Starting phenix.real_space_refine on Tue May 5 04:37:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uoe_64377/05_2026/9uoe_64377.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uoe_64377/05_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_64377/05_2026/9uoe_64377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uoe_64377/05_2026/9uoe_64377.map" model { file = "/net/cci-nas-00/data/ceres_data/9uoe_64377/05_2026/9uoe_64377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uoe_64377/05_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 5.63, per 1000 atoms: 0.22 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 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: 0.85 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: 5.31 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 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: 0.02 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: 3.660 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.270 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 covalent geometry : bond 0.00359 (26444) covalent geometry : angle 0.54780 (35868) hydrogen bonds : bond 0.15051 ( 1358) hydrogen bonds : angle 6.56850 ( 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 : 0.951 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: 0.6733 time to fit residues: 279.5156 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 : 0.631 ------------------------------------------------------------------------------- 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: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 0.0020 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN B 162 ASN B 248 ASN B 561 ASN C 123 ASN C 159 ASN C 237 GLN C 536 ASN C 755 GLN D 162 ASN D 229 ASN D 237 GLN D 248 ASN D 561 ASN D 600 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.156255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135335 restraints weight = 30558.261| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.51 r_work: 0.3404 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.161 26444 Z= 0.314 Angle : 1.067 28.249 35868 Z= 0.577 Chirality : 0.054 0.740 3888 Planarity : 0.010 0.110 4672 Dihedral : 8.222 88.633 3665 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.27 % Favored : 96.54 % Rotamer: Outliers : 4.15 % Allowed : 18.29 % Favored : 77.56 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.76 (0.14), residues: 3176 helix: -0.24 (0.12), residues: 1676 sheet: 0.21 (0.23), residues: 484 loop : -1.06 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG D 583 TYR 0.235 0.006 TYR D 400 PHE 0.110 0.008 PHE C 461 TRP 0.082 0.006 TRP D 780 HIS 0.045 0.003 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00672 (26444) covalent geometry : angle 1.06699 (35868) hydrogen bonds : bond 0.07093 ( 1358) hydrogen bonds : angle 5.87248 ( 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 419 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 304 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7439 (m-80) REVERT: A 328 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7882 (mt) REVERT: A 376 LYS cc_start: 0.8452 (tttp) cc_final: 0.8213 (ttpm) REVERT: A 391 TYR cc_start: 0.8111 (t80) cc_final: 0.7797 (t80) REVERT: A 501 ASN cc_start: 0.7567 (t0) cc_final: 0.7096 (m-40) REVERT: A 529 GLU cc_start: 0.7768 (tt0) cc_final: 0.7525 (tp30) REVERT: A 680 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: A 683 ASP cc_start: 0.7824 (m-30) cc_final: 0.7525 (m-30) REVERT: A 801 LYS cc_start: 0.7946 (mttt) cc_final: 0.7542 (mtpt) REVERT: B 26 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8072 (tpp) REVERT: B 39 HIS cc_start: 0.6850 (m90) cc_final: 0.6606 (m90) REVERT: B 57 TRP cc_start: 0.6886 (t60) cc_final: 0.6481 (t60) REVERT: B 259 LYS cc_start: 0.8776 (mttt) cc_final: 0.8215 (mppt) REVERT: B 279 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7707 (mtp180) REVERT: B 280 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7839 (tt0) REVERT: B 348 GLU cc_start: 0.7754 (tt0) cc_final: 0.7451 (mm-30) REVERT: B 362 MET cc_start: 0.7994 (mmm) cc_final: 0.7443 (mpp) REVERT: B 376 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8639 (tttt) REVERT: B 405 ASP cc_start: 0.6875 (m-30) cc_final: 0.6615 (t0) REVERT: B 440 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7858 (mp) REVERT: B 455 LYS cc_start: 0.7650 (ptpp) cc_final: 0.7446 (ptpp) REVERT: B 701 GLU cc_start: 0.7805 (tp30) cc_final: 0.7314 (tm-30) REVERT: B 745 ASP cc_start: 0.8417 (m-30) cc_final: 0.8069 (t0) REVERT: B 785 MET cc_start: 0.8308 (mtm) cc_final: 0.7957 (mtp) REVERT: C 29 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8328 (mt) REVERT: C 52 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.6475 (mmt180) REVERT: C 440 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8034 (pp) REVERT: C 501 ASN cc_start: 0.7515 (t0) cc_final: 0.6984 (m-40) REVERT: C 529 GLU cc_start: 0.7789 (tt0) cc_final: 0.7516 (tp30) REVERT: C 680 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: C 683 ASP cc_start: 0.7850 (m-30) cc_final: 0.7572 (m-30) REVERT: C 801 LYS cc_start: 0.7895 (mttt) cc_final: 0.7525 (mtpt) REVERT: D 26 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8022 (tpp) REVERT: D 57 TRP cc_start: 0.6810 (t60) cc_final: 0.6386 (t60) REVERT: D 174 GLU cc_start: 0.8144 (tt0) cc_final: 0.7650 (tm-30) REVERT: D 202 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7006 (tptp) REVERT: D 259 LYS cc_start: 0.8720 (mttt) cc_final: 0.8123 (mtmt) REVERT: D 280 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7843 (tt0) REVERT: D 348 GLU cc_start: 0.7708 (tt0) cc_final: 0.7484 (mm-30) REVERT: D 362 MET cc_start: 0.8011 (mmm) cc_final: 0.7460 (mpp) REVERT: D 397 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6879 (mt0) REVERT: D 439 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8002 (tp30) REVERT: D 440 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7868 (mp) REVERT: D 455 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7454 (ptpp) REVERT: D 529 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7795 (tp30) REVERT: D 600 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.8350 (t70) REVERT: D 699 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7440 (mt-10) REVERT: D 701 GLU cc_start: 0.7747 (tp30) cc_final: 0.7261 (tm-30) REVERT: D 745 ASP cc_start: 0.8374 (m-30) cc_final: 0.7957 (t0) REVERT: D 785 MET cc_start: 0.8268 (mtm) cc_final: 0.7908 (mtp) outliers start: 115 outliers final: 30 residues processed: 384 average time/residue: 0.6489 time to fit residues: 287.6642 Evaluate side-chains 329 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 282 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 328 ILE 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 