54780 / 0.33 (35868) hydrogen bonds : bond 0.15051 / 9.97 ( 1358) hydrogen bonds : angle 6.56850 / 4.82 ( 3852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 312 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7711 (ttt) REVERT: A 171 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: A 187 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7801 (ptt180) REVERT: A 362 MET cc_start: 0.6472 (pmm) cc_final: 0.5783 (ttt) REVERT: A 376 LYS cc_start: 0.8473 (tttp) cc_final: 0.8223 (ttpm) REVERT: A 391 TYR cc_start: 0.8100 (t80) cc_final: 0.7807 (t80) REVERT: A 440 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8001 (pp) REVERT: A 501 ASN cc_start: 0.7605 (t0) cc_final: 0.7028 (m110) REVERT: A 529 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7471 (tp30) REVERT: A 680 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: A 683 ASP cc_start: 0.7869 (m-30) cc_final: 0.7588 (m-30) REVERT: A 801 LYS cc_start: 0.7926 (mttt) cc_final: 0.7528 (mtpt) REVERT: B 39 HIS cc_start: 0.6916 (m90) cc_final: 0.6456 (m-70) REVERT: B 52 ARG cc_start: 0.7583 (mtp85) cc_final: 0.7331 (mpt180) REVERT: B 57 TRP cc_start: 0.6891 (t60) cc_final: 0.6516 (t60) REVERT: B 202 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7142 (tptp) REVERT: B 257 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: B 259 LYS cc_start: 0.8786 (mttt) cc_final: 0.8206 (mppt) REVERT: B 280 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7846 (tt0) REVERT: B 348 GLU cc_start: 0.7779 (tt0) cc_final: 0.7460 (mm-30) REVERT: B 362 MET cc_start: 0.7969 (mmm) cc_final: 0.7394 (mpp) REVERT: B 363 SER cc_start: 0.8180 (t) cc_final: 0.7694 (p) REVERT: B 376 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8669 (tttt) REVERT: B 405 ASP cc_start: 0.6841 (m-30) cc_final: 0.6597 (t0) REVERT: B 455 LYS cc_start: 0.7673 (ptpp) cc_final: 0.7473 (ptpp) REVERT: B 699 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7404 (mt-10) REVERT: B 701 GLU cc_start: 0.7802 (tp30) cc_final: 0.7266 (tm-30) REVERT: B 745 ASP cc_start: 0.8447 (m-30) cc_final: 0.8105 (t0) REVERT: B 785 MET cc_start: 0.8339 (mtm) cc_final: 0.8000 (mtp) REVERT: C 171 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: C 187 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7800 (ptt180) REVERT: C 362 MET cc_start: 0.6471 (pmm) cc_final: 0.5782 (ttt) REVERT: C 376 LYS cc_start: 0.8471 (tttp) cc_final: 0.8221 (ttpm) REVERT: C 391 TYR cc_start: 0.8098 (t80) cc_final: 0.7805 (t80) REVERT: C 440 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.8001 (pp) REVERT: C 501 ASN cc_start: 0.7607 (t0) cc_final: 0.7028 (m110) REVERT: C 529 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7470 (tp30) REVERT: C 680 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: C 683 ASP cc_start: 0.7869 (m-30) cc_final: 0.7586 (m-30) REVERT: C 801 LYS cc_start: 0.7927 (mttt) cc_final: 0.7530 (mtpt) REVERT: D 39 HIS cc_start: 0.6916 (m90) cc_final: 0.6458 (m-70) REVERT: D 52 ARG cc_start: 0.7589 (mtp85) cc_final: 0.7339 (mpt180) REVERT: D 57 TRP cc_start: 0.6889 (t60) cc_final: 0.6511 (t60) REVERT: D 202 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7143 (tptp) REVERT: D 257 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: D 259 LYS cc_start: 0.8784 (mttt) cc_final: 0.8205 (mppt) REVERT: D 280 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7821 (tt0) REVERT: D 348 GLU cc_start: 0.7771 (tt0) cc_final: 0.7464 (mm-30) REVERT: D 362 MET cc_start: 0.7968 (mmm) cc_final: 0.7394 (mpp) REVERT: D 363 SER cc_start: 0.8179 (t) cc_final: 0.7695 (p) REVERT: D 405 ASP cc_start: 0.6841 (m-30) cc_final: 0.6597 (t0) REVERT: D 455 LYS cc_start: 0.7674 (ptpp) cc_final: 0.7474 (ptpp) REVERT: D 699 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7402 (mt-10) REVERT: D 701 GLU cc_start: 0.7802 (tp30) cc_final: 0.7267 (tm-30) REVERT: D 745 ASP cc_start: 0.8448 (m-30) cc_final: 0.8107 (t0) REVERT: D 785 MET cc_start: 0.8342 (mtm) cc_final: 0.8004 (mtp) outliers start: 74 outliers final: 39 residues processed: 361 average time/residue: 0.7038 time to fit residues: 292.8253 Evaluate side-chains 349 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 295 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 785 MET Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 597 MET Chi-restraints excluded: chain D residue 660 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 GLN A 536 ASN B 162 ASN B 248 ASN B 561 ASN C 198 GLN C 536 ASN D 162 ASN D 248 ASN D 561 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.155396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.134354 restraints weight = 30533.477| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.51 r_work: 0.3392 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26444 Z= 0.111 Angle : 0.468 5.867 35868 Z= 0.253 Chirality : 0.039 0.142 3888 Planarity : 0.003 0.045 4672 Dihedral : 7.440 81.611 3665 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 3.17 % Allowed : 18.00 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 3176 helix: 1.15 (0.13), residues: 1688 sheet: 0.05 (0.23), residues: 476 loop : -0.63 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.012 0.001 TYR D 400 PHE 0.013 0.001 PHE B 156 TRP 0.011 0.001 TRP B 473 HIS 0.004 0.001 HIS B 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (26444) covalent geometry : angle 0.46753 / 0.25 (35868) hydrogen bonds : bond 0.04330 / 2.86 ( 1358) hydrogen bonds : angle 4.89239 / 3.56 ( 3852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 303 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7760 (ttt) REVERT: A 171 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: A 241 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: A 338 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: A 376 LYS cc_start: 0.8470 (tttp) cc_final: 0.8233 (ttpm) REVERT: A 440 LEU cc_start: 0.8296 (pt) cc_final: 0.8045 (pp) REVERT: A 501 ASN cc_start: 0.7706 (t0) cc_final: 0.7157 (m-40) REVERT: A 529 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7549 (tp30) REVERT: A 680 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: A 698 GLU cc_start: 0.6932 (pp20) cc_final: 0.6681 (mp0) REVERT: A 801 LYS cc_start: 0.8027 (mttt) cc_final: 0.7643 (mtpt) REVERT: B 39 HIS cc_start: 0.6850 (m90) cc_final: 0.6581 (m90) REVERT: B 52 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7331 (mpt180) REVERT: B 57 TRP cc_start: 0.6896 (t60) cc_final: 0.6504 (t60) REVERT: B 259 LYS cc_start: 0.8739 (mttt) cc_final: 0.8171 (mppt) REVERT: B 280 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7902 (tt0) REVERT: B 348 GLU cc_start: 0.7748 (tt0) cc_final: 0.7460 (mm-30) REVERT: B 362 MET cc_start: 0.7815 (mmm) cc_final: 0.7406 (mpp) REVERT: B 376 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8631 (tttt) REVERT: B 405 ASP cc_start: 0.6881 (m-30) cc_final: 0.6624 (t0) REVERT: B 529 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: B 701 GLU cc_start: 0.7795 (tp30) cc_final: 0.7246 (tm-30) REVERT: B 785 MET cc_start: 0.8316 (mtm) cc_final: 0.7992 (mtp) REVERT: C 26 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7643 (ttt) REVERT: C 171 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7424 (m-80) REVERT: C 338 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7353 (mt-10) REVERT: C 376 LYS cc_start: 0.8460 (tttp) cc_final: 0.8225 (ttpm) REVERT: C 440 LEU cc_start: 0.8283 (pt) cc_final: 0.8031 (pp) REVERT: C 501 ASN cc_start: 0.7723 (t0) cc_final: 0.7179 (m-40) REVERT: C 680 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: C 698 GLU cc_start: 0.6939 (pp20) cc_final: 0.6670 (mp0) REVERT: C 801 LYS cc_start: 0.8009 (mttt) cc_final: 0.7626 (mtpt) REVERT: D 39 HIS cc_start: 0.6851 (m90) cc_final: 0.6578 (m90) REVERT: D 57 TRP cc_start: 0.6894 (t60) cc_final: 0.6500 (t60) REVERT: D 259 LYS cc_start: 0.8755 (mttt) cc_final: 0.8176 (mppt) REVERT: D 280 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7879 (tt0) REVERT: D 348 GLU cc_start: 0.7753 (tt0) cc_final: 0.7457 (mm-30) REVERT: D 362 MET cc_start: 0.7870 (mmm) cc_final: 0.7450 (mpp) REVERT: D 405 ASP cc_start: 0.6862 (m-30) cc_final: 0.6624 (t0) REVERT: D 529 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7882 (tp30) REVERT: D 701 GLU cc_start: 0.7768 (tp30) cc_final: 0.7230 (tm-30) REVERT: D 785 MET cc_start: 0.8310 (mtm) cc_final: 0.7984 (mtp) outliers start: 88 outliers final: 33 residues processed: 364 average time/residue: 0.5869 time to fit residues: 248.1138 Evaluate side-chains 331 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 286 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 529 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 143 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 292 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN B 162 ASN B 248 ASN B 323 HIS B 561 ASN C 229 ASN C 536 ASN D 162 ASN D 248 ASN D 323 HIS D 561 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127646 restraints weight = 30649.568| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.50 r_work: 0.3306 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 26444 Z= 0.269 Angle : 0.626 6.185 35868 Z= 0.339 Chirality : 0.047 0.171 3888 Planarity : 0.005 0.059 4672 Dihedral : 7.034 82.890 3592 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 5.19 % Allowed : 17.21 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 3176 helix: 0.58 (0.12), residues: 1688 sheet: 0.13 (0.23), residues: 468 loop : -0.73 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 70 TYR 0.019 0.003 TYR C 302 PHE 0.022 0.003 PHE D 156 TRP 0.018 0.002 TRP D 473 HIS 0.005 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.27 (26444) covalent geometry : angle 0.62581 / 0.34 (35868) hydrogen bonds : bond 0.05978 / 3.93 ( 1358) hydrogen bonds : angle 5.09871 / 3.72 ( 3852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 297 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7929 (ttm) REVERT: A 52 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6615 (mmt90) REVERT: A 171 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: A 241 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: A 338 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: A 376 LYS cc_start: 0.8535 (tttp) cc_final: 0.8302 (ttpm) REVERT: A 391 TYR cc_start: 0.8248 (t80) cc_final: 0.7988 (t80) REVERT: A 432 HIS cc_start: 0.7446 (t70) cc_final: 0.6287 (p90) REVERT: A 440 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8104 (pp) REVERT: A 529 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7526 (tp30) REVERT: A 620 ASP cc_start: 0.7779 (m-30) cc_final: 0.7569 (m-30) REVERT: A 683 ASP cc_start: 0.7761 (m-30) cc_final: 0.7472 (m-30) REVERT: A 698 GLU cc_start: 0.6920 (pp20) cc_final: 0.6638 (mp0) REVERT: A 801 LYS cc_start: 0.8026 (mttt) cc_final: 0.7660 (mtpt) REVERT: B 39 HIS cc_start: 0.7148 (m90) cc_final: 0.6831 (m90) REVERT: B 57 TRP cc_start: 0.6981 (t60) cc_final: 0.6534 (t60) REVERT: B 110 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6911 (mm-30) REVERT: B 134 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7807 (mp) REVERT: B 171 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: B 259 LYS cc_start: 0.8718 (mttt) cc_final: 0.8201 (mppt) REVERT: B 279 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7826 (mtp180) REVERT: B 280 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7972 (tt0) REVERT: B 348 GLU cc_start: 0.7897 (tt0) cc_final: 0.7570 (mm-30) REVERT: B 362 MET cc_start: 0.7794 (mmm) cc_final: 0.7329 (mpp) REVERT: B 376 LYS cc_start: 0.8951 (ttpp) cc_final: 0.8692 (tttt) REVERT: B 405 ASP cc_start: 0.6866 (m-30) cc_final: 0.6605 (t0) REVERT: B 514 HIS cc_start: 0.7226 (t-170) cc_final: 0.6834 (t70) REVERT: B 529 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: B 600 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.8251 (t-170) REVERT: B 617 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7696 (tp40) REVERT: B 701 GLU cc_start: 0.7940 (tp30) cc_final: 0.7350 (tm-30) REVERT: B 778 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7009 (mt-10) REVERT: B 807 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8340 (mp) REVERT: C 52 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.6603 (mmt90) REVERT: C 171 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: C 241 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: C 338 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: C 376 LYS cc_start: 0.8513 (tttp) cc_final: 0.8278 (ttpm) REVERT: C 391 TYR cc_start: 0.8242 (t80) cc_final: 0.7985 (t80) REVERT: C 432 HIS cc_start: 0.7434 (t70) cc_final: 0.6270 (p90) REVERT: C 440 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8113 (pp) REVERT: C 620 ASP cc_start: 0.7766 (m-30) cc_final: 0.7553 (m-30) REVERT: C 683 ASP cc_start: 0.7763 (m-30) cc_final: 0.7512 (m-30) REVERT: C 698 GLU cc_start: 0.6931 (pp20) cc_final: 0.6650 (mp0) REVERT: C 801 LYS cc_start: 0.8030 (mttt) cc_final: 0.7648 (mtpt) REVERT: D 39 HIS cc_start: 0.7128 (m90) cc_final: 0.6812 (m90) REVERT: D 57 TRP cc_start: 0.6987 (t60) cc_final: 0.6527 (t60) REVERT: D 110 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6911 (mm-30) REVERT: D 134 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7802 (mp) REVERT: D 171 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: D 259 LYS cc_start: 0.8730 (mttt) cc_final: 0.8185 (mppt) REVERT: D 280 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7979 (tt0) REVERT: D 348 GLU cc_start: 0.7895 (tt0) cc_final: 0.7586 (mm-30) REVERT: D 362 MET cc_start: 0.7837 (mmm) cc_final: 0.7381 (mpp) REVERT: D 405 ASP cc_start: 0.6850 (m-30) cc_final: 0.6610 (t0) REVERT: D 514 HIS cc_start: 0.7225 (t-170) cc_final: 