Starting phenix.real_space_refine on Wed Mar 4 02:41:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk7_32561/03_2026/7wk7_32561.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk7_32561/03_2026/7wk7_32561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wk7_32561/03_2026/7wk7_32561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk7_32561/03_2026/7wk7_32561.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wk7_32561/03_2026/7wk7_32561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk7_32561/03_2026/7wk7_32561.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6658 2.51 5 N 1684 2.21 5 O 1822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10206 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.33, per 1000 atoms: 0.23 Number of scatterers: 10206 At special positions: 0 Unit cell: (86.818, 127.612, 118.198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1822 8.00 N 1684 7.00 C 6658 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: 0.78 Conformation dependent library (CDL) restraints added in 507.3 milliseconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 66.5% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.609A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.849A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 79 through 106 removed outlier: 4.950A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 3.968A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.786A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 206 removed outlier: 3.935A pdb=" N ALA A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.508A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 241 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.777A pdb=" N ALA A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 374 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.716A pdb=" N GLU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.901A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.610A pdb=" N ILE A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 436 " --> pdb=" O MET A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 457 removed outlier: 3.826A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.676A pdb=" N LYS A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.786A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.581A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.834A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 4.131A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.624A pdb=" N LYS A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.507A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.824A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.805A pdb=" N LEU B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.606A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.892A pdb=" N TRP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 105 removed outlier: 3.633A pdb=" N LEU B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.920A pdb=" N LEU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 119' Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.685A pdb=" N VAL B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.685A pdb=" N HIS B 160 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 161' Processing helix chain 'B' and resid 180 through 206 removed outlier: 4.099A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 213 removed outlier: 3.565A pdb=" N VAL B 212 " --> pdb=" O GLY B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.627A pdb=" N PHE B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 removed outlier: 3.617A pdb=" N ALA B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.727A pdb=" N THR B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 374 removed outlier: 3.941A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 397 removed outlier: 3.993A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.552A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.539A pdb=" N VAL B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 457 removed outlier: 3.808A pdb=" N LEU B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 474 removed outlier: 3.651A pdb=" N LYS B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.770A pdb=" N ILE B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 515 removed outlier: 3.564A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 571 removed outlier: 3.612A pdb=" N LYS B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 571 " --> pdb=" O ASN B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 removed outlier: 3.885A pdb=" N TYR B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 686 removed outlier: 4.855A pdb=" N SER B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 3.824A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.525A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 removed outlier: 3.820A pdb=" N ALA B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 3.545A pdb=" N VAL B 22 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 164 removed outlier: 3.995A pdb=" N VAL A 163 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 175 " --> pdb=" O VAL A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA5, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.573A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'B' and resid 163 through 164 removed outlier: 4.235A pdb=" N VAL B 163 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR B 175 " --> pdb=" O VAL B 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AA9, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.556A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP B 661 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 548 " --> pdb=" O ASP B 661 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1650 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: 1.40 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3203 1.34 - 1.46: 1355 1.46 - 1.57: 5784 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10406 Sorted by residual: bond pdb=" C BCT B 800 " pdb=" O3 BCT B 800 " ideal model delta sigma weight residual 1.389 1.436 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C BCT A 800 " pdb=" O3 BCT A 800 " ideal model delta sigma weight residual 1.389 1.435 -0.046 2.00e-02 2.50e+03 5.34e+00 bond pdb=" C VAL B 653 " pdb=" N PRO B 654 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.24e-01 bond pdb=" C VAL A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.354 -0.021 2.34e-02 1.83e+03 7.75e-01 bond pdb=" N ASN A 167 " pdb=" CA ASN A 167 " ideal model delta sigma weight residual 1.457 1.468 -0.010 1.29e-02 6.01e+03 6.27e-01 ... (remaining 10401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 13718 1.01 - 2.02: 308 2.02 - 3.03: 69 3.03 - 4.04: 29 4.04 - 5.05: 18 Bond angle restraints: 14142 Sorted by residual: angle pdb=" C ARG B 79 " pdb=" N VAL B 80 " pdb=" CA VAL B 80 " ideal model delta sigma weight residual 120.62 124.97 -4.35 1.64e+00 3.72e-01 7.03e+00 angle pdb=" N LEU A 521 " pdb=" CA LEU A 521 " pdb=" C LEU A 521 " ideal model delta sigma weight residual 110.42 113.96 -3.54 1.46e+00 4.69e-01 5.86e+00 angle pdb=" N LEU B 521 " pdb=" CA LEU B 521 " pdb=" C LEU B 521 " ideal model delta sigma weight residual 110.42 113.93 -3.51 1.46e+00 4.69e-01 5.79e+00 angle pdb=" C ALA B 434 " pdb=" N ILE B 435 " pdb=" CA ILE B 435 " ideal model delta sigma weight residual 122.66 120.34 2.32 9.70e-01 1.06e+00 5.71e+00 angle pdb=" C GLY A 520 " pdb=" N LEU A 521 " pdb=" CA LEU A 521 " ideal model delta sigma weight residual 121.56 125.25 -3.69 1.56e+00 4.11e-01 5.59e+00 ... (remaining 14137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 5994 17.24 - 34.49: 153 34.49 - 51.73: 24 51.73 - 68.97: 3 68.97 - 86.22: 8 