627 ILE Chi-restraints excluded: chain A residue 680 GLU 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 279 ARG Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 497 LEU 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 658 THR Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 660 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 143 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 292 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN B 162 ASN B 248 ASN B 561 ASN C 71 GLN C 198 GLN C 237 GLN C 536 ASN D 162 ASN D 237 GLN D 561 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.151013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129733 restraints weight = 30653.589| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.50 r_work: 0.3333 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26444 Z= 0.205 Angle : 0.577 9.816 35868 Z= 0.311 Chirality : 0.044 0.157 3888 Planarity : 0.005 0.046 4672 Dihedral : 6.602 84.024 3590 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 4.15 % Allowed : 17.46 % Favored : 78.39 % 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: -0.08 (0.15), residues: 3176 helix: 0.46 (0.12), residues: 1688 sheet: 0.28 (0.24), residues: 456 loop : -0.90 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 526 TYR 0.018 0.002 TYR A 356 PHE 0.021 0.002 PHE D 27 TRP 0.016 0.002 TRP D 473 HIS 0.005 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00478 (26444) covalent geometry : angle 0.57667 (35868) hydrogen bonds : bond 0.05311 ( 1358) hydrogen bonds : angle 5.06479 ( 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 410 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 295 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.6554 (mmt90) REVERT: A 171 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: A 187 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7932 (ptt180) REVERT: A 241 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: A 328 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7967 (mt) REVERT: A 338 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: A 376 LYS cc_start: 0.8504 (tttp) cc_final: 0.8289 (ttpm) REVERT: A 391 TYR cc_start: 0.8207 (t80) cc_final: 0.7925 (t80) REVERT: A 501 ASN cc_start: 0.7724 (t0) cc_final: 0.7130 (m-40) REVERT: A 620 ASP cc_start: 0.7749 (m-30) cc_final: 0.7537 (m-30) REVERT: A 680 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: A 683 ASP cc_start: 0.7908 (m-30) cc_final: 0.7639 (m-30) REVERT: A 801 LYS cc_start: 0.8032 (mttt) cc_final: 0.7622 (mtpt) REVERT: B 26 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7973 (tpp) REVERT: B 39 HIS cc_start: 0.7047 (m90) cc_final: 0.6739 (m90) REVERT: B 57 TRP cc_start: 0.6941 (t60) cc_final: 0.6524 (t60) REVERT: B 171 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8225 (m-80) REVERT: B 257 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: B 259 LYS cc_start: 0.8752 (mttt) cc_final: 0.8248 (mppt) REVERT: B 280 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7975 (tt0) REVERT: B 348 GLU cc_start: 0.7881 (tt0) cc_final: 0.7600 (mm-30) REVERT: B 362 MET cc_start: 0.7801 (mmm) cc_final: 0.7339 (mpp) REVERT: B 376 LYS cc_start: 0.8942 (ttpp) cc_final: 0.8686 (tttt) REVERT: B 405 ASP cc_start: 0.6855 (m-30) cc_final: 0.6620 (t0) REVERT: B 514 HIS cc_start: 0.7108 (t-170) cc_final: 0.6743 (t70) REVERT: B 617 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7693 (tp40) REVERT: B 701 GLU cc_start: 0.7883 (tp30) cc_final: 0.7333 (tm-30) REVERT: B 745 ASP cc_start: 0.8482 (m-30) cc_final: 0.8100 (t0) REVERT: B 807 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8299 (mp) REVERT: C 52 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.6555 (mmt90) REVERT: C 171 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: C 187 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7902 (ptt180) REVERT: C 338 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: C 391 TYR cc_start: 0.8190 (t80) cc_final: 0.7979 (t80) REVERT: C 440 LEU cc_start: 0.8313 (pt) cc_final: 0.8062 (pp) REVERT: C 529 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7519 (tp30) REVERT: C 680 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: C 683 ASP cc_start: 0.7888 (m-30) cc_final: 0.7577 (m-30) REVERT: C 801 LYS cc_start: 0.8030 (mttt) cc_final: 0.7621 (mtpt) REVERT: D 26 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.8034 (tpp) REVERT: D 39 HIS cc_start: 0.7130 (m90) cc_final: 0.6824 (m90) REVERT: D 57 TRP cc_start: 0.6931 (t60) cc_final: 0.6465 (t60) REVERT: D 174 GLU cc_start: 0.8142 (tt0) cc_final: 0.7720 (tm-30) REVERT: D 259 LYS cc_start: 0.8736 (mttt) cc_final: 0.8149 (mppt) REVERT: D 280 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7982 (tt0) REVERT: D 348 GLU cc_start: 0.7871 (tt0) cc_final: 0.7613 (mm-30) REVERT: D 362 MET cc_start: 0.7792 (mmm) cc_final: 0.7324 (mpp) REVERT: D 395 THR cc_start: 0.8572 (m) cc_final: 0.8319 (m) REVERT: D 511 MET cc_start: 0.5838 (OUTLIER) cc_final: 0.4482 (pp-130) REVERT: D 514 HIS cc_start: 0.7105 (t-170) cc_final: 0.6761 (t70) REVERT: D 529 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: D 617 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7677 (tp40) REVERT: D 701 GLU cc_start: 0.7872 (tp30) cc_final: 0.7307 (tm-30) REVERT: D 716 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7376 (ttmt) REVERT: D 745 ASP cc_start: 0.8519 (m-30) cc_final: 0.8097 (t0) outliers start: 115 outliers final: 55 residues processed: 368 average time/residue: 0.6603 time to fit residues: 279.4188 Evaluate side-chains 366 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 290 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 315 ILE Chi-restraints excluded: chain A residue 328 ILE 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 504 GLN Chi-restraints excluded: chain A residue 511 MET 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 706 GLN Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain B residue 26 MET 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 257 GLU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 503 LEU 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 168 SER 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 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 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 627 ILE Chi-restraints excluded: chain C residue 680 GLU 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 118 ASP Chi-restraints excluded: chain D residue 171 TYR 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 404 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 511 MET Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain D residue 716 LYS Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain D residue 796 SER Chi-restraints excluded: chain D residue 800 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 227 optimal weight: 5.9990 chunk 84 optimal weight: 0.1980 chunk 296 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 174 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN B 162 ASN B 561 ASN C 417 ASN C 536 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 561 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.154908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.134039 restraints weight = 30548.634| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.49 r_work: 0.3387 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26444 Z= 0.103 Angle : 0.458 5.875 35868 Z= 0.247 Chirality : 0.039 0.146 3888 Planarity : 0.003 0.039 4672 Dihedral : 6.044 79.133 3577 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 3.10 % Allowed : 18.94 % Favored : 77.96 % 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: 0.45 (0.15), residues: 3176 helix: 1.01 (0.13), residues: 1688 sheet: 0.03 (0.23), residues: 476 loop : -0.65 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 279 TYR 0.019 0.001 TYR C 555 PHE 0.013 0.001 PHE C 156 TRP 0.011 0.001 TRP D 473 HIS 0.003 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00218 (26444) covalent geometry : angle 0.45755 (35868) hydrogen bonds : bond 0.03823 ( 1358) hydrogen bonds : angle 4.61670 ( 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 391 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 305 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7813 (mmm) REVERT: A 52 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6606 (mmt180) REVERT: A 171 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: A 241 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: A 680 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: A 801 LYS cc_start: 0.8043 (mttt) cc_final: 0.7350 (mtpt) REVERT: B 39 HIS cc_start: 0.6853 (m90) cc_final: 0.6611 (m90) REVERT: B 57 TRP cc_start: 0.6896 (t60) cc_final: 0.6477 (t60) REVERT: B 259 LYS cc_start: 0.8773 (mttt) cc_final: 0.8190 (mppt) REVERT: B 279 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7721 (mtp180) REVERT: B 280 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7951 (tt0) REVERT: B 348 GLU cc_start: 0.7803 (tt0) cc_final: 0.7506 (mm-30) REVERT: B 362 MET cc_start: 0.7881 (mmm) cc_final: 0.7447 (mpp) REVERT: B 376 LYS cc_start: 0.8910 (ttpp) cc_final: 0.8656 (tttt) REVERT: B 405 ASP cc_start: 0.6830 (m-30) cc_final: 0.6564 (t0) REVERT: B 701 GLU cc_start: 0.7788 (tp30) cc_final: 0.7301 (tm-30) REVERT: C 52 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.6602 (mmt180) REVERT: C 338 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7404 (mt-10) REVERT: C 440 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8085 (pp) REVERT: C 801 LYS cc_start: 0.7994 (mttt) cc_final: 0.7324 (mtpt) REVERT: D 39 HIS cc_start: 0.6971 (m90) cc_final: 0.6639 (m90) REVERT: D 52 ARG cc_start: 0.7612 (mtp85) cc_final: 0.7372 (mpt90) REVERT: D 57 TRP cc_start: 0.6866 (t60) cc_final: 0.6433 (t60) REVERT: D 174 GLU cc_start: 0.8077 (tt0) cc_final: 0.7651 (tm-30) REVERT: D 259 LYS cc_start: 0.8724 (mttt) cc_final: 0.8085 (mppt) REVERT: D 280 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7950 (tt0) REVERT: D 321 ASP cc_start: 0.7612 (t70) cc_final: 0.7401 (t0) REVERT: D 348 GLU cc_start: 0.7763 (tt0) cc_final: 0.7545 (mm-30) REVERT: D 362 MET cc_start: 0.7892 (mmm) cc_final: 0.7450 (mpp) REVERT: D 395 THR cc_start: 0.8491 (m) cc_final: 0.8238 (m) REVERT: D 511 MET cc_start: 0.5655 (OUTLIER) cc_final: 0.4329 (pp-130) REVERT: D 699 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7456 (mt-10) REVERT: D 701 GLU cc_start: 0.7827 (tp30) cc_final: 0.7262 (tm-30) REVERT: D 778 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7084 (mt-10) outliers start: 86 outliers final: 30 residues processed: 362 average time/residue: 0.6445 time to fit residues: 268.3481 Evaluate side-chains 334 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 293 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 52 ARG Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 TYR 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 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 627 ILE Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain B residue 34 VAL 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 C residue 17 LEU 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 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 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 706 GLN Chi-restraints excluded: chain D residue 511 MET 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: 0.6980 chunk 157 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 143 optimal weight: 0.2980 chunk 303 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 536 ASN A 561 ASN B 162 ASN B 248 ASN B 561 ASN C 536 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 248 ASN D 488 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 = 0.3711 r_free = 0.3711 target = 0.152152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.130992 restraints weight = 30404.629| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.50 r_work: 0.3351 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26444 Z= 0.156 Angle : 0.517 6.001 35868 Z= 0.280 Chirality : 0.042 0.152 3888 Planarity : 0.004 0.036 4672 Dihedral : 6.072 81.440 3572 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 3.68 % Allowed : 18.72 % 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: 0.38 (0.15), residues: 3176 helix: 0.93 (0.13), residues: 1692 sheet: 0.03 (0.23), residues: 476 loop : -0.64 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.019 0.002 TYR C 555 PHE 0.018 0.002 PHE D 156 TRP 0.013 0.001 TRP D 473 HIS 0.004 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00357 (26444) covalent geometry : angle 0.51744 (35868) hydrogen bonds : bond 0.04590 ( 1358) hydrogen bonds : angle 4.69110 ( 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 399 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 297 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.6558 (mmt90) REVERT: A 171 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7340 (m-80) REVERT: A 187 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7911 (ptt180) REVERT: A 241 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: A 338 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: A 391 TYR cc_start: 0.8193 (t80) cc_final: 0.7963 (t80) REVERT: A 440 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7860 (pp) REVERT: A 620 ASP cc_start: 0.7724 (m-30) cc_final: 0.7494 (m-30) REVERT: A 680 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: A 801 LYS cc_start: 0.7938 (mttt) cc_final: 0.7564 (mtpt) REVERT: B 39 HIS cc_start: 0.6862 (m90) cc_final: 0.6614 (m90) REVERT: B 57 TRP cc_start: 0.6919 (t60) cc_final: 0.6489 (t60) REVERT: B 259 LYS cc_start: 0.8752 (mttt) cc_final: 0.8229 (mppt) REVERT: B 279 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7791 (mtp180) REVERT: B 280 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7978 (tt0) REVERT: B 348 GLU cc_start: 0.7868 (tt0) cc_final: 0.7605 (mm-30) REVERT: B 362 MET cc_start: 0.7855 (mmm) cc_final: 0.7421 (mpp) REVERT: B 376 LYS cc_start: 0.8929 (ttpp) cc_final: 0.8687 (tttt) REVERT: B 405 ASP cc_start: 0.6871 (m-30) cc_final: 0.6586 (t0) REVERT: B 514 HIS cc_start: 0.7100 (t-170) cc_final: 0.6745 (t70) REVERT: B 617 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7680 (tp40) REVERT: B 701 GLU cc_start: 0.7836 (tp30) cc_final: 0.7308 (tm-30) REVERT: C 52 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.6584 (mmt90) REVERT: C 187 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7923 (ptt180) REVERT: C 338 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: C 440 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8117 (pp) REVERT: C 801 LYS cc_start: 0.7971 (mttt) cc_final: 0.7603 (mtpt) REVERT: D 39 HIS cc_start: 0.7033 (m90) cc_final: 0.6733 (m90) REVERT: D 52 ARG cc_start: 0.7633 (mtp85) cc_final: 0.7371 (mpt90) REVERT: D 57 TRP cc_start: 0.6900 (t60) cc_final: 0.6428 (t60) REVERT: D 114 ASP cc_start: 0.7445 (m-30) cc_final: 0.7240 (m-30) REVERT: D 259 LYS cc_start: 0.8722 (mttt) cc_final: 0.8170 (mppt) REVERT: D 280 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7949 (tt0) REVERT: D 348 GLU cc_start: 0.7846 (tt0) cc_final: 0.7594 (mm-30) REVERT: D 362 MET cc_start: 0.7839 (mmm) cc_final: 0.7456 (mpp) REVERT: D 395 THR cc_start: 0.8564 (m) cc_final: 0.8313 (m) REVERT: D 511 MET cc_start: 0.5768 (OUTLIER) cc_final: 0.4481 (pp-130) REVERT: D 514 HIS cc_start: 0.7107 (t-170) cc_final: 0.6772 (t70) REVERT: D 617 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7674 (tp40) REVERT: D 701 GLU cc_start: 0.7853 (tp30) cc_final: 0.7286 (tm-30) REVERT: D 778 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: D 807 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8258 (mp) outliers start: 102 outliers final: 51 residues processed: 362 average time/residue: 0.6611 time to fit residues: 274.6576 Evaluate side-chains 360 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 294 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 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 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 171 TYR Chi-restraints excluded: chain B residue 187 ARG 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 398 GLU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 17 LEU 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 159 ASN Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 196 ILE 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 372 ASP Chi-restraints excluded: chain C residue 425 TRP 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 706 GLN Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 511 MET Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 800 ILE 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: 5.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 232 optimal weight: 3.9990 chunk 281 optimal weight: 0.0670 chunk 138 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN B 162 ASN B 561 ASN C 536 ASN D 162 ASN D 248 ASN D 488 HIS D 561 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130418 restraints weight = 30627.985| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.47 r_work: 0.3356 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26444 Z= 0.169 Angle : 0.528 5.896 35868 Z= 0.286 Chirality : 0.042 0.151 3888 Planarity : 0.004 0.038 4672 Dihedral : 6.173 80.379 3572 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.74 % Favored : 97.20 % Rotamer: Outliers : 4.44 % Allowed : 18.15 % Favored : 77.42 % 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: 0.29 (0.15), residues: 3176 helix: 0.85 (0.13), residues: 1692 sheet: -0.03 (0.22), residues: 480 loop : -0.66 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 187 TYR 0.019 0.002 TYR C 555 PHE 0.018 0.002 PHE D 156 TRP 0.015 0.001 TRP D 473 HIS 0.004 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00389 (26444) covalent geometry : angle 0.52787 (35868) hydrogen bonds : bond 0.04752 ( 1358) hydrogen bonds : angle 4.71390 ( 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 411 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 288 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.6588 (mmt90) REVERT: A 108 ASN cc_start: 0.6531 (p0) cc_final: 0.5975 (t0) REVERT: A 171 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: A 187 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7937 (ptt180) REVERT: A 241 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: A 338 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: A 391 TYR cc_start: 0.8203 (t80) cc_final: 0.7977 (t80) REVERT: A 432 HIS cc_start: 0.7367 (t70) cc_final: 0.6252 (p90) REVERT: A 440 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7880 (pp) REVERT: A 801 LYS cc_start: 0.7967 (mttt) cc_final: 0.7597 (mtpt) REVERT: B 26 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7804 (tpt) REVERT: B 39 HIS cc_start: 0.6929 (m90) cc_final: 0.6656 (m90) REVERT: B 57 TRP cc_start: 0.6909 (t60) cc_final: 0.6479 (t60) REVERT: B 257 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: B 259 LYS cc_start: 0.8736 (mttt) cc_final: 0.8237 (mppt) REVERT: B 279 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7789 (mtp180) REVERT: B 280 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7945 (tt0) REVERT: B 348 GLU cc_start: 0.7896 (tt0) cc_final: 0.7620 (mm-30) REVERT: B 362 MET cc_start: 0.7974 (mmm) cc_final: 0.7405 (mpp) REVERT: B 376 LYS cc_start: 0.8933 (ttpp) cc_final: 0.8691 (tttt) REVERT: B 405 ASP cc_start: 0.6830 (m-30) cc_final: 0.6587 (t0) REVERT: B 514 HIS cc_start: 0.7116 (t-170) cc_final: 0.6763 (t70) REVERT: B 600 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.8273 (t-170) REVERT: B 617 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7689 (tp40) REVERT: B 701 GLU cc_start: 0.7837 (tp30) cc_final: 0.7352 (tm-30) REVERT: B 778 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6963 (mt-10) REVERT: B 807 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8263 (mp) REVERT: C 52 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.6630 (mmt90) REVERT: C 187 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7973 (ptt180) REVERT: C 338 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: C 440 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8134 (pp) REVERT: C 801 LYS cc_start: 0.7974 (mttt) cc_final: 0.7609 (mtpt) REVERT: D 39 HIS cc_start: 