0.6835 (t70) REVERT: D 529 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: D 600 HIS cc_start: 0.8577 (OUTLIER) cc_final: 0.8247 (t-170) REVERT: D 617 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7723 (tp40) REVERT: D 701 GLU cc_start: 0.7906 (tp30) cc_final: 0.7328 (tm-30) REVERT: D 716 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7403 (ttmt) REVERT: D 778 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7070 (mt-10) REVERT: D 807 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8349 (mp) outliers start: 144 outliers final: 56 residues processed: 392 average time/residue: 0.6732 time to fit residues: 304.2490 Evaluate side-chains 374 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 290 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 425 TRP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 706 GLN Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 716 LYS Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 796 SER Chi-restraints excluded: chain D residue 807 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 227 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 208 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN A 536 ASN B 162 ASN C 159 ASN C 229 ASN C 536 ASN D 162 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.152975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131910 restraints weight = 30434.768| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.50 r_work: 0.3360 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26444 Z= 0.121 Angle : 0.480 5.669 35868 Z= 0.260 Chirality : 0.040 0.146 3888 Planarity : 0.003 0.038 4672 Dihedral : 6.673 78.573 3590 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.29 % Rotamer: Outliers : 3.93 % Allowed : 18.58 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 3176 helix: 0.90 (0.13), residues: 1696 sheet: -0.05 (0.23), residues: 476 loop : -0.64 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 279 TYR 0.015 0.002 TYR D 400 PHE 0.013 0.001 PHE A 156 TRP 0.013 0.001 TRP D 473 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (26444) covalent geometry : angle 0.47953 / 0.26 (35868) hydrogen bonds : bond 0.04219 / 2.77 ( 1358) hydrogen bonds : angle 4.66433 / 3.39 ( 3852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 304 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7829 (ttt) REVERT: A 52 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.6633 (mmt180) REVERT: A 171 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: A 187 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7940 (ptt180) REVERT: A 241 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: A 432 HIS cc_start: 0.7372 (t70) cc_final: 0.6224 (p90) REVERT: A 440 LEU cc_start: 0.8357 (pt) cc_final: 0.8116 (pp) REVERT: A 529 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7441 (tp30) REVERT: A 680 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: A 683 ASP cc_start: 0.7622 (m-30) cc_final: 0.7383 (m-30) REVERT: A 698 GLU cc_start: 0.6897 (pp20) cc_final: 0.6590 (mp0) REVERT: A 801 LYS cc_start: 0.8019 (mttt) cc_final: 0.7382 (mtpt) REVERT: B 39 HIS cc_start: 0.6930 (m90) cc_final: 0.6655 (m90) REVERT: B 52 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7387 (mpt90) REVERT: B 57 TRP cc_start: 0.6901 (t60) cc_final: 0.6488 (t60) REVERT: B 110 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6902 (mm-30) REVERT: B 259 LYS cc_start: 0.8741 (mttt) cc_final: 0.8204 (mppt) REVERT: B 279 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7762 (mtp180) REVERT: B 280 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7943 (tt0) REVERT: B 348 GLU cc_start: 0.7820 (tt0) cc_final: 0.7564 (mm-30) REVERT: B 362 MET cc_start: 0.7851 (mmm) cc_final: 0.7451 (mpp) REVERT: B 376 LYS cc_start: 0.8895 (ttpp) cc_final: 0.8658 (tttt) REVERT: B 405 ASP cc_start: 0.6839 (m-30) cc_final: 0.6577 (t0) REVERT: B 617 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7655 (tp40) REVERT: B 701 GLU cc_start: 0.7857 (tp30) cc_final: 0.7336 (tm-30) REVERT: B 778 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6948 (mt-10) REVERT: C 26 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7813 (mmm) REVERT: C 52 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.6653 (mmt180) REVERT: C 171 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: C 187 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7963 (ptt180) REVERT: C 376 LYS cc_start: 0.8470 (tttp) cc_final: 0.8260 (ttpm) REVERT: C 432 HIS cc_start: 0.7346 (t70) cc_final: 0.6198 (p90) REVERT: C 440 LEU cc_start: 0.8354 (pt) cc_final: 0.8114 (pp) REVERT: C 680 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: C 683 ASP cc_start: 0.7625 (m-30) cc_final: 0.7398 (m-30) REVERT: C 698 GLU cc_start: 0.6911 (pp20) cc_final: 0.6598 (mp0) REVERT: C 801 LYS cc_start: 0.8020 (mttt) cc_final: 0.7382 (mtpt) REVERT: D 39 HIS cc_start: 0.6936 (m90) cc_final: 0.6659 (m90) REVERT: D 52 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7404 (mpt90) REVERT: D 57 TRP cc_start: 0.6919 (t60) cc_final: 0.6497 (t60) REVERT: D 110 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6904 (mm-30) REVERT: D 259 LYS cc_start: 0.8742 (mttt) cc_final: 0.8198 (mppt) REVERT: D 279 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7789 (mtp180) REVERT: D 280 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7955 (tt0) REVERT: D 348 GLU cc_start: 0.7808 (tt0) cc_final: 0.7571 (mm-30) REVERT: D 362 MET cc_start: 0.7856 (mmm) cc_final: 0.7432 (mpp) REVERT: D 405 ASP cc_start: 0.6788 (m-30) cc_final: 0.6582 (t0) REVERT: D 617 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7672 (tp40) REVERT: D 701 GLU cc_start: 0.7853 (tp30) cc_final: 0.7309 (tm-30) REVERT: D 778 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7026 (mt-10) outliers start: 109 outliers final: 43 residues processed: 383 average time/residue: 0.6254 time to fit residues: 276.1553 Evaluate side-chains 349 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 288 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 706 GLN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 778 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 213 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 296 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN B 159 ASN B 162 ASN B 561 ASN C 536 ASN D 159 ASN D 162 ASN D 561 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.146962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124940 restraints weight = 28851.699| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.47 r_work: 0.3251 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 26444 Z= 0.217 Angle : 0.570 5.992 35868 Z= 0.309 Chirality : 0.044 0.155 3888 Planarity : 0.004 0.046 4672 Dihedral : 6.924 81.735 3590 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 4.76 % Allowed : 18.33 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3176 helix: 0.65 (0.12), residues: 1696 sheet: 0.13 (0.23), residues: 468 loop : -0.73 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 187 TYR 0.017 0.002 TYR C 302 PHE 0.020 0.002 PHE D 156 TRP 0.015 0.002 TRP D 473 HIS 0.004 0.001 HIS B 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (26444) covalent geometry : angle 0.57003 / 0.31 (35868) hydrogen bonds : bond 0.05289 / 3.48 ( 1358) hydrogen bonds : angle 4.85709 / 3.54 ( 3852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 292 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7978 (ttm) REVERT: A 52 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.6604 (mmt90) REVERT: A 171 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: A 187 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7981 (ptt180) REVERT: A 241 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: A 338 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: A 391 TYR cc_start: 0.8195 (t80) cc_final: 0.7959 (t80) REVERT: A 432 HIS cc_start: 0.7331 (t70) cc_final: 0.6259 (p90) REVERT: A 440 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8090 (pp) REVERT: A 529 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7395 (tp30) REVERT: A 620 ASP cc_start: 0.7746 (m-30) cc_final: 0.7537 (m-30) REVERT: A 683 ASP cc_start: 0.7688 (m-30) cc_final: 0.7379 (m-30) REVERT: A 698 GLU cc_start: 0.6952 (pp20) cc_final: 0.6615 (mp0) REVERT: A 801 LYS cc_start: 0.8029 (mttt) cc_final: 0.7651 (mtpt) REVERT: B 39 HIS cc_start: 0.7024 (m90) cc_final: 0.6712 (m90) REVERT: B 57 TRP cc_start: 0.6933 (t60) cc_final: 0.6508 (t60) REVERT: B 110 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: B 171 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: B 259 LYS cc_start: 0.8737 (mttt) cc_final: 0.8183 (mppt) REVERT: B 279 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7801 (mtp180) REVERT: B 280 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8053 (tt0) REVERT: B 348 GLU cc_start: 0.7967 (tt0) cc_final: 0.7576 (mm-30) REVERT: B 362 MET cc_start: 0.7843 (mmm) cc_final: 0.7422 (mpp) REVERT: B 405 ASP cc_start: 0.6823 (m-30) cc_final: 0.6546 (t0) REVERT: B 514 HIS cc_start: 0.7157 (t-170) cc_final: 0.6742 (t70) REVERT: B 522 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: B 529 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7932 (tp30) REVERT: B 617 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7681 (tp40) REVERT: B 778 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: B 807 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8350 (mp) REVERT: C 52 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.6597 (mmt90) REVERT: C 171 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: C 187 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7999 (ptt180) REVERT: C 338 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: C 376 LYS cc_start: 0.8540 (tttp) cc_final: 0.8287 (ttpm) REVERT: C 391 TYR cc_start: 0.8189 (t80) cc_final: 0.7949 (t80) REVERT: C 432 HIS cc_start: 0.7335 (t70) cc_final: 0.6244 (p90) REVERT: C 440 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8095 (pp) REVERT: C 620 ASP cc_start: 0.7765 (m-30) cc_final: 0.7554 (m-30) REVERT: C 683 ASP cc_start: 0.7687 (m-30) cc_final: 0.7372 (m-30) REVERT: C 698 GLU cc_start: 0.6948 (pp20) cc_final: 0.6612 (mp0) REVERT: C 801 LYS cc_start: 0.8027 (mttt) cc_final: 0.7649 (mtpt) REVERT: D 39 HIS cc_start: 0.7018 (m90) cc_final: 0.6718 (m90) REVERT: D 57 TRP cc_start: 0.6943 (t60) cc_final: 0.6503 (t60) REVERT: D 110 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6960 (mm-30) REVERT: D 259 LYS cc_start: 0.8726 (mttt) cc_final: 0.8183 (mppt) REVERT: D 279 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7807 (mtp180) REVERT: D 280 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8034 (tt0) REVERT: D 348 GLU cc_start: 0.7992 (tt0) cc_final: 0.7590 (mm-30) REVERT: D 362 MET cc_start: 0.7818 (mmm) cc_final: 0.7419 (mpp) REVERT: D 405 ASP cc_start: 0.6821 (m-30) cc_final: 0.6567 (t0) REVERT: D 514 HIS cc_start: 0.7172 (t-170) cc_final: 0.6762 (t70) REVERT: D 529 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: D 617 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7683 (tp40) REVERT: D 778 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: D 807 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8345 (mp) outliers start: 132 outliers final: 67 residues processed: 378 average time/residue: 0.6125 time to fit residues: 266.7305 Evaluate side-chains 383 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 291 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 425 TRP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 706 GLN Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain D residue 597 MET Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 796 SER Chi-restraints excluded: chain D residue 807 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 152 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 0.0770 chunk 232 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN B 162 ASN C 536 ASN D 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.149533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127671 restraints weight = 28926.210| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.46 r_work: 0.3285 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26444 Z= 0.133 Angle : 0.488 5.676 35868 Z= 0.265 Chirality : 0.040 0.146 3888 Planarity : 0.003 0.036 4672 Dihedral : 6.504 78.809 3582 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.36 % Rotamer: Outliers : 3.97 % Allowed : 19.23 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3176 helix: 0.88 (0.13), residues: 1696 sheet: -0.10 (0.22), residues: 476 loop : -0.65 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 TYR 0.013 0.002 TYR A 302 PHE 0.014 0.002 PHE D 156 TRP 0.013 0.001 TRP B 473 HIS 0.003 0.001 HIS B 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (26444) covalent geometry : angle 0.48755 / 0.26 (35868) hydrogen bonds : bond 0.04306 / 2.83 ( 1358) hydrogen bonds : angle 4.62589 / 3.36 ( 3852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 298 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7860 (ttt) REVERT: A 52 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6548 (mmt90) REVERT: A 108 ASN cc_start: 0.6493 (p0) cc_final: 0.5920 (t0) REVERT: A 171 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: A 187 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7985 (ptt180) REVERT: A 241 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: A 338 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: A 432 HIS cc_start: 0.7307 (t70) cc_final: 0.6204 (p-80) REVERT: A 440 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8090 (pp) REVERT: A 529 