Dihedral angle restraints: 6182 sinusoidal: 2346 harmonic: 3836 Sorted by residual: dihedral pdb=" N LEU A 496 " pdb=" CA LEU A 496 " pdb=" CB LEU A 496 " pdb=" CG LEU A 496 " ideal model delta sinusoidal sigma weight residual -180.00 -123.81 -56.19 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CB GLU A 303 " pdb=" CG GLU A 303 " pdb=" CD GLU A 303 " pdb=" OE1 GLU A 303 " ideal model delta sinusoidal sigma weight residual 0.00 -82.21 82.21 1 3.00e+01 1.11e-03 9.22e+00 dihedral pdb=" N LEU B 727 " pdb=" CA LEU B 727 " pdb=" CB LEU B 727 " pdb=" CG LEU B 727 " ideal model delta sinusoidal sigma weight residual -180.00 -127.36 -52.64 3 1.50e+01 4.44e-03 9.13e+00 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 975 0.026 - 0.052: 469 0.052 - 0.077: 181 0.077 - 0.103: 75 0.103 - 0.129: 18 Chirality restraints: 1718 Sorted by residual: chirality pdb=" CA PRO B 553 " pdb=" N PRO B 553 " pdb=" C PRO B 553 " pdb=" CB PRO B 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA PRO A 553 " pdb=" N PRO A 553 " pdb=" C PRO A 553 " pdb=" CB PRO A 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA LEU A 668 " pdb=" N LEU A 668 " pdb=" C LEU A 668 " pdb=" CB LEU A 668 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1715 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 552 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO B 553 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 553 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 300 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO B 301 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.017 5.00e-02 4.00e+02 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1077 2.74 - 3.28: 10847 3.28 - 3.82: 16622 3.82 - 4.36: 19625 4.36 - 4.90: 33392 Nonbonded interactions: 81563 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.206 3.040 nonbonded pdb=" OG SER A 90 " pdb=" O GLY A 417 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASN B 475 " pdb=" OG1 THR B 477 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASN A 475 " pdb=" OG1 THR A 477 " model vdw 2.229 3.040 nonbonded pdb=" O THR A 485 " pdb=" OG SER A 489 " model vdw 2.237 3.040 ... (remaining 81558 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.520 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.180 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 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 : 0.002 0.047 10406 Z= 0.093 Angle : 0.440 5.051 14142 Z= 0.246 Chirality : 0.037 0.129 1718 Planarity : 0.003 0.031 1760 Dihedral : 8.683 86.216 3710 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.39 % Rotamer: Outliers : 3.12 % Allowed : 5.17 % Favored : 91.71 % 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: -3.90 (0.18), residues: 1322 helix: -2.07 (0.14), residues: 838 sheet: -4.06 (0.61), residues: 34 loop : -3.22 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.009 0.001 TYR A 127 PHE 0.009 0.001 PHE B 555 TRP 0.004 0.000 TRP A 83 HIS 0.001 0.000 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00176 (10406) covalent geometry : angle 0.43952 (14142) hydrogen bonds : bond 0.23070 ( 562) hydrogen bonds : angle 6.98527 ( 1650) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 438 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8008 (t70) cc_final: 0.7682 (p0) REVERT: A 195 LEU cc_start: 0.8361 (tp) cc_final: 0.8161 (tp) REVERT: A 213 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7424 (mtm-85) REVERT: A 236 LEU cc_start: 0.8466 (tp) cc_final: 0.8144 (tt) REVERT: A 237 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8377 (tttt) REVERT: A 244 THR cc_start: 0.8102 (p) cc_final: 0.7341 (p) REVERT: A 245 LYS cc_start: 0.7687 (ttmm) cc_final: 0.7344 (ttmm) REVERT: A 247 TYR cc_start: 0.7572 (m-10) cc_final: 0.6639 (m-10) REVERT: A 262 GLN cc_start: 0.7474 (mt0) cc_final: 0.7184 (mt0) REVERT: A 276 LEU cc_start: 0.8432 (tp) cc_final: 0.7941 (tt) REVERT: A 280 ILE cc_start: 0.8409 (mt) cc_final: 0.8033 (mm) REVERT: A 350 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6449 (tm) REVERT: A 361 TYR cc_start: 0.8286 (t80) cc_final: 0.8029 (t80) REVERT: A 369 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7733 (mmtt) REVERT: A 384 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6573 (mm-30) REVERT: A 385 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.8005 (t80) REVERT: A 391 SER cc_start: 0.8553 (m) cc_final: 0.8224 (p) REVERT: A 394 PHE cc_start: 0.8343 (t80) cc_final: 0.7437 (t80) REVERT: A 398 PHE cc_start: 0.7707 (m-80) cc_final: 0.7392 (m-80) REVERT: A 432 MET cc_start: 0.7318 (tpt) cc_final: 0.6933 (tpt) REVERT: A 447 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8322 (mtpp) REVERT: A 448 SER cc_start: 0.9040 (m) cc_final: 0.8530 (t) REVERT: A 470 ARG cc_start: 0.7426 (tpp80) cc_final: 0.7180 (tpp80) REVERT: A 475 ASN cc_start: 0.7165 (t0) cc_final: 0.6658 (t0) REVERT: A 478 ASP cc_start: 0.6763 (m-30) cc_final: 0.6187 (m-30) REVERT: A 484 PHE cc_start: 0.8603 (t80) cc_final: 0.8345 (t80) REVERT: A 503 LEU cc_start: 0.8278 (mt) cc_final: 0.7953 (mp) REVERT: A 556 TYR cc_start: 0.8097 (p90) cc_final: 0.7760 (p90) REVERT: A 560 ASP cc_start: 0.7818 (m-30) cc_final: 0.6417 (m-30) REVERT: A 563 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8109 (mtpp) REVERT: A 684 GLN cc_start: 0.8627 (tp40) cc_final: 0.8384 (tp-100) REVERT: A 698 ASP cc_start: 0.7124 (t0) cc_final: 0.6828 (t0) REVERT: B 71 ILE cc_start: 0.8640 (tt) cc_final: 0.8374 (tp) REVERT: B 105 TYR cc_start: 0.8456 (m-10) cc_final: 0.8240 (m-80) REVERT: B 160 HIS cc_start: 0.7694 (t-90) cc_final: 0.7386 (t-90) REVERT: B 195 LEU cc_start: 0.8254 (tp) cc_final: 0.7987 (tp) REVERT: B 207 GLN cc_start: 0.7978 (tp40) cc_final: 0.7354 (mm110) REVERT: B 213 ARG cc_start: 0.7589 (mtt180) cc_final: 0.7183 (mtt180) REVERT: B 244 THR cc_start: 0.7957 (p) cc_final: 0.7295 (p) REVERT: B 247 TYR cc_start: 0.7667 (m-10) cc_final: 0.6907 (m-10) REVERT: B 276 LEU cc_start: 0.8647 (tp) cc_final: 0.8312 (tt) REVERT: B 277 LEU cc_start: 0.8523 (tp) cc_final: 0.8257 (tp) REVERT: B 286 LYS cc_start: 0.8721 (tppt) cc_final: 0.8360 (ttmm) REVERT: B 287 GLU cc_start: 0.7710 (tp30) cc_final: 0.6739 (tp30) REVERT: B 303 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: B 309 ILE cc_start: 0.8478 (tp) cc_final: 0.8240 (pt) REVERT: B 311 THR cc_start: 0.7679 (p) cc_final: 0.7411 (t) REVERT: B 355 SER cc_start: 0.8654 (m) cc_final: 0.8059 (p) REVERT: B 366 SER cc_start: 0.8430 (t) cc_final: 0.7883 (p) REVERT: B 377 TYR cc_start: 0.7857 (p90) cc_final: 0.7190 (p90) REVERT: B 378 VAL cc_start: 0.8437 (t) cc_final: 0.7893 (p) REVERT: B 391 SER cc_start: 0.8479 (m) cc_final: 0.8137 (p) REVERT: B 394 PHE cc_start: 0.8446 (t80) cc_final: 0.7315 (t80) REVERT: B 398 PHE cc_start: 0.7613 (m-80) cc_final: 0.7390 (m-80) REVERT: B 414 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6768 (tm-30) REVERT: B 422 VAL cc_start: 0.7738 (t) cc_final: 0.7268 (p) REVERT: B 432 MET cc_start: 0.7454 (tpt) cc_final: 0.7085 (tpt) REVERT: B 447 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8307 (mtpt) REVERT: B 448 SER cc_start: 0.9105 (m) cc_final: 0.8706 (t) REVERT: B 473 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8125 (mtpt) REVERT: B 475 ASN cc_start: 0.7284 (t0) cc_final: 0.6543 (t0) REVERT: B 478 ASP cc_start: 0.7002 (m-30) cc_final: 0.6217 (m-30) REVERT: B 503 LEU cc_start: 0.8397 (mt) cc_final: 0.8103 (mp) REVERT: B 573 ASP cc_start: 0.7590 (t0) cc_final: 0.5764 (t0) REVERT: B 727 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7623 (mm) outliers start: 35 outliers final: 9 residues processed: 464 average time/residue: 0.1154 time to fit residues: 72.0292 Evaluate side-chains 380 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 367 