0.7041 (m90) cc_final: 0.6732 (m90) REVERT: D 57 TRP cc_start: 0.6949 (t60) cc_final: 0.6487 (t60) REVERT: D 110 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6728 (mm-30) REVERT: D 114 ASP cc_start: 0.7454 (m-30) cc_final: 0.7238 (m-30) REVERT: D 259 LYS cc_start: 0.8746 (mttt) cc_final: 0.8187 (mppt) REVERT: D 280 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7943 (tt0) REVERT: D 348 GLU cc_start: 0.7866 (tt0) cc_final: 0.7644 (mm-30) REVERT: D 362 MET cc_start: 0.7846 (mmm) cc_final: 0.7472 (mpp) REVERT: D 395 THR cc_start: 0.8578 (m) cc_final: 0.8326 (m) REVERT: D 511 MET cc_start: 0.5820 (OUTLIER) cc_final: 0.4558 (pp-130) REVERT: D 514 HIS cc_start: 0.7123 (t-170) cc_final: 0.6778 (t70) REVERT: D 617 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7722 (tp40) REVERT: D 701 GLU cc_start: 0.7806 (tp30) cc_final: 0.7280 (tm-30) REVERT: D 778 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7023 (mt-10) REVERT: D 807 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8284 (mp) outliers start: 123 outliers final: 61 residues processed: 370 average time/residue: 0.6592 time to fit residues: 280.7390 Evaluate side-chains 361 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 280 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 214 VAL 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 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 171 TYR Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 257 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 398 GLU 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 796 SER Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain C residue 17 LEU 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 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 525 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 680 GLU 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 210 GLU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 511 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 146 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 264 optimal weight: 0.6980 chunk 245 optimal weight: 3.9990 chunk 56 optimal weight: 0.0010 chunk 257 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN B 159 ASN B 162 ASN B 561 ASN C 536 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 488 HIS D 749 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.153147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.132167 restraints weight = 30487.576| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.50 r_work: 0.3366 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 0.033 26444 Z= 0.124 Angle : 0.481 5.757 35868 Z= 0.260 Chirality : 0.040 0.145 3888 Planarity : 0.003 0.037 4672 Dihedral : 5.996 79.157 3572 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 3.79 % Allowed : 19.37 % Favored : 76.84 % 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: 0.46 (0.15), residues: 3176 helix: 1.01 (0.13), residues: 1692 sheet: 0.02 (0.23), residues: 476 loop : -0.60 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.020 0.002 TYR C 555 PHE 0.014 0.001 PHE B 156 TRP 0.013 0.001 TRP D 473 HIS 0.003 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00275 (26444) covalent geometry : angle 0.48143 (35868) hydrogen bonds : bond 0.04111 ( 1358) hydrogen bonds : angle 4.56033 ( 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 397 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 292 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7836 (mmm) REVERT: A 52 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.6624 (mmt180) REVERT: A 108 ASN cc_start: 0.6448 (p0) cc_final: 0.5984 (t0) REVERT: A 171 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: A 187 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7956 (ptt180) REVERT: A 338 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: A 391 TYR cc_start: 0.8126 (t80) cc_final: 0.7900 (t80) REVERT: A 440 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7887 (pp) REVERT: A 801 LYS cc_start: 0.7940 (mttt) cc_final: 0.7555 (mtpt) REVERT: B 39 HIS cc_start: 0.6829 (m90) cc_final: 0.6588 (m90) REVERT: B 57 TRP cc_start: 0.6921 (t60) cc_final: 0.6484 (t60) REVERT: B 257 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: B 259 LYS cc_start: 0.8723 (mttt) cc_final: 0.8216 (mppt) REVERT: B 279 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7790 (mtp180) REVERT: B 280 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7945 (tt0) REVERT: B 348 GLU cc_start: 0.7872 (tt0) cc_final: 0.7589 (mm-30) REVERT: B 362 MET cc_start: 0.7984 (mmm) cc_final: 0.7429 (mpp) REVERT: B 376 LYS cc_start: 0.8908 (ttpp) cc_final: 0.8660 (tttt) REVERT: B 405 ASP cc_start: 0.6799 (m-30) cc_final: 0.6553 (t0) REVERT: B 522 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: B 600 HIS cc_start: 0.8587 (OUTLIER) cc_final: 0.8266 (t-170) REVERT: B 617 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7655 (tp40) REVERT: B 701 GLU cc_start: 0.7779 (tp30) cc_final: 0.7291 (tm-30) REVERT: B 778 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: C 52 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.6624 (mmt180) REVERT: C 108 ASN cc_start: 0.6457 (p0) cc_final: 0.5993 (t0) REVERT: C 187 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7931 (ptt180) REVERT: C 338 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: C 440 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8117 (pp) REVERT: C 741 ARG cc_start: 0.7555 (tpp80) cc_final: 0.6957 (mmm-85) REVERT: C 801 LYS cc_start: 0.7963 (mttt) cc_final: 0.7601 (mtpt) REVERT: D 39 HIS cc_start: 0.6953 (m90) cc_final: 0.6677 (m90) REVERT: D 52 ARG cc_start: 0.7640 (mtp85) cc_final: 0.7391 (mpt90) REVERT: D 57 TRP cc_start: 0.6891 (t60) cc_final: 0.6418 (t60) REVERT: D 114 ASP cc_start: 0.7426 (m-30) cc_final: 0.7214 (m-30) REVERT: D 259 LYS cc_start: 0.8750 (mttt) cc_final: 0.8194 (mppt) REVERT: D 280 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7940 (tt0) REVERT: D 348 GLU cc_start: 0.7828 (tt0) cc_final: 0.7595 (mm-30) REVERT: D 362 MET cc_start: 0.8007 (mmm) cc_final: 0.7424 (mpp) REVERT: D 395 THR cc_start: 0.8514 (m) cc_final: 0.8260 (m) REVERT: D 511 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.4403 (pp-130) REVERT: D 617 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7610 (tp40) REVERT: D 699 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7474 (mt-10) REVERT: D 701 GLU cc_start: 0.7798 (tp30) cc_final: 0.7266 (tm-30) REVERT: D 778 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7003 (mt-10) REVERT: D 807 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8248 (mp) outliers start: 105 outliers final: 55 residues processed: 358 average time/residue: 0.6538 time to fit residues: 268.5838 Evaluate side-chains 354 