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: A 683 ASP cc_start: 0.7681 (m-30) cc_final: 0.7384 (m-30) REVERT: A 698 GLU cc_start: 0.6938 (pp20) cc_final: 0.6591 (mp0) REVERT: A 801 LYS cc_start: 0.8030 (mttt) cc_final: 0.7657 (mtpt) REVERT: B 39 HIS cc_start: 0.6928 (m90) cc_final: 0.6653 (m90) REVERT: B 52 ARG cc_start: 0.7557 (mtp85) cc_final: 0.7350 (mpt90) REVERT: B 57 TRP cc_start: 0.6914 (t60) cc_final: 0.6501 (t60) REVERT: B 110 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6780 (mm-30) REVERT: B 202 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.6841 (tptp) REVERT: B 259 LYS cc_start: 0.8759 (mttt) cc_final: 0.8201 (mppt) REVERT: B 279 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7753 (mtp180) REVERT: B 280 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8006 (tt0) REVERT: B 348 GLU cc_start: 0.7966 (tt0) cc_final: 0.7613 (mm-30) REVERT: B 362 MET cc_start: 0.8026 (mmm) cc_final: 0.7443 (mpp) REVERT: B 405 ASP cc_start: 0.6779 (m-30) cc_final: 0.6511 (t0) REVERT: B 514 HIS cc_start: 0.7086 (t-170) cc_final: 0.6685 (t70) REVERT: B 600 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.8264 (t-170) REVERT: B 617 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7642 (tp40) REVERT: B 778 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7066 (mt-10) REVERT: B 807 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8275 (mp) REVERT: C 26 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7864 (mmm) REVERT: C 52 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.6562 (mmt90) REVERT: C 108 ASN cc_start: 0.6492 (p0) cc_final: 0.5923 (t0) REVERT: C 171 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7364 (m-80) REVERT: C 187 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7992 (ptt180) REVERT: C 241 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: C 338 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: C 376 LYS cc_start: 0.8512 (tttp) cc_final: 0.8267 (ttpm) REVERT: C 432 HIS cc_start: 0.7322 (t70) cc_final: 0.6189 (p-80) REVERT: C 440 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8099 (pp) REVERT: C 683 ASP cc_start: 0.7679 (m-30) cc_final: 0.7374 (m-30) REVERT: C 698 GLU cc_start: 0.6940 (pp20) cc_final: 0.6597 (mp0) REVERT: C 801 LYS cc_start: 0.8043 (mttt) cc_final: 0.7674 (mtpt) REVERT: D 39 HIS cc_start: 0.6928 (m90) cc_final: 0.6653 (m90) REVERT: D 52 ARG cc_start: 0.7597 (mtt180) cc_final: 0.7352 (mpt90) REVERT: D 57 TRP cc_start: 0.6933 (t60) cc_final: 0.6503 (t60) REVERT: D 110 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6775 (mm-30) REVERT: D 202 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.6834 (tptp) REVERT: D 259 LYS cc_start: 0.8740 (mttt) cc_final: 0.8196 (mppt) REVERT: D 279 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7748 (mtp180) REVERT: D 280 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7977 (tt0) REVERT: D 348 GLU cc_start: 0.7990 (tt0) cc_final: 0.7624 (mm-30) REVERT: D 362 MET cc_start: 0.8049 (mmm) cc_final: 0.7452 (mpp) REVERT: D 405 ASP cc_start: 0.6799 (m-30) cc_final: 0.6540 (t0) REVERT: D 514 HIS cc_start: 0.7097 (t-170) cc_final: 0.6694 (t70) REVERT: D 522 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: D 600 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.8266 (t-170) REVERT: D 617 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7631 (tp40) REVERT: D 778 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: D 807 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8267 (mp) outliers start: 110 outliers final: 59 residues processed: 370 average time/residue: 0.6997 time to fit residues: 297.8051 Evaluate side-chains 374 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 287 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 706 GLN Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 807 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 146 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 264 optimal weight: 0.7980 chunk 245 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 257 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 192 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN B 162 ASN B 561 ASN B 749 ASN C 536 ASN D 162 ASN D 561 ASN D 749 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.128831 restraints weight = 28800.590| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.47 r_work: 0.3299 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26444 Z= 0.113 Angle : 0.463 5.576 35868 Z= 0.251 Chirality : 0.039 0.143 3888 Planarity : 0.003 0.036 4672 Dihedral : 6.339 77.921 3582 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.29 % Rotamer: Outliers : 4.04 % Allowed : 19.19 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 3176 helix: 1.04 (0.13), residues: 1696 sheet: -0.07 (0.22), residues: 476 loop : -0.57 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 50 TYR 0.016 0.001 TYR C 95 PHE 0.013 0.001 PHE A 156 TRP 0.012 0.001 TRP D 473 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (26444) covalent geometry : angle 0.46309 / 0.25 (35868) hydrogen bonds : bond 0.03942 / 2.60 ( 1358) hydrogen bonds : angle 4.50308 / 3.27 ( 3852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 301 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7906 (ttt) REVERT: A 52 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.6576 (mmt180) REVERT: A 108 ASN cc_start: 0.6440 (p0) cc_final: 0.5916 (t0) REVERT: A 171 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: A 187 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8225 (ptp-170) REVERT: A 241 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: A 338 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: A 432 HIS cc_start: 0.7294 (t70) cc_final: 0.6177 (p-80) REVERT: A 440 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8096 (pp) REVERT: A 529 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: A 683 ASP cc_start: 0.7672 (m-30) cc_final: 0.7415 (m-30) REVERT: A 698 GLU cc_start: 0.6974 (pp20) cc_final: 0.6622 (mp0) REVERT: A 796 SER cc_start: 0.7895 (OUTLIER) cc_final: 0.7459 (p) REVERT: A 801 LYS cc_start: 0.8019 (mttt) cc_final: 0.7642 (mtpt) REVERT: B 39 HIS cc_start: 0.6922 (m90) cc_final: 0.6657 (m90) REVERT: B 52 ARG cc_start: 0.7621 (mtp85) cc_final: 0.7379 (mpt90) REVERT: B 57 TRP cc_start: 0.6885 (t60) cc_final: 0.6482 (t60) REVERT: B 110 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6879 (mm-30) REVERT: B 202 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6912 (tptp) REVERT: B 259 LYS cc_start: 0.8784 (mttt) cc_final: 0.8224 (mppt) REVERT: B 279 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7788 (mtp180) REVERT: B 280 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7997 (tt0) REVERT: B 348 GLU cc_start: 0.7962 (tt0) cc_final: 0.7574 (mm-30) REVERT: B 362 MET cc_start: 0.8034 (mmm) cc_final: 0.7449 (mpp) REVERT: B 376 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8688 (tttt) REVERT: B 405 ASP cc_start: 0.6768 (m-30) cc_final: 0.6529 (t0) REVERT: B 522 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: B 600 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.8249 (t-170) REVERT: B 617 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7611 (tp40) REVERT: B 701 GLU cc_start: 0.7495 (tp30) cc_final: 0.6722 (tm-30) REVERT: B 778 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: B 807 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8280 (mp) REVERT: C 26 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7853 (mmm) REVERT: C 52 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.6590 (mmt180) REVERT: C 108 ASN cc_start: 0.6445 (p0) cc_final: 0.5930 (t0) REVERT: C 171 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: C 187 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8240 (ptp-170) REVERT: C 241 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: C 338 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: C 376 LYS cc_start: 0.8509 (tttp) cc_final: 0.8264 (ttpm) REVERT: C 432 HIS cc_start: 0.7309 (t70) cc_final: 0.6169 (p-80) REVERT: C 440 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8090 (pp) REVERT: C 683 ASP cc_start: 0.7672 (m-30) cc_final: 0.7411 (m-30) REVERT: C 698 GLU cc_start: 0.6963 (pp20) cc_final: 0.6612 (mp0) REVERT: C 796 SER cc_start: 0.7897 (OUTLIER) cc_final: 0.7459 (p) REVERT: C 801 LYS cc_start: 0.8038 (mttt) cc_final: 0.7657 (mtpt) REVERT: D 39 HIS cc_start: 0.6921 (m90) cc_final: 0.6659 (m90) REVERT: D 52 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7357 (mpt90) REVERT: D 57 TRP cc_start: 0.6893 (t60) cc_final: 0.6478 (t60) REVERT: D 110 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6838 (mm-30) REVERT: D 202 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.6922 (tptp) REVERT: D 259 LYS cc_start: 0.8757 (mttt) cc_final: 0.8211 (mppt) REVERT: D 279 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7762 (mtp180) REVERT: D 280 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7982 (tt0) REVERT: D 348 GLU cc_start: 0.7979 (tt0) cc_final: 0.7586 (mm-30) REVERT: D 362 MET cc_start: 0.8053 (mmm) cc_final: 0.7468 (mpp) REVERT: D 405 ASP cc_start: 0.6778 (m-30) cc_final: 0.6521 (t0) REVERT: D 522 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: D 600 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.8249 (t-170) REVERT: D 617 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7607 (tp40) REVERT: D 701 GLU cc_start: 0.7504 (tp30) cc_final: 0.6715 (tm-30) REVERT: D 778 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: D 807 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8271 (mp) outliers start: 112 outliers final: 57 residues processed: 374 average time/residue: 0.6968 time to fit residues: 300.1254 Evaluate side-chains 375 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 287 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 706 GLN Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 807 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 249 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 295 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 274 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 160 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN B 162 ASN B 248 ASN B 561 ASN C 536 ASN D 162 ASN D 248 ASN D 561 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.151353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129749 restraints weight = 28794.901| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.49 r_work: 0.3307 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26444 Z= 0.109 Angle : 0.459 5.579 35868 Z= 0.249 Chirality : 0.039 0.143 3888 Planarity : 0.003 0.035 4672 Dihedral : 6.206 77.153 3582 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 3.68 % Allowed : 19.84 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 3176 helix: 1.09 (0.13), residues: 1700 sheet: -0.03 (0.23), residues: 476 loop : -0.50 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 TYR 0.016 0.001 TYR D 400 PHE 0.014 0.001 PHE A 156 TRP 0.011 0.001 TRP D 473 HIS 0.003 0.001 HIS B 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (26444) covalent geometry : angle 0.45934 / 0.25 (35868) hydrogen bonds : bond 0.03825 / 2.52 ( 1358) hydrogen bonds : angle 4.44663 / 3.23 ( 3852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 291 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7880 (ttt) REVERT: A 52 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.6563 (mmt180) REVERT: A 108 ASN cc_start: 0.6404 (p0) cc_final: 0.5923 (t0) REVERT: A 171 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: A 187 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8216 (ptp-170) REVERT: A 241 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: A 432 HIS cc_start: 0.7307 (t70) cc_final: 0.6182 (p-80) REVERT: A 440 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8084 (pp) REVERT: A 698 GLU cc_start: 0.6952 (pp20) cc_final: 0.6594 (mp0) REVERT: A 796 SER cc_start: 0.7875 (OUTLIER) cc_final: 0.7455 (p) REVERT: A 801 LYS cc_start: 0.8013 (mttt) cc_final: 0.7640 (mtpt) REVERT: B 39 HIS cc_start: 0.6895 (m90) cc_final: 0.6627 (m90) REVERT: B 52 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7377 (mpt90) REVERT: B 57 TRP cc_start: 0.6875 (t60) cc_final: 0.6467 (t60) REVERT: B 110 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: B 202 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.6947 (tptp) REVERT: B 259 LYS cc_start: 0.8775 (mttt) cc_final: 0.8220 (mppt) REVERT: B 279 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7833 (mtp180) REVERT: B 280 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7974 (tt0) REVERT: B 348 GLU cc_start: 0.7911 (tt0) cc_final: 0.7555 (mm-30) REVERT: B 362 MET cc_start: 0.8016 (mmm) cc_final: 0.7463 (mpp) REVERT: B 376 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8689 (tttt) REVERT: B 522 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: B 600 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.8244 (t-170) REVERT: B 617 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7612 (tp40) REVERT: B 701 GLU cc_start: 0.7524 (tp30) cc_final: 0.6756 (tm-30) REVERT: B 778 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: B 807 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8275 (mp) REVERT: C 26 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7834 (mmm) REVERT: C 52 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.6586 (mmt180) REVERT: C 108 ASN cc_start: 0.6425 (p0) cc_final: 0.5947 (t0) REVERT: C 171 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: C 187 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8228 (ptp-170) REVERT: C 241 