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 382 ASN A 656 HIS B 101 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN B 457 ASN B 464 GLN B 474 GLN B 731 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.123276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104453 restraints weight = 17973.576| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.87 r_work: 0.3268 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10406 Z= 0.164 Angle : 0.617 9.477 14142 Z= 0.317 Chirality : 0.043 0.147 1718 Planarity : 0.005 0.038 1760 Dihedral : 6.030 80.116 1443 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.19 % Allowed : 15.86 % Favored : 79.95 % 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: -2.07 (0.22), residues: 1322 helix: -0.49 (0.17), residues: 836 sheet: -3.61 (0.74), residues: 36 loop : -2.79 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 576 TYR 0.015 0.001 TYR A 377 PHE 0.021 0.001 PHE A 130 TRP 0.005 0.001 TRP A 74 HIS 0.013 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00366 (10406) covalent geometry : angle 0.61657 (14142) hydrogen bonds : bond 0.04954 ( 562) hydrogen bonds : angle 4.38964 ( 1650) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 379 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7752 (m-10) cc_final: 0.7530 (m-10) REVERT: A 48 ASP cc_start: 0.8175 (t70) cc_final: 0.7799 (p0) REVERT: A 87 ASP cc_start: 0.7243 (m-30) cc_final: 0.6833 (t0) REVERT: A 94 THR cc_start: 0.8254 (m) cc_final: 0.7863 (p) REVERT: A 195 LEU cc_start: 0.8552 (tp) cc_final: 0.8290 (tp) REVERT: A 213 ARG cc_start: 0.8139 (mtt180) cc_final: 0.7929 (mtm180) REVERT: A 236 LEU cc_start: 0.8680 (tp) cc_final: 0.8173 (tt) REVERT: A 244 THR cc_start: 0.8394 (p) cc_final: 0.8186 (t) REVERT: A 245 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7811 (ttmm) REVERT: A 247 TYR cc_start: 0.8115 (m-10) cc_final: 0.7345 (m-10) REVERT: A 263 ASN cc_start: 0.8495 (t0) cc_final: 0.8197 (t0) REVERT: A 349 MET cc_start: 0.6700 (ptp) cc_final: 0.6500 (ptp) REVERT: A 369 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7831 (mmtt) REVERT: A 370 VAL cc_start: 0.8514 (t) cc_final: 0.8309 (p) REVERT: A 378 VAL cc_start: 0.8246 (t) cc_final: 0.7920 (p) REVERT: A 384 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7133 (mm-30) REVERT: A 385 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7887 (t80) REVERT: A 391 SER cc_start: 0.8692 (m) cc_final: 0.8322 (p) REVERT: A 394 PHE cc_start: 0.8587 (t80) cc_final: 0.7757 (t80) REVERT: A 398 PHE cc_start: 0.8076 (m-80) cc_final: 0.7695 (m-80) REVERT: A 432 MET cc_start: 0.7837 (tpt) cc_final: 0.7389 (tpt) REVERT: A 436 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8477 (m) REVERT: A 447 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8443 (mtpp) REVERT: A 484 PHE cc_start: 0.8733 (t80) cc_final: 0.8507 (t80) REVERT: A 556 TYR cc_start: 0.8552 (p90) cc_final: 0.8042 (p90) REVERT: A 560 ASP cc_start: 0.8394 (m-30) cc_final: 0.7160 (m-30) REVERT: A 573 ASP cc_start: 0.7878 (t0) cc_final: 0.7631 (t0) REVERT: A 581 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7794 (mtp85) REVERT: A 677 ARG cc_start: 0.8197 (ptm-80) cc_final: 0.7849 (ttt-90) REVERT: A 698 ASP cc_start: 0.7702 (t0) cc_final: 0.7357 (t0) REVERT: B 66 LYS cc_start: 0.8339 (tppt) cc_final: 0.8094 (tppt) REVERT: B 69 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8292 (mt) REVERT: B 100 LEU cc_start: 0.8983 (tp) cc_final: 0.8702 (tp) REVERT: B 195 LEU cc_start: 0.8584 (tp) cc_final: 0.8180 (tp) REVERT: B 207 GLN cc_start: 0.8216 (tp40) cc_final: 0.8005 (mm110) REVERT: B 213 ARG cc_start: 0.8206 (mtt180) cc_final: 0.7671 (mtt180) REVERT: B 244 THR cc_start: 0.8415 (p) cc_final: 0.7871 (p) REVERT: B 276 LEU cc_start: 0.8665 (tp) cc_final: 0.8415 (tt) REVERT: B 287 GLU cc_start: 0.8040 (tp30) cc_final: 0.7054 (tp30) REVERT: B 309 ILE cc_start: 0.8437 (tp) cc_final: 0.8226 (pt) REVERT: B 318 ASN cc_start: 0.8386 (t0) cc_final: 0.8171 (t0) REVERT: B 355 SER cc_start: 0.8597 (m) cc_final: 0.8158 (p) REVERT: B 361 TYR cc_start: 0.8505 (t80) cc_final: 0.8104 (t80) REVERT: B 366 SER cc_start: 0.8554 (t) cc_final: 0.8327 (p) REVERT: B 367 VAL cc_start: 0.8783 (t) cc_final: 0.8463 (m) REVERT: B 370 VAL cc_start: 0.9027 (t) cc_final: 0.8795 (p) REVERT: B 382 ASN cc_start: 0.8559 (m-40) cc_final: 0.7648 (t0) REVERT: B 391 SER cc_start: 0.8680 (m) cc_final: 0.8367 (p) REVERT: B 394 PHE cc_start: 0.8540 (t80) cc_final: 0.7415 (t80) REVERT: B 398 PHE cc_start: 0.8016 (m-80) cc_final: 0.7649 (m-80) REVERT: B 414 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7088 (tm-30) REVERT: B 432 MET cc_start: 0.8048 (tpt) cc_final: 0.7621 (tpt) REVERT: B 447 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8448 (mtpt) REVERT: B 473 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8350 (mtpt) REVERT: B 560 ASP cc_start: 0.8119 (m-30) cc_final: 0.7900 (m-30) REVERT: B 587 ARG cc_start: 0.7393 (mmm160) cc_final: 0.7150 (tpt170) REVERT: B 702 LYS cc_start: 0.8191 (tptp) cc_final: 0.7407 (ttmm) outliers start: 47 outliers final: 27 residues processed: 404 average time/residue: 0.1114 time to fit residues: 60.9101 Evaluate side-chains 374 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 344 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 681 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 94 optimal weight: 0.0030 chunk 78 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 684 GLN B 34 GLN B 135 HIS B 160 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.120802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.101683 restraints weight = 17824.864| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.84 r_work: 0.3227 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10406 Z= 0.164 Angle : 0.631 9.931 14142 Z= 0.324 Chirality : 0.043 0.189 1718 Planarity : 0.004 0.040 1760 Dihedral : 5.484 80.957 1433 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.46 % Allowed : 19.07 % Favored : 76.47 % 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: -1.38 (0.23), residues: 1322 helix: 0.01 (0.17), residues: 848 sheet: -3.25 (0.76), residues: 36 loop : -2.48 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 38 TYR 0.014 0.001 TYR B 578 PHE 0.018 0.001 PHE B 272 TRP 0.004 0.001 TRP A 74 HIS 0.014 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00362 (10406) covalent geometry : angle 0.63130 (14142) hydrogen bonds : bond 0.04322 ( 562) hydrogen bonds : angle 4.16578 ( 1650) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 351 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8163 (tpp-160) cc_final: 0.7798 (mpp-170) REVERT: A 87 ASP cc_start: 0.7261 (m-30) cc_final: 0.6986 (t0) REVERT: A 94 THR cc_start: 0.8359 (m) cc_final: 0.8007 (p) REVERT: A 195 LEU cc_start: 0.8644 (tp) cc_final: 0.8312 (tp) REVERT: A 236 LEU cc_start: 0.8752 (tp) cc_final: 0.8324 (tt) REVERT: A 240 LEU cc_start: 0.8516 (mm) cc_final: 0.8273 (mp) REVERT: A 244 THR cc_start: 0.8387 (p) cc_final: 0.8153 (p) REVERT: A 245 LYS cc_start: 0.8218 (ttmm) cc_final: 0.7848 (ttmm) REVERT: A 247 TYR cc_start: 0.8139 (m-10) cc_final: 0.7368 (m-10) REVERT: A 251 LEU cc_start: 0.8818 (mm) cc_final: 0.8369 (mm) REVERT: A 369 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8082 (mmtt) REVERT: A 370 VAL cc_start: 0.8636 (t) cc_final: 0.8431 (p) REVERT: A 384 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7105 (mm-30) REVERT: A 385 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7866 (t80) REVERT: A 391 SER cc_start: 0.8635 (m) cc_final: 0.8258 (p) REVERT: A 394 PHE cc_start: 0.8503 (t80) cc_final: 0.7665 (t80) REVERT: A 398 PHE cc_start: 0.8024 (m-80) cc_final: 0.7600 (m-80) REVERT: A 432 MET cc_start: 0.7748 (tpt) cc_final: 0.7377 (tpt) REVERT: A 436 