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 281 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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 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 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 34 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 257 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 398 GLU 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 C residue 17 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 159 ASN 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 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 525 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 680 GLU 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 118 ASP Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 511 MET Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 800 ILE 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: 3.9990 chunk 24 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 295 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 274 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN B 162 ASN B 248 ASN B 561 ASN C 536 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 488 HIS D 561 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.152412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131334 restraints weight = 30481.705| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.50 r_work: 0.3353 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26444 Z= 0.144 Angle : 0.500 5.804 35868 Z= 0.271 Chirality : 0.041 0.148 3888 Planarity : 0.003 0.036 4672 Dihedral : 6.040 79.431 3572 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.83 % Favored : 97.10 % Rotamer: Outliers : 3.90 % Allowed : 19.41 % Favored : 76.70 % 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: 0.40 (0.15), residues: 3176 helix: 0.95 (0.13), residues: 1692 sheet: -0.02 (0.23), residues: 476 loop : -0.61 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 187 TYR 0.020 0.002 TYR C 555 PHE 0.016 0.002 PHE B 156 TRP 0.013 0.001 TRP B 473 HIS 0.004 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00326 (26444) covalent geometry : angle 0.50045 (35868) hydrogen bonds : bond 0.04370 ( 1358) hydrogen bonds : angle 4.59693 ( 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 397 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 289 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.6565 (mmt90) REVERT: A 108 ASN cc_start: 0.6477 (p0) cc_final: 0.5960 (t0) REVERT: A 171 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7364 (m-80) REVERT: A 187 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7926 (ptt180) REVERT: A 241 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: A 338 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: A 432 HIS cc_start: 0.7309 (t70) cc_final: 0.6201 (p-80) REVERT: A 440 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7889 (pp) REVERT: A 698 GLU cc_start: 0.7031 (pp20) cc_final: 0.6702 (mp0) REVERT: A 801 LYS cc_start: 0.7958 (mttt) cc_final: 0.7590 (mtpt) REVERT: B 39 HIS cc_start: 0.6879 (m90) cc_final: 0.6629 (m90) REVERT: B 57 TRP cc_start: 0.6937 (t60) cc_final: 0.6489 (t60) REVERT: B 257 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: B 259 LYS cc_start: 0.8729 (mttt) cc_final: 0.8217 (mppt) REVERT: B 279 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7791 (mtp180) REVERT: B 280 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7952 (tt0) REVERT: B 348 GLU cc_start: 0.7879 (tt0) cc_final: 0.7580 (mm-30) REVERT: B 362 MET cc_start: 0.7971 (mmm) cc_final: 0.7414 (mpp) REVERT: B 376 LYS cc_start: 0.8914 (ttpp) cc_final: 0.8681 (tttt) REVERT: B 405 ASP cc_start: 0.6818 (m-30) cc_final: 0.6552 (t0) REVERT: B 514 HIS cc_start: 0.7104 (t-170) cc_final: 0.6727 (t70) REVERT: B 522 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: B 600 HIS cc_start: 0.8583 (OUTLIER) cc_final: 0.8260 (t-170) REVERT: B 617 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7649 (tp40) REVERT: B 701 GLU cc_start: 0.7786 (tp30) cc_final: 0.7309 (tm-30) REVERT: B 778 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6919 (mt-10) REVERT: B 807 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8244 (mp) REVERT: C 52 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.6648 (mmt180) REVERT: C 108 ASN cc_start: 0.6465 (p0) cc_final: 0.5976 (t0) REVERT: C 187 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7963 (ptt180) REVERT: C 338 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: C 440 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8110 (pp) REVERT: C 801 LYS cc_start: 0.7969 (mttt) cc_final: 0.7602 (mtpt) REVERT: D 39 HIS cc_start: 0.6915 (m90) cc_final: 0.6642 (m90) REVERT: D 52 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7361 (mpt90) REVERT: D 57 TRP cc_start: 0.6896 (t60) cc_final: 0.6402 (t60) REVERT: D 114 ASP cc_start: 0.7418 (m-30) cc_final: 0.7185 (m-30) REVERT: D 257 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: D 259 LYS cc_start: 0.8767 (mttt) cc_final: 0.8216 (mppt) REVERT: D 280 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7956 (tt0) REVERT: D 348 GLU cc_start: 0.7831 (tt0) cc_final: 0.7614 (mm-30) REVERT: D 362 MET cc_start: 0.7970 (mmm) cc_final: 0.7418 (mpp) REVERT: D 395 THR cc_start: 0.8540 (m) cc_final: 0.8293 (m) REVERT: D 514 HIS cc_start: 0.7087 (t-170) cc_final: 0.6737 (t70) REVERT: D 600 HIS cc_start: 0.8587 (OUTLIER) cc_final: 0.8308 (t-170) REVERT: D 617 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7650 (tp40) REVERT: D 699 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7499 (mt-10) REVERT: D 701 GLU cc_start: 0.7812 (tp30) cc_final: 0.7263 (tm-30) REVERT: D 778 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7003 (mt-10) REVERT: D 807 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8267 (mp) outliers start: 108 outliers final: 62 residues processed: 357 average time/residue: 0.6739 time to fit residues: 277.5713 Evaluate side-chains 367 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 285 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 214 VAL 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 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 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 171 TYR Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 257 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 398 GLU 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 772 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 35 VAL Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 52 ARG 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 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 525 LYS Chi-restraints excluded: chain C residue 597 MET 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 