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: C 376 LYS cc_start: 0.8505 (tttp) cc_final: 0.8251 (ttpm) REVERT: C 432 HIS cc_start: 0.7304 (t70) cc_final: 0.6165 (p-80) REVERT: C 440 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8089 (pp) REVERT: C 698 GLU cc_start: 0.6944 (pp20) cc_final: 0.6583 (mp0) REVERT: C 796 SER cc_start: 0.7875 (OUTLIER) cc_final: 0.7454 (p) REVERT: C 801 LYS cc_start: 0.8020 (mttt) cc_final: 0.7643 (mtpt) REVERT: D 39 HIS cc_start: 0.6897 (m90) cc_final: 0.6630 (m90) REVERT: D 52 ARG cc_start: 0.7563 (mtt180) cc_final: 0.7356 (mpt90) REVERT: D 57 TRP cc_start: 0.6881 (t60) cc_final: 0.6460 (t60) REVERT: D 110 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6843 (mm-30) REVERT: D 202 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.6942 (tptp) REVERT: D 259 LYS cc_start: 0.8753 (mttt) cc_final: 0.8214 (mppt) REVERT: D 279 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7718 (mtp180) REVERT: D 280 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7975 (tt0) REVERT: D 348 GLU cc_start: 0.7930 (tt0) cc_final: 0.7567 (mm-30) REVERT: D 362 MET cc_start: 0.8037 (mmm) cc_final: 0.7484 (mpp) REVERT: D 405 ASP cc_start: 0.6789 (m-30) cc_final: 0.6521 (t0) REVERT: D 522 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: D 600 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.8245 (t-170) REVERT: D 617 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7611 (tp40) REVERT: D 701 GLU cc_start: 0.7535 (tp30) cc_final: 0.6750 (tm-30) REVERT: D 778 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: D 807 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8268 (mp) outliers start: 102 outliers final: 50 residues processed: 355 average time/residue: 0.6809 time to fit residues: 278.5731 Evaluate side-chains 362 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 284 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 706 GLN Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 807 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 46 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 294 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 276 optimal weight: 0.8980 chunk 210 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN B 162 ASN B 248 ASN B 561 ASN C 536 ASN D 162 ASN D 248 ASN D 561 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.151772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130078 restraints weight = 28883.426| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.47 r_work: 0.3314 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26444 Z= 0.104 Angle : 0.455 7.428 35868 Z= 0.245 Chirality : 0.039 0.142 3888 Planarity : 0.003 0.035 4672 Dihedral : 5.996 76.224 3579 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 3.25 % Allowed : 20.42 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 3176 helix: 1.18 (0.13), residues: 1696 sheet: 0.01 (0.23), residues: 476 loop : -0.47 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 TYR 0.016 0.001 TYR A 95 PHE 0.014 0.001 PHE A 156 TRP 0.011 0.001 TRP D 473 HIS 0.003 0.001 HIS B 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (26444) covalent geometry : angle 0.45495 / 0.24 (35868) hydrogen bonds : bond 0.03700 / 2.44 ( 1358) hydrogen bonds : angle 4.40026 / 3.19 ( 3852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 289 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7814 (ttt) REVERT: A 52 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.6559 (mmt180) REVERT: A 108 ASN cc_start: 0.6403 (p0) cc_final: 0.5971 (t0) REVERT: A 171 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: A 187 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8208 (ptp-170) REVERT: A 241 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: A 432 HIS cc_start: 0.7290 (t70) cc_final: 0.6173 (p-80) REVERT: A 440 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8082 (pp) REVERT: A 796 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7458 (p) REVERT: A 801 LYS cc_start: 0.8049 (mttt) cc_final: 0.7651 (mtpt) REVERT: B 39 HIS cc_start: 0.6901 (m90) cc_final: 0.6474 (m90) REVERT: B 52 ARG cc_start: 0.7606 (mtp85) cc_final: 0.7386 (mpt90) REVERT: B 57 TRP cc_start: 0.6866 (t60) cc_final: 0.6480 (t60) REVERT: B 202 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.6939 (tptp) REVERT: B 259 LYS cc_start: 0.8780 (mttt) cc_final: 0.8222 (mppt) REVERT: B 279 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7791 (mtp180) REVERT: B 280 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7969 (tt0) REVERT: B 348 GLU cc_start: 0.7917 (tt0) cc_final: 0.7535 (mm-30) REVERT: B 362 MET cc_start: 0.8015 (mmm) cc_final: 0.7458 (mpp) REVERT: B 376 LYS cc_start: 0.8919 (ttpp) cc_final: 0.8691 (tttt) REVERT: B 405 ASP cc_start: 0.6795 (m-30) cc_final: 0.6506 (t0) REVERT: B 522 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: B 617 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7599 (tp40) REVERT: B 701 GLU cc_start: 0.7523 (tp30) cc_final: 0.6755 (tm-30) REVERT: B 807 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8319 (mp) REVERT: C 26 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7849 (mmm) REVERT: C 52 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6583 (mmt180) REVERT: C 108 ASN cc_start: 0.6396 (p0) cc_final: 0.5971 (t0) REVERT: C 171 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: C 187 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8232 (ptp-170) REVERT: C 241 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: C 376 LYS cc_start: 0.8500 (tttp) cc_final: 0.8251 (ttpm) REVERT: C 432 HIS cc_start: 0.7293 (t70) cc_final: 0.6165 (p-80) REVERT: C 440 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8082 (pp) REVERT: C 796 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7460 (p) REVERT: C 801 LYS cc_start: 0.8048 (mttt) cc_final: 0.7650 (mtpt) REVERT: D 39 HIS cc_start: 0.6910 (m90) cc_final: 0.6495 (m90) REVERT: D 57 TRP cc_start: 0.6877 (t60) cc_final: 0.6474 (t60) REVERT: D 202 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.6951 (tptp) REVERT: D 259 LYS cc_start: 0.8771 (mttt) cc_final: 0.8221 (mppt) REVERT: D 279 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7741 (mtp180) REVERT: D 280 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7950 (tt0) REVERT: D 348 GLU cc_start: 0.7925 (tt0) cc_final: 0.7545 (mm-30) REVERT: D 362 MET cc_start: 0.8027 (mmm) cc_final: 0.7471 (mpp) REVERT: D 405 ASP cc_start: 0.6778 (m-30) cc_final: 0.6516 (t0) REVERT: D 522 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: D 617 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7588 (tp40) REVERT: D 701 GLU cc_start: 0.7533 (tp30) cc_final: 0.6737 (tm-30) REVERT: D 807 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8314 (mp) outliers start: 90 outliers final: 45 residues processed: 350 average time/residue: 0.7141 time to fit residues: 288.0674 Evaluate side-chains 351 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 284 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 706 GLN Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 807 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 155 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 236 optimal weight: 0.8980 chunk 225 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 172 optimal weight: 2.9990 chunk 264 optimal weight: 0.0170 chunk 101 optimal weight: 6.