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8503 (m) REVERT: A 447 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8366 (ttmt) REVERT: A 470 ARG cc_start: 0.7977 (tpp80) cc_final: 0.7736 (tpp80) REVERT: A 475 ASN cc_start: 0.7187 (m-40) cc_final: 0.6949 (m-40) REVERT: A 478 ASP cc_start: 0.7249 (m-30) cc_final: 0.7012 (m-30) REVERT: A 531 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8177 (mmmm) REVERT: A 563 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8364 (mmmt) REVERT: A 573 ASP cc_start: 0.7970 (t0) cc_final: 0.7630 (t0) REVERT: A 677 ARG cc_start: 0.8270 (ptm-80) cc_final: 0.7704 (ttt90) REVERT: A 698 ASP cc_start: 0.7681 (t0) cc_final: 0.7307 (t0) REVERT: B 66 LYS cc_start: 0.8369 (tppt) cc_final: 0.8139 (tppt) REVERT: B 69 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8357 (mt) REVERT: B 71 ILE cc_start: 0.8632 (tt) cc_final: 0.8396 (tp) REVERT: B 155 MET cc_start: 0.8216 (mpp) cc_final: 0.7830 (mpp) REVERT: B 181 ARG cc_start: 0.8514 (tmm-80) cc_final: 0.8238 (ttt-90) REVERT: B 195 LEU cc_start: 0.8624 (tp) cc_final: 0.8251 (tp) REVERT: B 213 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7844 (mtt180) REVERT: B 244 THR cc_start: 0.8488 (p) cc_final: 0.7765 (t) REVERT: B 259 GLU cc_start: 0.8602 (tt0) cc_final: 0.8275 (tt0) REVERT: B 276 LEU cc_start: 0.8693 (tp) cc_final: 0.8481 (tt) REVERT: B 287 GLU cc_start: 0.8070 (tp30) cc_final: 0.7115 (tp30) REVERT: B 309 ILE cc_start: 0.8453 (tp) cc_final: 0.8227 (pt) REVERT: B 355 SER cc_start: 0.8598 (m) cc_final: 0.8162 (p) REVERT: B 361 TYR cc_start: 0.8581 (t80) cc_final: 0.8269 (t80) REVERT: B 366 SER cc_start: 0.8607 (t) cc_final: 0.8341 (p) REVERT: B 367 VAL cc_start: 0.8854 (t) cc_final: 0.8521 (m) REVERT: B 378 VAL cc_start: 0.8545 (t) cc_final: 0.8279 (m) REVERT: B 382 ASN cc_start: 0.8546 (m-40) cc_final: 0.7792 (t0) REVERT: B 384 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 391 SER cc_start: 0.8679 (m) cc_final: 0.8280 (p) REVERT: B 394 PHE cc_start: 0.8474 (t80) cc_final: 0.7410 (t80) REVERT: B 398 PHE cc_start: 0.7989 (m-80) cc_final: 0.7688 (m-80) REVERT: B 414 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 432 MET cc_start: 0.8041 (tpt) cc_final: 0.7649 (tpt) REVERT: B 447 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8461 (mtpt) REVERT: B 473 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8265 (mtpt) REVERT: B 478 ASP cc_start: 0.7479 (m-30) cc_final: 0.7275 (m-30) REVERT: B 531 LYS cc_start: 0.8439 (mmmt) cc_final: 0.7823 (mmmt) REVERT: B 682 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7800 (mt-10) REVERT: B 714 ARG cc_start: 0.8514 (mtm-85) cc_final: 0.8171 (mtm-85) outliers start: 50 outliers final: 35 residues processed: 379 average time/residue: 0.1149 time to fit residues: 58.0593 Evaluate side-chains 361 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 323 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 580 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 0.0470 chunk 55 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 248 ASN A 382 ASN A 475 ASN A 656 HIS A 684 GLN B 34 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.120762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101271 restraints weight = 17945.286| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.95 r_work: 0.3216 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10406 Z= 0.152 Angle : 0.611 9.659 14142 Z= 0.316 Chirality : 0.044 0.218 1718 Planarity : 0.004 0.040 1760 Dihedral : 5.563 81.560 1433 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.72 % Allowed : 20.77 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.23), residues: 1322 helix: 0.23 (0.18), residues: 852 sheet: -2.92 (0.81), residues: 36 loop : -2.31 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 38 TYR 0.011 0.001 TYR B 578 PHE 0.014 0.001 PHE A 484 TRP 0.006 0.001 TRP A 472 HIS 0.007 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00339 (10406) covalent geometry : angle 0.61115 (14142) hydrogen bonds : bond 0.04204 ( 562) hydrogen bonds : angle 4.02926 ( 1650) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 339 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8282 (tpp-160) cc_final: 0.7641 (mpp-170) REVERT: A 87 ASP cc_start: 0.7325 (m-30) cc_final: 0.7037 (t0) REVERT: A 88 ILE cc_start: 0.7457 (mm) cc_final: 0.7102 (mm) REVERT: A 94 THR cc_start: 0.8359 (m) cc_final: 0.7941 (p) REVERT: A 195 LEU cc_start: 0.8613 (tp) cc_final: 0.8339 (tp) REVERT: A 236 LEU cc_start: 0.8749 (tp) cc_final: 0.8313 (tt) REVERT: A 245 LYS cc_start: 0.8264 (ttmm) cc_final: 0.7911 (ttmm) REVERT: A 247 TYR cc_start: 0.8192 (m-10) cc_final: 0.7538 (m-10) REVERT: A 251 LEU cc_start: 0.8745 (mm) cc_final: 0.8451 (mm) REVERT: A 259 GLU cc_start: 0.8449 (tt0) cc_final: 0.8077 (tp30) REVERT: A 369 LYS cc_start: 0.8241 (mmtt) cc_final: 0.8033 (mmtt) REVERT: A 370 VAL cc_start: 0.8541 (t) cc_final: 0.8340 (p) REVERT: A 384 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7259 (mm-30) REVERT: A 385 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7855 (t80) REVERT: A 391 SER cc_start: 0.8729 (m) cc_final: 0.8323 (p) REVERT: A 394 PHE cc_start: 0.8568 (t80) cc_final: 0.7893 (t80) REVERT: A 398 PHE cc_start: 0.8046 (m-80) cc_final: 0.7693 (m-80) REVERT: A 414 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 432 MET cc_start: 0.7889 (tpt) cc_final: 0.7521 (tpt) REVERT: A 436 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8498 (m) REVERT: A 447 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8421 (ttmt) REVERT: A 470 ARG cc_start: 0.8000 (tpp80) cc_final: 0.7760 (tpp80) REVERT: A 475 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7381 (m-40) REVERT: A 531 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8098 (mmmm) REVERT: A 563 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8336 (mmmt) REVERT: A 573 ASP cc_start: 0.7965 (t0) cc_final: 0.7569 (t0) REVERT: A 581 ARG cc_start: 0.8056 (mmt180) cc_final: 0.7726 (mtp85) REVERT: A 677 ARG cc_start: 0.8363 (ptm-80) cc_final: 0.7832 (ttt90) REVERT: A 698 ASP cc_start: 0.7701 (t0) cc_final: 0.7314 (t0) REVERT: B 69 LEU cc_start: 0.8458 (mt) cc_final: 0.8251 (mt) REVERT: B 71 ILE cc_start: 0.8662 (tt) cc_final: 0.8310 (tp) REVERT: B 155 MET cc_start: 0.8283 (mpp) cc_final: 0.7965 (mpp) REVERT: B 195 LEU cc_start: 0.8619 (tp) cc_final: 0.8246 (tp) REVERT: B 213 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7925 (ttp-170) REVERT: B 244 THR cc_start: 0.8483 (p) cc_final: 0.7498 (t) REVERT: B 259 GLU cc_start: 0.8562 (tt0) cc_final: 0.8251 (tt0) REVERT: B 276 LEU cc_start: 0.8636 (tp) cc_final: 0.8430 (tt) REVERT: B 287 GLU cc_start: 0.8173 (tp30) cc_final: 0.7164 (tp30) REVERT: B 309 ILE cc_start: 0.8454 (tp) cc_final: 0.8199 (pt) REVERT: B 329 LYS cc_start: 0.8315 (pttt) cc_final: 0.8102 (pttt) REVERT: B 361 TYR cc_start: 0.8558 (t80) cc_final: 0.8230 (t80) REVERT: B 366 SER cc_start: 0.8509 (t) cc_final: 0.8292 (p) REVERT: B 367 VAL cc_start: 0.8708 (t) cc_final: 0.8507 (m) REVERT: B 373 THR cc_start: 0.8471 (m) cc_final: 0.8090 (t) REVERT: B 378 VAL cc_start: 0.8578 (t) cc_final: 0.8340 (m) REVERT: B 382 ASN cc_start: 0.8569 (m-40) cc_final: 0.8010 (t0) REVERT: B 384 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7531 (mm-30) REVERT: B 391 SER cc_start: 0.8740 (m) cc_final: 0.8317 (p) REVERT: B 394 PHE cc_start: 0.8540 (t80) cc_final: 0.7550 (t80) REVERT: B 398 PHE cc_start: 0.8013 (m-80) cc_final: 0.7660 (m-80) REVERT: B 432 MET cc_start: 0.8067 (tpt) cc_final: 0.7670 (tpt) REVERT: B 447 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8461 (mtpt) REVERT: B 473 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8303 (mtpt) REVERT: B 475 ASN cc_start: 0.7722 (m-40) cc_final: 0.7379 (m-40) REVERT: B 478 