762 SER 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 187 ARG Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 597 MET Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 800 ILE 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: 2.9990 chunk 21 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 276 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN B 162 ASN B 248 ASN B 561 ASN B 749 ASN C 536 ASN D 162 ASN D 488 HIS D 561 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.147618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125637 restraints weight = 28951.354| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.48 r_work: 0.3259 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26444 Z= 0.203 Angle : 0.562 5.997 35868 Z= 0.303 Chirality : 0.044 0.154 3888 Planarity : 0.004 0.042 4672 Dihedral : 6.284 81.010 3572 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 3.90 % Allowed : 19.37 % Favored : 76.73 % 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: 0.24 (0.15), residues: 3176 helix: 0.75 (0.12), residues: 1688 sheet: 0.07 (0.22), residues: 504 loop : -0.64 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 187 TYR 0.020 0.002 TYR C 555 PHE 0.020 0.002 PHE D 156 TRP 0.016 0.002 TRP B 473 HIS 0.005 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00475 (26444) covalent geometry : angle 0.56162 (35868) hydrogen bonds : bond 0.05108 ( 1358) hydrogen bonds : angle 4.77352 ( 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 396 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 288 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.6621 (mmt90) REVERT: A 171 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: A 187 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7972 (ptt180) REVERT: A 241 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: A 338 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: A 391 TYR cc_start: 0.8193 (t80) cc_final: 0.7966 (t80) REVERT: A 432 HIS cc_start: 0.7376 (t70) cc_final: 0.6241 (p90) REVERT: A 440 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7844 (pp) REVERT: A 698 GLU cc_start: 0.7025 (pp20) cc_final: 0.6673 (mp0) REVERT: A 801 LYS cc_start: 0.8041 (mttt) cc_final: 0.7669 (mtpt) REVERT: B 39 HIS cc_start: 0.6990 (m90) cc_final: 0.6706 (m90) REVERT: B 57 TRP cc_start: 0.6921 (t60) cc_final: 0.6475 (t60) REVERT: B 62 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7050 (ttp-110) REVERT: B 110 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6890 (mm-30) REVERT: B 171 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8214 (m-80) REVERT: B 257 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: B 259 LYS cc_start: 0.8751 (mttt) cc_final: 0.8217 (mppt) REVERT: B 279 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7783 (mtp180) REVERT: B 280 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8063 (tt0) REVERT: B 348 GLU cc_start: 0.7979 (tt0) cc_final: 0.7578 (mm-30) REVERT: B 362 MET cc_start: 0.8005 (mmm) cc_final: 0.7422 (mpp) REVERT: B 405 ASP cc_start: 0.6809 (m-30) cc_final: 0.6552 (t0) REVERT: B 514 HIS cc_start: 0.7151 (t-170) cc_final: 0.6753 (t70) REVERT: B 522 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: B 600 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.8255 (t-170) REVERT: B 617 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7688 (tp40) REVERT: B 778 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: B 807 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8328 (mp) REVERT: C 52 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.6630 (mmt90) REVERT: C 108 ASN cc_start: 0.6517 (p0) cc_final: 0.5902 (t0) REVERT: C 187 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7999 (ptt180) REVERT: C 338 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: C 432 HIS cc_start: 0.7326 (t70) cc_final: 0.6223 (p90) REVERT: C 440 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8096 (pp) REVERT: C 698 GLU cc_start: 0.7000 (pp20) cc_final: 0.6612 (mp0) REVERT: C 801 LYS cc_start: 0.8059 (mttt) cc_final: 0.7684 (mtpt) REVERT: D 39 HIS cc_start: 0.6999 (m90) cc_final: 0.6693 (m90) REVERT: D 57 TRP cc_start: 0.6941 (t60) cc_final: 0.6461 (t60) REVERT: D 114 ASP cc_start: 0.7441 (m-30) cc_final: 0.7190 (m-30) REVERT: D 257 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: D 259 LYS cc_start: 0.8732 (mttt) cc_final: 0.8205 (mppt) REVERT: D 280 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8035 (tt0) REVERT: D 348 GLU cc_start: 0.7977 (tt0) cc_final: 0.7599 (mm-30) REVERT: D 362 MET cc_start: 0.7980 (mmm) cc_final: 0.7398 (mpp) REVERT: D 395 THR cc_start: 0.8578 (m) cc_final: 0.8323 (m) REVERT: D 514 HIS cc_start: 0.7151 (t-170) cc_final: 0.6769 (t70) REVERT: D 600 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.8295 (t-170) REVERT: D 617 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7684 (tp40) REVERT: D 778 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: D 807 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8350 (mp) outliers start: 108 outliers final: 61 residues processed: 355 average time/residue: 0.6976 time to fit residues: 283.0044 Evaluate side-chains 368 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 284 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 203 THR Chi-restraints excluded: chain A residue 214 VAL 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 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 62 ARG Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 257 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 398 GLU 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 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 35 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 187 ARG 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 525 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 706 GLN Chi-restraints excluded: chain C residue 762 SER 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 187 ARG Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 597 MET Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 778 GLU Chi-restraints excluded: chain D residue 800 ILE 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: 0.9980 chunk 52 optimal weight: 0.1980 chunk 187 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 chunk 225 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 264 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN B 162 ASN C 536 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 488 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.150973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129365 restraints weight = 28783.391| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.46 r_work: 0.3304 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1231 