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN B 162 ASN B 248 ASN B 561 ASN C 536 ASN D 162 ASN D 248 ASN D 561 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130431 restraints weight = 28806.737| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.52 r_work: 0.3313 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26444 Z= 0.102 Angle : 0.451 5.968 35868 Z= 0.245 Chirality : 0.039 0.141 3888 Planarity : 0.003 0.035 4672 Dihedral : 5.798 75.582 3573 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 2.56 % Allowed : 21.00 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.15), residues: 3176 helix: 1.25 (0.13), residues: 1696 sheet: 0.05 (0.23), residues: 476 loop : -0.44 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 TYR 0.016 0.001 TYR D 400 PHE 0.013 0.001 PHE A 156 TRP 0.011 0.001 TRP B 473 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (26444) covalent geometry : angle 0.45131 / 0.24 (35868) hydrogen bonds : bond 0.03612 / 2.38 ( 1358) hydrogen bonds : angle 4.36534 / 3.17 ( 3852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 288 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6572 (mmt180) REVERT: A 108 ASN cc_start: 0.6381 (p0) cc_final: 0.5986 (t0) REVERT: A 171 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7423 (m-80) REVERT: A 187 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8229 (ptp-170) REVERT: A 432 HIS cc_start: 0.7301 (t70) cc_final: 0.6162 (p-80) REVERT: A 440 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8085 (pp) REVERT: A 741 ARG cc_start: 0.7607 (tpp80) cc_final: 0.7030 (mmm-85) REVERT: A 796 SER cc_start: 0.7838 (OUTLIER) cc_final: 0.7450 (p) REVERT: A 801 LYS cc_start: 0.8044 (mttt) cc_final: 0.7648 (mtpt) REVERT: B 39 HIS cc_start: 0.6907 (m90) cc_final: 0.6485 (m90) REVERT: B 52 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7386 (mpt90) REVERT: B 57 TRP cc_start: 0.6851 (t60) cc_final: 0.6435 (t60) REVERT: B 202 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.6955 (tptp) REVERT: B 259 LYS cc_start: 0.8791 (mttt) cc_final: 0.8229 (mppt) REVERT: B 279 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7788 (mtp180) REVERT: B 280 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7978 (tt0) REVERT: B 348 GLU cc_start: 0.7928 (tt0) cc_final: 0.7567 (mm-30) REVERT: B 362 MET cc_start: 0.8009 (mmm) cc_final: 0.7458 (mpp) REVERT: B 376 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8695 (tttt) REVERT: B 405 ASP cc_start: 0.6793 (m-30) cc_final: 0.6495 (t0) REVERT: B 522 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: B 617 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7582 (tp40) REVERT: B 701 GLU cc_start: 0.7558 (tp30) cc_final: 0.6759 (tm-30) REVERT: B 807 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8314 (mp) REVERT: C 26 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7805 (mmm) REVERT: C 52 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6584 (mmt180) REVERT: C 108 ASN cc_start: 0.6371 (p0) cc_final: 0.5991 (t0) REVERT: C 171 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: C 187 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8237 (ptp-170) REVERT: C 241 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: C 376 LYS cc_start: 0.8503 (tttp) cc_final: 0.8245 (ttpm) REVERT: C 432 HIS cc_start: 0.7296 (t70) cc_final: 0.6156 (p-80) REVERT: C 440 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8082 (pp) REVERT: C 741 ARG cc_start: 0.7604 (tpp80) cc_final: 0.7028 (mmm-85) REVERT: C 796 SER cc_start: 0.7838 (OUTLIER) cc_final: 0.7451 (p) REVERT: C 801 LYS cc_start: 0.8053 (mttt) cc_final: 0.7653 (mtpt) REVERT: D 39 HIS cc_start: 0.6920 (m90) cc_final: 0.6493 (m90) REVERT: D 57 TRP cc_start: 0.6870 (t60) cc_final: 0.6466 (t60) REVERT: D 202 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.6962 (tptp) REVERT: D 259 LYS cc_start: 0.8770 (mttt) cc_final: 0.8228 (mppt) REVERT: D 279 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7745 (mtp180) REVERT: D 280 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7954 (tt0) REVERT: D 348 GLU cc_start: 0.7937 (tt0) cc_final: 0.7583 (mm-30) REVERT: D 362 MET cc_start: 0.8032 (mmm) cc_final: 0.7468 (mpp) REVERT: D 405 ASP cc_start: 0.6784 (m-30) cc_final: 0.6489 (t0) REVERT: D 522 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: D 617 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7582 (tp40) REVERT: D 701 GLU cc_start: 0.7552 (tp30) cc_final: 0.6741 (tm-30) REVERT: D 807 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8306 (mp) outliers start: 71 outliers final: 42 residues processed: 331 average time/residue: 0.6677 time to fit residues: 254.1597 Evaluate side-chains 343 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 281 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 807 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 191 optimal weight: 5.9990 chunk 164 optimal weight: 0.3980 chunk 188 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 124 optimal weight: 0.0970 chunk 88 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 277 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 ASN B 248 ASN B 561 ASN D 162 ASN D 248 ASN D 561 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.152158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.130537 restraints weight = 28775.134| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.46 r_work: 0.3321 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26444 Z= 0.103 Angle : 0.451 5.782 35868 Z= 0.244 Chirality : 0.039 0.142 3888 Planarity : 0.003 0.036 4672 Dihedral : 5.475 75.116 3563 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 2.74 % Allowed : 21.10 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3176 helix: 1.26 (0.13), residues: 1700 sheet: 0.06 (0.23), residues: 476 loop : -0.42 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 50 TYR 0.016 0.001 TYR C 95 PHE 0.014 0.001 PHE C 156 TRP 0.011 0.001 TRP D 473 HIS 0.003 0.001 HIS D 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (26444) covalent geometry : angle 0.45087 / 0.24 (35868) hydrogen bonds : bond 0.03632 / 2.40 ( 1358) hydrogen bonds : angle 4.35966 / 3.16 ( 3852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9401.92 seconds wall clock time: 160 minutes 48.08 seconds (9648.08 seconds total)