ASP cc_start: 0.7627 (m-30) cc_final: 0.7293 (m-30) REVERT: B 681 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8345 (ttmm) REVERT: B 714 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.8168 (mtm-85) outliers start: 53 outliers final: 34 residues processed: 367 average time/residue: 0.1170 time to fit residues: 57.2975 Evaluate side-chains 361 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 323 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 112 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 0.0020 chunk 104 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.0060 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 457 ASN A 475 ASN A 656 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.121753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102534 restraints weight = 18060.865| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.93 r_work: 0.3233 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10406 Z= 0.136 Angle : 0.619 9.641 14142 Z= 0.315 Chirality : 0.043 0.183 1718 Planarity : 0.004 0.039 1760 Dihedral : 5.596 82.738 1433 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.46 % Allowed : 22.37 % Favored : 73.17 % 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: -0.82 (0.23), residues: 1322 helix: 0.40 (0.18), residues: 850 sheet: -2.44 (0.88), residues: 36 loop : -2.21 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 38 TYR 0.018 0.001 TYR B 105 PHE 0.011 0.001 PHE A 484 TRP 0.004 0.001 TRP A 472 HIS 0.012 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00304 (10406) covalent geometry : angle 0.61924 (14142) hydrogen bonds : bond 0.03997 ( 562) hydrogen bonds : angle 3.94006 ( 1650) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 318 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8209 (tpp-160) cc_final: 0.7614 (mpp-170) REVERT: A 87 ASP cc_start: 0.7324 (m-30) cc_final: 0.6964 (t0) REVERT: A 88 ILE cc_start: 0.7476 (mm) cc_final: 0.7268 (mm) REVERT: A 94 THR cc_start: 0.8365 (m) cc_final: 0.7972 (p) REVERT: A 103 MET cc_start: 0.8022 (mmm) cc_final: 0.7816 (mmm) REVERT: A 195 LEU cc_start: 0.8588 (tp) cc_final: 0.8334 (tp) REVERT: A 236 LEU cc_start: 0.8765 (tp) cc_final: 0.8428 (tt) REVERT: A 245 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7880 (ttmm) REVERT: A 247 TYR cc_start: 0.8132 (m-10) cc_final: 0.7575 (m-10) REVERT: A 251 LEU cc_start: 0.8667 (mm) cc_final: 0.8363 (mm) REVERT: A 370 VAL cc_start: 0.8599 (t) cc_final: 0.8381 (p) REVERT: A 384 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 385 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.7780 (t80) REVERT: A 391 SER cc_start: 0.8714 (m) cc_final: 0.8349 (p) REVERT: A 394 PHE cc_start: 0.8588 (t80) cc_final: 0.7951 (t80) REVERT: A 395 SER cc_start: 0.8154 (m) cc_final: 0.7949 (p) REVERT: A 398 PHE cc_start: 0.8054 (m-80) cc_final: 0.7702 (m-80) REVERT: A 414 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7392 (tm-30) REVERT: A 432 MET cc_start: 0.7719 (tpt) cc_final: 0.7349 (tpt) REVERT: A 436 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8513 (m) REVERT: A 447 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8467 (mtpt) REVERT: A 470 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7784 (tpp80) REVERT: A 475 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7378 (m-40) REVERT: A 478 ASP cc_start: 0.7595 (m-30) cc_final: 0.7389 (m-30) REVERT: A 531 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8101 (mmmm) REVERT: A 560 ASP cc_start: 0.8380 (m-30) cc_final: 0.7190 (m-30) REVERT: A 563 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8442 (mmmt) REVERT: A 573 ASP cc_start: 0.7949 (t0) cc_final: 0.7581 (t0) REVERT: A 581 ARG cc_start: 0.8039 (mmt180) cc_final: 0.7678 (mtp85) REVERT: A 677 ARG cc_start: 0.8318 (ptm-80) cc_final: 0.7836 (ttt90) REVERT: A 698 ASP cc_start: 0.7666 (t0) cc_final: 0.7297 (t0) REVERT: A 704 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7803 (tm-30) REVERT: B 71 ILE cc_start: 0.8609 (tt) cc_final: 0.8257 (tp) REVERT: B 155 MET cc_start: 0.8301 (mpp) cc_final: 0.8000 (mpp) REVERT: B 181 ARG cc_start: 0.8522 (tmm-80) cc_final: 0.8238 (ttt-90) REVERT: B 195 LEU cc_start: 0.8568 (tp) cc_final: 0.8215 (tp) REVERT: B 213 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7715 (mtt180) REVERT: B 240 LEU cc_start: 0.8863 (mm) cc_final: 0.8648 (mp) REVERT: B 244 THR cc_start: 0.8551 (p) cc_final: 0.8017 (p) REVERT: B 247 TYR cc_start: 0.7995 (m-80) cc_final: 0.7705 (m-10) REVERT: B 287 GLU cc_start: 0.8160 (tp30) cc_final: 0.7149 (tp30) REVERT: B 329 LYS cc_start: 0.8367 (pttt) cc_final: 0.8082 (ptmm) REVERT: B 367 VAL cc_start: 0.8635 (t) cc_final: 0.8415 (m) REVERT: B 373 THR cc_start: 0.8437 (m) cc_final: 0.8106 (t) REVERT: B 377 TYR cc_start: 0.8096 (p90) cc_final: 0.7609 (p90) REVERT: B 382 ASN cc_start: 0.8525 (m-40) cc_final: 0.7977 (t0) REVERT: B 391 SER cc_start: 0.8733 (m) cc_final: 0.8319 (p) REVERT: B 394 PHE cc_start: 0.8557 (t80) cc_final: 0.8127 (t80) REVERT: B 432 MET cc_start: 0.7987 (tpt) cc_final: 0.7606 (tpt) REVERT: B 473 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8198 (mtpp) REVERT: B 475 ASN cc_start: 0.7704 (m-40) cc_final: 0.7456 (m-40) REVERT: B 478 ASP cc_start: 0.7693 (m-30) cc_final: 0.7383 (m-30) REVERT: B 580 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7740 (mmmt) REVERT: B 677 ARG cc_start: 0.8538 (tpt-90) cc_final: 0.8197 (tpt-90) REVERT: B 681 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8190 (mttp) REVERT: B 714 ARG cc_start: 0.8527 (mtm-85) cc_final: 0.8174 (mtm-85) outliers start: 50 outliers final: 34 residues processed: 349 average time/residue: 0.1092 time to fit residues: 51.5666 Evaluate side-chains 341 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 135 HIS A 382 ASN A 457 ASN A 475 ASN A 656 HIS A 728 HIS B 34 GLN B 135 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.116971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097794 restraints weight = 18205.879| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.91 r_work: 0.3152 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 10406 Z= 0.277 Angle : 0.706 10.130 14142 Z= 0.365 Chirality : 0.048 0.214 1718 Planarity : 0.005 0.053 1760 Dihedral : 5.744 81.132 1431 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.35 % Allowed : 22.55 % Favored : 72.10 % 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: -0.94 (0.23), residues: 1322 helix: 0.26 (0.18), residues: 862 sheet: -2.22 (0.91), residues: 36 loop : -2.25 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 38 TYR 0.020 0.002 TYR B 20 PHE 0.015 0.001 PHE B 667 TRP 0.008 0.002 TRP B 518 HIS 0.013 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00603 (10406) covalent geometry : angle 0.70587 (14142) hydrogen bonds : bond 0.04641 ( 562) hydrogen bonds : angle 4.06926 ( 1650) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 321 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7341 (m-30) cc_final: 0.7094 (t0) REVERT: A 88 ILE cc_start: 0.7551 (mm) cc_final: 0.7309 (mm) REVERT: A 195 LEU cc_start: 0.8622 (tp) cc_final: 0.8347 (tp) REVERT: A 236 LEU cc_start: 0.8802 (tp) cc_final: 0.8397 (tt) REVERT: A 245 LYS cc_start: 0.8379 (ttmm) cc_final: 0.7954 (ttmm) REVERT: A 247 TYR cc_start: 0.8206 (m-10) cc_final: 0.7527 (m-10) REVERT: A 277 LEU cc_start: 0.8712 (tp) cc_final: 0.8462 (tp) REVERT: A 369 LYS cc_start: 0.8361 (mmtt) cc_final: 0.8016 (mmtt) REVERT: A 384 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7404 (mm-30) REVERT: A 385 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7739 (t80) REVERT: A 391 SER cc_start: 0.8753 (m) cc_final: 0.8364 (p) REVERT: A 394 PHE cc_start: 0.8642 (t80) cc_final: 0.8432 (t80) REVERT: A 395 SER cc_start: 0.8278 (m) cc_final: 0.8043 (p) REVERT: A 414 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7515 (tm-30) REVERT: A 432 MET cc_start: 0.7874 (tpt) cc_final: 0.7516 (tpt) REVERT: A 436 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8544 (m) REVERT: A 447 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8498 (ttmt) REVERT: A 463 MET cc_start: 0.8558 (tpp) cc_final: 0.8229 (mmm) REVERT: A 470 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7869 (tpp80) REVERT: A 573 ASP cc_start: 0.8071 (t0) cc_final: 0.7714 (t0) REVERT: A 677 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8090 (ttt-90) REVERT: A 698 ASP cc_start: 0.7750 (t0) cc_final: 0.7366 (t0) REVERT: B 71 ILE cc_start: 0.8752 (tt) cc_final: 0.8409 (tp) REVERT: B 134 ARG cc_start: 0.8306 (mtt90) cc_final: 0.8098 (mtt-85) REVERT: B 155 MET cc_start: 0.8345 (mpp) cc_final: 0.7998 (mpp) REVERT: B 195 LEU cc_start: 0.8622 (tp) cc_final: 0.8269 (tp) REVERT: B 207 GLN cc_start: 0.8407 (mm110) cc_final: 0.8171 (mm-40) REVERT: B 213 ARG cc_start: 0.8208 (mtt180) cc_final: 0.7945 (mtt180) REVERT: B 240 LEU cc_start: 0.8922 (mm) cc_final: 0.8695 (mp) REVERT: B 244 THR cc_start: 0.8483 (p) cc_final: 0.8219 (p) REVERT: B 287 GLU cc_start: 0.8227 (tp30) cc_final: 0.7240 (tp30) REVERT: B 292 PHE cc_start: 0.7985 (m-10) cc_final: 0.7704 (m-10) REVERT: B 329 LYS cc_start: 0.8529 (pttt) cc_final: 0.8225 (ptmm) REVERT: B 367 VAL cc_start: 0.8697 (t) cc_final: 0.8496 (m) REVERT: B 378 VAL cc_start: 0.8577 (t) cc_final: 0.8299 (p) REVERT: B 382 ASN cc_start: 0.8581 (m-40) cc_final: 0.8072 (t0) REVERT: B 391 SER cc_start: 0.8783 (m) cc_final: 0.8340 (p) REVERT: B 394 PHE cc_start: 0.8613 (t80) cc_final: 0.8224 (t80) REVERT: B 432 MET cc_start: 0.8117 (tpt) cc_final: 0.7720 (tpt) REVERT: B 473 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8236 (mtpp) REVERT: B 554 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7911 (pt) REVERT: B 563 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8488 (mmmt) REVERT: B 580 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7799 (mmmt) REVERT: B 681 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8291 (mttp) REVERT: B 714 ARG cc_start: 0.8527 (mtm-85) cc_final: 0.8165 (mtm-85) outliers start: 60 outliers final: 40 residues processed: 358 average time/residue: 0.1126 time to fit residues: 54.1732 Evaluate side-chains 358 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 313 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 78 optimal weight: 0.5980 chunk 72 optimal weight: 0.0970 chunk 57 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 1 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 382 ASN A 457 ASN A 475 ASN A 656 HIS B 34 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.120074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100855 restraints weight = 17996.675| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.92 r_work: 0.3200 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10406 Z= 0.148 Angle : 0.649 9.879 14142 Z= 0.329 Chirality : 0.044 0.187 1718 Planarity : 0.004 0.043 1760 Dihedral : 5.708 83.245 1431 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.81 % Allowed : 24.15 % Favored : 71.03 % 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: -0.68 (0.24), residues: 1322 helix: 0.46 (0.18), residues: 852 sheet: -1.84 (0.95), residues: 36 loop : -2.14 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 38 TYR 0.015 0.001 TYR B 105 PHE 0.011 0.001 PHE B 667 TRP 0.008 0.001 TRP A 472 HIS 0.010 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00334 (10406) covalent geometry : angle 0.64929 (14142) hydrogen bonds : bond 0.04105 ( 562) hydrogen bonds : angle 3.96001 ( 1650) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 313 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8258 (tpp-160) cc_final: 0.7339 (mpp-170) REVERT: A 48 ASP cc_start: 0.8220 (t70) cc_final: 0.7881 (p0) REVERT: A 87 ASP cc_start: 0.7335 (m-30) cc_final: 0.6961 (t0) REVERT: A 88 ILE cc_start: 0.7558 (mm) cc_final: 0.7341 (mm) REVERT: A 94 THR cc_start: 0.8509 (t) cc_final: 0.8224 (p) REVERT: A 195 LEU cc_start: 0.8551 (tp) cc_final: 0.8287 (tp) REVERT: A 236 LEU cc_start: 0.8780 (tp) cc_final: 0.8385 (tt) REVERT: A 245 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7932 (ttmm) REVERT: A 247 TYR cc_start: 0.8143 (m-10) cc_final: 0.7523 (m-10) REVERT: A 277 LEU cc_start: 0.8653 (tp) cc_final: 0.8411 (tp) REVERT: A 369 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7952 (mmtt) REVERT: A 378 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7860 (p) REVERT: A 391 SER cc_start: 0.8742 (m) cc_final: 0.8343 (p) REVERT: A 394 PHE cc_start: 0.8612 (t80) cc_final: 0.8377 (t80) REVERT: A 414 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7446 (tm-30) REVERT: A 432 MET cc_start: 0.7780 (tpt) cc_final: 0.7402 (tpt) REVERT: A 436 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8517 (m) REVERT: A 447 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8455 (mtpt) REVERT: A 470 ARG cc_start: 0.8059 (tpp80) cc_final: 0.7812 (tpp80) REVERT: A 560 ASP cc_start: 0.8309 (m-30) cc_final: 0.7323 (m-30) REVERT: A 563 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8415 (mmmt) REVERT: A 573 ASP cc_start: 0.8012 (t0) cc_final: 0.7665 (t0) REVERT: A 677 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7567 (ttt-90) REVERT: A 681 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7944 (mptt) REVERT: A 698 ASP cc_start: 0.7659 (t0) cc_final: 0.7299 (t0) REVERT: B 71 ILE cc_start: 0.8685 (tt) cc_final: 0.8340 (tp) REVERT: B 155 MET cc_start: 0.8322 (mpp) cc_final: 0.7994 (mpp) REVERT: B 195 LEU cc_start: 0.8611 (tp) cc_final: 0.8263 (tp) REVERT: B 207 GLN cc_start: 0.8324 (mm110) cc_final: 0.8079 (mm110) REVERT: B 213 ARG cc_start: 0.8205 (mtt180) cc_final: 0.7816 (mtt180) REVERT: B 240 LEU cc_start: 0.8912 (mm) cc_final: 0.8603 (mp) REVERT: B 287 GLU cc_start: 0.8175 (tp30) cc_final: 0.7202 (tp30) REVERT: B 292 PHE cc_start: 0.7996 (m-10) cc_final: 0.7688 (m-10) REVERT: B 329 LYS cc_start: 0.8447 (pttt) cc_final: 0.8102 (ptmm) REVERT: B 373 THR cc_start: 0.8323 (m) cc_final: 0.8089 (t) REVERT: B 378 VAL cc_start: 0.8549 (t) cc_final: 0.8275 (p) REVERT: B 380 ASP cc_start: 0.8251 (t0) cc_final: 0.8022 (t0) REVERT: B 382 ASN cc_start: 0.8599 (m-40) cc_final: 0.8205 (t0) REVERT: B 391 SER cc_start: 0.8786 (m) cc_final: 0.8366 (p) REVERT: B 394 PHE cc_start: 0.8564 (t80) cc_final: 0.8180 (t80) REVERT: B 432 MET cc_start: 0.8032 (tpt) cc_final: 0.7647 (tpt) REVERT: B 473 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8208 (mtpp) REVERT: B 478 ASP cc_start: 0.7614 (m-30) cc_final: 0.7236 (m-30) REVERT: B 563 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8409 (mmmt) REVERT: B 573 ASP cc_start: 0.7319 (t70) cc_final: 0.6751 (p0) REVERT: B 580 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7781 (mmmt) REVERT: B 681 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8245 (mttp) REVERT: B 714 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.8182 (mtm-85) outliers start: 54 outliers final: 40 residues processed: 345 average time/residue: 0.1145 time to fit residues: 53.3459 Evaluate side-chains 352 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 307 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 128 optimal weight: 0.4980 chunk 69 optimal weight: 10.0000 chunk 10 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 160 HIS A 382 ASN A 457 ASN A 656 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.119631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100481 restraints weight = 17960.341| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.91 r_work: 0.3206 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10406 Z= 0.165 Angle : 0.662 9.753 