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= 0.110 Angle : 0.471 6.062 35868 Z= 0.254 Chirality : 0.040 0.145 3888 Planarity : 0.003 0.037 4672 Dihedral : 5.930 77.579 3572 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 3.32 % Allowed : 20.09 % Favored : 76.59 % 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: 0.46 (0.15), residues: 3176 helix: 1.02 (0.13), residues: 1692 sheet: -0.05 (0.23), residues: 476 loop : -0.58 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 711 TYR 0.021 0.001 TYR C 555 PHE 0.015 0.001 PHE C 156 TRP 0.013 0.001 TRP B 473 HIS 0.004 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00237 (26444) covalent geometry : angle 0.47123 (35868) hydrogen bonds : bond 0.03942 ( 1358) hydrogen bonds : angle 4.52241 ( 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 383 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 291 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7838 (mmm) REVERT: A 52 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.6623 (mmt180) REVERT: A 108 ASN cc_start: 0.6391 (p0) cc_final: 0.5935 (t0) REVERT: A 171 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: A 187 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7973 (ptt180) REVERT: A 241 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: A 432 HIS cc_start: 0.7314 (t70) cc_final: 0.6198 (p-80) REVERT: A 440 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7844 (pp) REVERT: A 698 GLU cc_start: 0.6995 (pp20) cc_final: 0.6658 (mp0) REVERT: A 796 SER cc_start: 0.7904 (OUTLIER) cc_final: 0.7452 (p) REVERT: A 801 LYS cc_start: 0.8003 (mttt) cc_final: 0.7629 (mtpt) REVERT: B 39 HIS cc_start: 0.6869 (m90) cc_final: 0.6634 (m90) REVERT: B 57 TRP cc_start: 0.6865 (t60) cc_final: 0.6464 (t60) REVERT: B 202 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.6846 (tptp) REVERT: B 257 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: B 259 LYS cc_start: 0.8769 (mttt) cc_final: 0.8234 (mppt) REVERT: B 279 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7741 (mtp180) REVERT: B 280 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7997 (tt0) REVERT: B 348 GLU cc_start: 0.7951 (tt0) cc_final: 0.7553 (mm-30) REVERT: B 362 MET cc_start: 0.8010 (mmm) cc_final: 0.7428 (mpp) REVERT: B 376 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8687 (tttt) REVERT: B 405 ASP cc_start: 0.6793 (m-30) cc_final: 0.6522 (t0) REVERT: B 522 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: B 600 HIS cc_start: 0.8574 (OUTLIER) cc_final: 0.8255 (t-170) REVERT: B 617 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7635 (tp40) REVERT: B 701 GLU cc_start: 0.7483 (tp30) cc_final: 0.6688 (tm-30) REVERT: B 807 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8317 (mp) REVERT: C 52 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6581 (mmt180) REVERT: C 108 ASN cc_start: 0.6428 (p0) cc_final: 0.5966 (t0) REVERT: C 187 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7963 (ptt180) REVERT: C 440 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8094 (pp) REVERT: C 741 ARG cc_start: 0.7573 (tpp80) cc_final: 0.6994 (mmm-85) REVERT: C 796 SER cc_start: 0.7910 (OUTLIER) cc_final: 0.7455 (p) REVERT: C 801 LYS cc_start: 0.8016 (mttt) cc_final: 0.7656 (mtpt) REVERT: D 39 HIS cc_start: 0.6917 (m90) cc_final: 0.6660 (m90) REVERT: D 52 ARG cc_start: 0.7584 (mtp85) cc_final: 0.7346 (mpt90) REVERT: D 57 TRP cc_start: 0.6817 (t60) cc_final: 0.6369 (t60) REVERT: D 114 ASP cc_start: 0.7412 (m-30) cc_final: 0.7152 (m-30) REVERT: D 257 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: D 259 LYS cc_start: 0.8735 (mttt) cc_final: 0.8200 (mppt) REVERT: D 280 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7990 (tt0) REVERT: D 348 GLU cc_start: 0.7953 (tt0) cc_final: 0.7589 (mm-30) REVERT: D 362 MET cc_start: 0.7989 (mmm) cc_final: 0.7415 (mpp) REVERT: D 395 THR cc_start: 0.8506 (m) cc_final: 0.8256 (m) REVERT: D 514 HIS cc_start: 0.7091 (t-170) cc_final: 0.6710 (t70) REVERT: D 617 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7564 (tp40) REVERT: D 699 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7476 (mt-10) REVERT: D 701 GLU cc_start: 0.7435 (tp30) cc_final: 0.6692 (tm-30) REVERT: D 807 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8265 (mp) outliers start: 92 outliers final: 44 residues processed: 354 average time/residue: 0.6948 time to fit residues: 281.9091 Evaluate side-chains 343 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 280 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 203 THR Chi-restraints excluded: chain A residue 214 VAL 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 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 706 GLN 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 187 ARG 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 279 ARG Chi-restraints excluded: chain B residue 360 THR 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 807 ILE Chi-restraints excluded: chain C residue 17 LEU 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 187 ARG Chi-restraints excluded: chain C residue 203 THR 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 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 706 GLN Chi-restraints excluded: chain C residue 762 SER 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 187 ARG Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 503 LEU 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: 0.9990 chunk 164 optimal weight: 0.2980 chunk 188 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN B 162 ASN B 248 ASN B 561 ASN C 536 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 488 HIS D 561 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.150761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129093 restraints weight = 28747.119| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.46 r_work: 0.3301 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26444 Z= 0.120 Angle : 0.479 5.961 35868 Z= 0.259 Chirality : 0.040 0.143 3888 Planarity : 0.003 0.037 4672 Dihedral : 5.660 77.910 3566 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 2.74 % Allowed : 20.74 % Favored : 76.52 % 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: 0.53 (0.15), residues: 3176 helix: 1.05 (0.13), residues: 1696 sheet: 0.03 (0.23), residues: 472 loop : -0.54 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 50 TYR 0.021 0.002 TYR C 555 PHE 0.016 0.001 PHE A 156 TRP 0.013 0.001 TRP B 473 HIS 0.003 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00265 (26444) covalent geometry : angle 0.47941 (35868) hydrogen bonds : bond 0.04013 ( 1358) hydrogen bonds : angle 4.50547 ( 3852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9030.80 seconds wall clock time: 154 minutes 17.87 seconds (9257.87 seconds total)