Starting phenix.real_space_refine on Fri Feb 14 13:15:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk7_32561/02_2025/7wk7_32561.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk7_32561/02_2025/7wk7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wk7_32561/02_2025/7wk7_32561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk7_32561/02_2025/7wk7_32561.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk7_32561/02_2025/7wk7_32561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk7_32561/02_2025/7wk7_32561.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.25, per 1000 atoms: 0.61 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: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.06 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: 3.26 Time building geometry restraints manager: 3.06 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: 0.05 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.410 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.260 ------------------------------------------------------------------------------- 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= 0.110 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.000 TRP A 83 HIS 0.001 0.000 HIS B 656 PHE 0.009 0.001 PHE B 555 TYR 0.009 0.001 TYR A 127 ARG 0.001 0.000 ARG A 512 *********************** 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 : 1.013 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: 0.6770 (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: 0.7819 (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: 0.8455 (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: 0.7678 (p) cc_final: 0.7410 (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: 0.7316 (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: 0.6769 (tm-30) REVERT: B 422 VAL cc_start: 0.7738 (t) cc_final: 0.7268 (p) REVERT: B 432 MET cc_start: 0.7453 (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: 0.2615 time to fit residues: 160.8462 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 : 1.196 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 77 optimal weight: 0.0000 chunk 119 optimal weight: 0.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.123946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105273 restraints weight = 17781.001| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.84 r_work: 0.3280 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10406 Z= 0.218 Angle : 0.609 9.389 14142 Z= 0.314 Chirality : 0.043 0.180 1718 Planarity : 0.005 0.039 1760 Dihedral : 6.020 80.226 1443 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.01 % Allowed : 15.95 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.22), residues: 1322 helix: -0.45 (0.17), residues: 836 sheet: -3.74 (0.60), residues: 48 loop : -2.73 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.013 0.001 HIS A 656 PHE 0.023 0.001 PHE A 130 TYR 0.016 0.001 TYR A 377 ARG 0.006 0.001 ARG B 576 *********************** 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 421 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 376 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7181 (m-30) cc_final: 0.6807 (t0) REVERT: A 195 LEU cc_start: 0.8545 (tp) cc_final: 0.8279 (tp) REVERT: A 213 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7914 (mtm180) REVERT: A 236 LEU cc_start: 0.8683 (tp) cc_final: 0.8190 (tt) REVERT: A 237 LYS cc_start: 0.8596 (ttpp) cc_final: 0.8391 (ttpt) REVERT: A 244 THR cc_start: 0.8387 (p) cc_final: 0.8181 (t) REVERT: A 245 LYS cc_start: 0.8122 (ttmm) cc_final: 0.7804 (ttmm) REVERT: A 247 TYR cc_start: 0.8105 (m-10) cc_final: 0.7351 (m-10) REVERT: A 263 ASN cc_start: 0.8547 (t0) cc_final: 0.8243 (t0) REVERT: A 369 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7838 (mmtt) REVERT: A 370 VAL cc_start: 0.8508 (t) cc_final: 0.8304 (p) REVERT: A 378 VAL cc_start: 0.8253 (t) cc_final: 0.7927 (p) REVERT: A 384 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7080 (mm-30) REVERT: A 385 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7887 (t80) REVERT: A 391 SER cc_start: 0.8689 (m) cc_final: 0.8319 (p) REVERT: A 394 PHE cc_start: 0.8579 (t80) cc_final: 0.7649 (t80) REVERT: A 398 PHE cc_start: 0.8060 (m-80) cc_final: 0.7576 (m-80) REVERT: A 432 MET cc_start: 0.7820 (tpt) cc_final: 0.7367 (tpt) REVERT: A 436 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8475 (m) REVERT: A 447 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8429 (mtpp) REVERT: A 473 LYS cc_start: 0.8734 (mtpt) cc_final: 0.8119 (mtpt) REVERT: A 556 TYR cc_start: 0.8524 (p90) cc_final: 0.8025 (p90) REVERT: A 560 ASP cc_start: 0.8384 (m-30) cc_final: 0.7149 (m-30) REVERT: A 573 ASP cc_start: 0.7874 (t0) cc_final: 0.7636 (t0) REVERT: A 581 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7796 (mtp85) REVERT: A 677 