14142 Z= 0.335 Chirality : 0.044 0.190 1718 Planarity : 0.004 0.045 1760 Dihedral : 5.726 82.753 1431 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.08 % Allowed : 24.24 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.24), residues: 1322 helix: 0.45 (0.18), residues: 858 sheet: -1.67 (0.98), residues: 36 loop : -2.10 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 38 TYR 0.013 0.001 TYR B 105 PHE 0.013 0.001 PHE A 115 TRP 0.007 0.001 TRP A 472 HIS 0.014 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00372 (10406) covalent geometry : angle 0.66152 (14142) hydrogen bonds : bond 0.04030 ( 562) hydrogen bonds : angle 3.95333 ( 1650) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 311 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8225 (t70) cc_final: 0.7884 (p0) REVERT: A 87 ASP cc_start: 0.7341 (m-30) cc_final: 0.6952 (t0) REVERT: A 88 ILE cc_start: 0.7564 (mm) cc_final: 0.7326 (mm) REVERT: A 94 THR cc_start: 0.8529 (t) cc_final: 0.8229 (p) REVERT: A 195 LEU cc_start: 0.8566 (tp) cc_final: 0.8296 (tp) REVERT: A 236 LEU cc_start: 0.8783 (tp) cc_final: 0.8389 (tt) REVERT: A 245 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7931 (ttmm) REVERT: A 247 TYR cc_start: 0.8140 (m-10) cc_final: 0.7510 (m-10) REVERT: A 277 LEU cc_start: 0.8636 (tp) cc_final: 0.8399 (tp) REVERT: A 304 VAL cc_start: 0.8562 (t) cc_final: 0.8310 (m) REVERT: A 369 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7988 (mmtt) REVERT: A 378 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7828 (p) REVERT: A 391 SER cc_start: 0.8752 (m) cc_final: 0.8350 (p) REVERT: A 394 PHE cc_start: 0.8633 (t80) cc_final: 0.8405 (t80) REVERT: A 414 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 432 MET cc_start: 0.7800 (tpt) cc_final: 0.7414 (tpt) REVERT: A 447 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8445 (mtpt) REVERT: A 470 ARG cc_start: 0.8074 (tpp80) cc_final: 0.7831 (tpp80) REVERT: A 560 ASP cc_start: 0.8296 (m-30) cc_final: 0.7520 (m-30) REVERT: A 563 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8399 (mmmt) REVERT: A 573 ASP cc_start: 0.7980 (t0) cc_final: 0.7650 (t0) REVERT: A 677 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7575 (ttt-90) REVERT: A 681 LYS cc_start: 0.8317 (tptt) cc_final: 0.7948 (mptt) REVERT: A 698 ASP cc_start: 0.7640 (t0) cc_final: 0.7289 (t0) REVERT: B 71 ILE cc_start: 0.8711 (tt) cc_final: 0.8398 (tp) REVERT: B 155 MET cc_start: 0.8302 (mpp) cc_final: 0.7970 (mpp) REVERT: B 195 LEU cc_start: 0.8604 (tp) cc_final: 0.8263 (tp) REVERT: B 207 GLN cc_start: 0.8336 (mm110) cc_final: 0.8082 (mm110) REVERT: B 213 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7929 (mtt180) REVERT: B 240 LEU cc_start: 0.8884 (mm) cc_final: 0.8597 (mp) REVERT: B 287 GLU cc_start: 0.8186 (tp30) cc_final: 0.7226 (tp30) REVERT: B 292 PHE cc_start: 0.7994 (m-10) cc_final: 0.7650 (m-10) REVERT: B 329 LYS cc_start: 0.8413 (pttt) cc_final: 0.8092 (ptmm) REVERT: B 373 THR cc_start: 0.8333 (m) cc_final: 0.8106 (t) REVERT: B 378 VAL cc_start: 0.8559 (t) cc_final: 0.8229 (p) REVERT: B 380 ASP cc_start: 0.8246 (t0) cc_final: 0.7998 (t0) REVERT: B 382 ASN cc_start: 0.8650 (m-40) cc_final: 0.8269 (t0) REVERT: B 391 SER cc_start: 0.8785 (m) cc_final: 0.8352 (p) REVERT: B 394 PHE cc_start: 0.8567 (t80) cc_final: 0.8188 (t80) REVERT: B 432 MET cc_start: 0.7970 (tpt) cc_final: 0.7597 (tpt) REVERT: B 473 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8231 (mtpp) REVERT: B 478 ASP cc_start: 0.7632 (m-30) cc_final: 0.7285 (m-30) REVERT: B 563 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8371 (mmmt) REVERT: B 573 ASP cc_start: 0.7312 (t70) cc_final: 0.6745 (p0) REVERT: B 580 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7808 (mmmt) REVERT: B 668 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.5990 (mt) REVERT: B 681 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8252 (mttp) REVERT: B 714 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.8167 (mtm-85) outliers start: 57 outliers final: 43 residues processed: 347 average time/residue: 0.1166 time to fit residues: 54.3770 Evaluate side-chains 353 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 306 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 97 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 160 HIS A 382 ASN A 656 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100626 restraints weight = 18033.270| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.92 r_work: 0.3200 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10406 Z= 0.160 Angle : 0.662 9.762 14142 Z= 0.336 Chirality : 0.044 0.189 1718 Planarity : 0.004 0.046 1760 Dihedral : 5.723 83.009 1431 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.26 % Allowed : 24.42 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.24), residues: 1322 helix: 0.50 (0.18), residues: 860 sheet: -1.51 (1.00), residues: 36 loop : -2.06 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 38 TYR 0.017 0.001 TYR B 377 PHE 0.013 0.001 PHE B 667 TRP 0.007 0.001 TRP A 472 HIS 0.011 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00361 (10406) covalent geometry : angle 0.66238 (14142) hydrogen bonds : bond 0.03976 ( 562) hydrogen bonds : angle 3.91473 ( 1650) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 325 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8279 (tpp-160) cc_final: 0.7392 (mpp-170) REVERT: A 48 ASP cc_start: 0.8240 (t70) cc_final: 0.7866 (p0) REVERT: A 87 ASP cc_start: 0.7351 (m-30) cc_final: 0.6743 (t0) REVERT: A 94 THR cc_start: 0.8516 (t) cc_final: 0.8181 (p) REVERT: A 195 LEU cc_start: 0.8545 (tp) cc_final: 0.8253 (tp) REVERT: A 236 LEU cc_start: 0.8777 (tp) cc_final: 0.8370 (tt) REVERT: A 241 ASN cc_start: 0.8983 (t0) cc_final: 0.8693 (t0) REVERT: A 245 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7943 (ttmm) REVERT: A 247 TYR cc_start: 0.8151 (m-10) cc_final: 0.7542 (m-10) REVERT: A 277 LEU cc_start: 0.8631 (tp) cc_final: 0.8395 (tp) REVERT: A 303 GLU cc_start: 0.8013 (mp0) cc_final: 0.7741 (mp0) REVERT: A 324 ASN cc_start: 0.8731 (t0) cc_final: 0.8385 (t0) REVERT: A 369 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7984 (mmtt) REVERT: A 391 SER cc_start: 0.8776 (m) cc_final: 0.8376 (p) REVERT: A 394 PHE cc_start: 0.8637 (t80) cc_final: 0.8392 (t80) REVERT: A 414 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 432 MET cc_start: 0.7781 (tpt) cc_final: 0.7393 (tpt) REVERT: A 447 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8469 (mtpt) REVERT: A 470 ARG cc_start: 0.8061 (tpp80) cc_final: 0.7809 (tpp80) REVERT: A 560 ASP cc_start: 0.8306 (m-30) cc_final: 0.7578 (m-30) REVERT: A 563 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8128 (mmmt) REVERT: A 567 ASN cc_start: 0.8187 (m-40) cc_final: 0.7823 (m110) REVERT: A 573 ASP cc_start: 0.7923 (t0) cc_final: 0.7571 (t0) REVERT: A 581 ARG cc_start: 0.8038 (mmt180) cc_final: 0.7654 (mtp85) REVERT: A 677 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7577 (ttt-90) REVERT: A 681 LYS cc_start: 0.8300 (tptt) cc_final: 0.7947 (mptt) REVERT: A 698 ASP cc_start: 0.7626 (t0) cc_final: 0.7306 (t0) REVERT: B 66 LYS cc_start: 0.8204 (tppp) cc_final: 0.7944 (tppt) REVERT: B 71 ILE cc_start: 0.8707 (tt) cc_final: 0.8374 (tp) REVERT: B 155 MET cc_start: 0.8286 (mpp) cc_final: 0.7954 (mpp) REVERT: B 195 LEU cc_start: 0.8599 (tp) cc_final: 0.8256 (tp) REVERT: B 207 GLN cc_start: 0.8347 (mm110) cc_final: 0.8087 (mm110) REVERT: B 213 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7922 (mtt180) REVERT: B 240 LEU cc_start: 0.8890 (mm) cc_final: 0.8605 (mp) REVERT: B 263 ASN cc_start: 0.8452 (t0) cc_final: 0.8223 (t0) REVERT: B 287 GLU cc_start: 0.8199 (tp30) cc_final: 0.7238 (tp30) REVERT: B 292 PHE cc_start: 0.8007 (m-10) cc_final: 0.7617 (m-10) REVERT: B 329 LYS cc_start: 0.8424 (pttt) cc_final: 0.8191 (ptmm) REVERT: B 373 THR cc_start: 0.8291 (m) cc_final: 0.8081 (t) REVERT: B 378 VAL cc_start: 0.8531 (t) cc_final: 0.8258 (p) REVERT: B 380 ASP cc_start: 0.8245 (t0) cc_final: 0.7991 (t0) REVERT: B 382 ASN cc_start: 0.8645 (m-40) cc_final: 0.8265 (t0) REVERT: B 391 SER cc_start: 0.8798 (m) cc_final: 0.8367 (p) REVERT: B 394 PHE cc_start: 0.8590 (t80) cc_final: 0.8239 (t80) REVERT: B 432 MET cc_start: 0.7919 (tpt) cc_final: 0.7523 (tpt) REVERT: B 473 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8242 (mtpp) REVERT: B 478 ASP cc_start: 0.7671 (m-30) cc_final: 0.7328 (m-30) REVERT: B 563 LYS cc_start: 0.8712 (mmmm) cc_final: 0.8338 (mmmt) REVERT: B 573 ASP cc_start: 0.7271 (t70) cc_final: 0.6650 (p0) REVERT: B 580 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7830 (mmmt) REVERT: B 668 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5948 (mt) REVERT: B 681 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8210 (mttp) REVERT: B 714 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.8164 (mtm-85) outliers start: 59 outliers final: 45 residues processed: 363 average time/residue: 0.1146 time to fit residues: 55.8835 Evaluate side-chains 366 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 318 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 43 optimal weight: 0.5980 chunk 108 optimal weight: 0.0040 chunk 121 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 160 HIS A 382 ASN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.119598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100126 restraints weight = 17961.344| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.96 r_work: 0.3199 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10406 Z= 0.165 Angle : 0.682 9.645 14142 Z= 0.346 Chirality : 0.044 0.194 1718 Planarity : 0.004 0.049 1760 Dihedral : 5.773 82.891 1431 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.37 % Allowed : 26.29 % Favored : 69.34 % 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: -0.55 (0.24), residues: 1322 helix: 0.53 (0.18), residues: 860 sheet: -1.49 (1.00), residues: 36 loop : -2.07 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 38 TYR 0.019 0.001 TYR B 377 PHE 0.013 0.001 PHE A 115 TRP 0.006 0.001 TRP A 472 HIS 0.012 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00373 (10406) covalent geometry : angle 0.68243 (14142) hydrogen bonds : bond 0.04031 ( 562) hydrogen bonds : angle 3.92570 ( 1650) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 321 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8233 (t70) cc_final: 0.7820 (p0) REVERT: A 87 ASP cc_start: 0.7367 (m-30) cc_final: 0.6758 (t0) REVERT: A 88 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7279 (mm) REVERT: A 94 THR cc_start: 0.8512 (t) cc_final: 0.8228 (p) REVERT: A 195 LEU cc_start: 0.8563 (tp) cc_final: 0.8287 (tp) REVERT: A 236 LEU cc_start: 0.8780 (tp) cc_final: 0.8372 (tt) REVERT: A 241 ASN cc_start: 0.8981 (t0) cc_final: 0.8689 (t0) REVERT: A 245 LYS cc_start: 0.8338 (ttmm) cc_final: 0.7958 (ttmm) REVERT: A 247 TYR cc_start: 0.8169 (m-10) cc_final: 0.7557 (m-10) REVERT: A 277 LEU cc_start: 0.8620 (tp) cc_final: 0.8382 (tp) REVERT: A 303 GLU cc_start: 0.8041 (mp0) cc_final: 0.7754 (mp0) REVERT: A 324 ASN cc_start: 0.8676 (t0) cc_final: 0.8291 (t0) REVERT: A 369 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7981 (mmtt) REVERT: A 384 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7399 (mm-30) REVERT: A 391 SER cc_start: 0.8768 (m) cc_final: 0.8367 (p) REVERT: A 394 PHE cc_start: 0.8648 (t80) cc_final: 0.8164 (t80) REVERT: A 398 PHE cc_start: 0.8163 (m-80) cc_final: 0.7622 (m-80) REVERT: A 414 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7512 (tm-30) REVERT: A 432 MET cc_start: 0.7787 (tpt) cc_final: 0.7395 (tpt) REVERT: A 447 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8466 (mtpt) REVERT: A 470 ARG cc_start: 0.8085 (tpp80) cc_final: 0.7840 (tpp80) REVERT: A 560 ASP cc_start: 0.8311 (m-30) cc_final: 0.7581 (m-30) REVERT: A 563 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8148 (mmmt) REVERT: A 567 ASN cc_start: 0.8191 (m-40) cc_final: 0.7840 (m110) REVERT: A 573 ASP cc_start: 0.7927 (t0) cc_final: 0.7588 (t0) REVERT: A 581 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7660 (mtp85) REVERT: A 677 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7528 (ttt-90) REVERT: A 681 LYS cc_start: 0.8320 (tptt) cc_final: 0.7947 (mptt) REVERT: A 698 ASP cc_start: 0.7623 (t0) cc_final: 0.7313 (t0) REVERT: B 71 ILE cc_start: 0.8715 (tt) cc_final: 0.8382 (tp) REVERT: B 155 MET cc_start: 0.8299 (mpp) cc_final: 0.7960 (mpp) REVERT: B 195 LEU cc_start: 0.8603 (tp) cc_final: 0.8264 (tp) REVERT: B 207 GLN cc_start: 0.8332 (mm110) cc_final: 0.8068 (mm110) REVERT: B 213 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7916 (mtt180) REVERT: B 236 LEU cc_start: 0.8796 (tp) cc_final: 0.8457 (tt) REVERT: B 240 LEU cc_start: 0.8849 (mm) cc_final: 0.8605 (mp) REVERT: B 263 ASN cc_start: 0.8493 (t0) cc_final: 0.8215 (t0) REVERT: B 287 GLU cc_start: 0.8229 (tp30) cc_final: 0.7253 (tp30) REVERT: B 292 PHE cc_start: 0.7999 (m-10) cc_final: 0.7565 (m-10) REVERT: B 329 LYS cc_start: 0.8429 (pttt) cc_final: 0.8205 (ptmm) REVERT: B 373 THR cc_start: 0.8297 (m) cc_final: 0.8088 (t) REVERT: B 378 VAL cc_start: 0.8527 (t) cc_final: 0.8270 (p) REVERT: B 380 ASP cc_start: 0.8258 (t0) cc_final: 0.8015 (t0) REVERT: B 382 ASN cc_start: 0.8660 (m-40) cc_final: 0.8278 (t0) REVERT: B 391 SER cc_start: 0.8801 (m) cc_final: 0.8381 (p) REVERT: B 394 PHE cc_start: 0.8600 (t80) cc_final: 0.8249 (t80) REVERT: B 432 MET cc_start: 0.7945 (tpt) cc_final: 0.7584 (tpt) REVERT: B 473 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8260 (mtpp) REVERT: B 478 ASP cc_start: 0.7669 (m-30) cc_final: 0.7330 (m-30) REVERT: B 563 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8339 (mmmt) REVERT: B 573 ASP cc_start: 0.7282 (t70) cc_final: 0.6649 (p0) REVERT: B 580 LYS cc_start: 0.8094 (mmtt) cc_final: 0.7843 (mmmt) REVERT: B 668 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6041 (mt) REVERT: B 677 ARG cc_start: 0.8576 (tpt-90) cc_final: 0.8160 (tpt-90) REVERT: B 681 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8156 (mttp) REVERT: B 714 ARG cc_start: 0.8523 (mtm-85) cc_final: 0.8166 (mtm-85) outliers start: 49 outliers final: 43 residues processed: 350 average time/residue: 0.1138 time to fit residues: 53.4117 Evaluate side-chains 364 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 317 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 0.0040 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 160 HIS A 382 ASN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100358 restraints weight = 17959.817| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.92 r_work: 0.3196 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10406 Z= 0.170 Angle : 0.691 9.931 14142 Z= 0.348 Chirality : 0.045 0.197 1718 Planarity : 0.004 0.049 1760 Dihedral : 5.767 83.016 1431 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.46 % Allowed : 26.65 % Favored : 68.89 % 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: -0.54 (0.24), residues: 1322 helix: 0.54 (0.18), residues: 860 sheet: -1.47 (1.01), residues: 36 loop : -2.08 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 38 TYR 0.019 0.001 TYR B 377 PHE 0.013 0.001 PHE B 667 TRP 0.006 0.001 TRP A 472 HIS 0.017 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00384 (10406) covalent geometry : angle 0.69105 (14142) hydrogen bonds : bond 0.04012 ( 562) hydrogen bonds : angle 3.91071 ( 1650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.91 seconds wall clock time: 39 minutes 26.09 seconds (2366.09 seconds total)