ARG cc_start: 0.8171 (ptm-80) cc_final: 0.7823 (ttt-90) REVERT: A 698 ASP cc_start: 0.7697 (t0) cc_final: 0.7354 (t0) REVERT: B 34 GLN cc_start: 0.8409 (mt0) cc_final: 0.8205 (mt0) REVERT: B 66 LYS cc_start: 0.8343 (tppt) cc_final: 0.8099 (tppt) REVERT: B 69 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8311 (mt) REVERT: B 100 LEU cc_start: 0.8992 (tp) cc_final: 0.8697 (tp) REVERT: B 195 LEU cc_start: 0.8583 (tp) cc_final: 0.8185 (tp) REVERT: B 213 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7681 (mtt180) REVERT: B 244 THR cc_start: 0.8402 (p) cc_final: 0.7878 (t) REVERT: B 259 GLU cc_start: 0.8556 (tt0) cc_final: 0.8163 (tt0) REVERT: B 276 LEU cc_start: 0.8668 (tp) cc_final: 0.8417 (tt) REVERT: B 287 GLU cc_start: 0.8032 (tp30) cc_final: 0.7047 (tp30) REVERT: B 309 ILE cc_start: 0.8429 (tp) cc_final: 0.8217 (pt) REVERT: B 318 ASN cc_start: 0.8356 (t0) cc_final: 0.8142 (t0) REVERT: B 355 SER cc_start: 0.8592 (m) cc_final: 0.8151 (p) REVERT: B 361 TYR cc_start: 0.8493 (t80) cc_final: 0.8137 (t80) REVERT: B 366 SER cc_start: 0.8538 (t) cc_final: 0.8315 (p) REVERT: B 367 VAL cc_start: 0.8746 (t) cc_final: 0.8425 (m) REVERT: B 370 VAL cc_start: 0.9031 (t) cc_final: 0.8800 (p) REVERT: B 391 SER cc_start: 0.8673 (m) cc_final: 0.8366 (p) REVERT: B 394 PHE cc_start: 0.8533 (t80) cc_final: 0.7489 (t80) REVERT: B 398 PHE cc_start: 0.8006 (m-80) cc_final: 0.7645 (m-10) REVERT: B 414 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7059 (tm-30) REVERT: B 432 MET cc_start: 0.8010 (tpt) cc_final: 0.7582 (tpt) REVERT: B 447 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8438 (mtpt) REVERT: B 473 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8362 (mtpt) REVERT: B 560 ASP cc_start: 0.8106 (m-30) cc_final: 0.7891 (m-30) REVERT: B 587 ARG cc_start: 0.7441 (mmm160) cc_final: 0.7192 (tpt170) REVERT: B 702 LYS cc_start: 0.8165 (tptp) cc_final: 0.7388 (ttmm) outliers start: 45 outliers final: 25 residues processed: 400 average time/residue: 0.2664 time to fit residues: 142.6758 Evaluate side-chains 391 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 363 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 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 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 10 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 135 HIS B 160 HIS B 382 ASN B 457 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.120740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101588 restraints weight = 17913.411| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.83 r_work: 0.3227 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10406 Z= 0.236 Angle : 0.630 9.861 14142 Z= 0.324 Chirality : 0.043 0.177 1718 Planarity : 0.004 0.040 1760 Dihedral : 5.483 80.955 1433 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.23), residues: 1322 helix: -0.03 (0.17), residues: 856 sheet: -3.25 (0.77), residues: 36 loop : -2.54 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 74 HIS 0.013 0.001 HIS B 160 PHE 0.018 0.001 PHE B 272 TYR 0.013 0.001 TYR B 578 ARG 0.008 0.001 ARG B 38 *********************** 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 397 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 347 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8167 (tpp-160) cc_final: 0.7816 (mpp-170) REVERT: A 87 ASP cc_start: 0.7273 (m-30) cc_final: 0.6993 (t0) REVERT: A 195 LEU cc_start: 0.8643 (tp) cc_final: 0.8324 (tp) REVERT: A 236 LEU cc_start: 0.8771 (tp) cc_final: 0.8315 (tt) REVERT: A 240 LEU cc_start: 0.8539 (mm) cc_final: 0.8279 (mp) REVERT: A 245 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7829 (ttmm) REVERT: A 247 TYR cc_start: 0.8119 (m-10) cc_final: 0.7348 (m-10) REVERT: A 251 LEU cc_start: 0.8821 (mm) cc_final: 0.8360 (mm) REVERT: A 276 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 369 LYS cc_start: 0.8309 (mmtt) cc_final: 0.8096 (mmtt) REVERT: A 384 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7081 (mm-30) REVERT: A 385 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7852 (t80) REVERT: A 391 SER cc_start: 0.8624 (m) cc_final: 0.8241 (p) REVERT: A 394 PHE cc_start: 0.8488 (t80) cc_final: 0.7651 (t80) REVERT: A 398 PHE cc_start: 0.8012 (m-80) cc_final: 0.7599 (m-80) REVERT: A 432 MET cc_start: 0.7718 (tpt) cc_final: 0.7351 (tpt) REVERT: A 436 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8505 (m) REVERT: A 447 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8369 (ttmt) REVERT: A 470 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7718 (tpp80) REVERT: A 475 ASN cc_start: 0.7210 (m-40) cc_final: 0.6985 (m-40) REVERT: A 478 ASP cc_start: 0.7238 (m-30) cc_final: 0.6984 (m-30) REVERT: A 531 LYS cc_start: 0.8367 (mmmt) cc_final: 0.7829 (mmmt) REVERT: A 563 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8363 (mmmt) REVERT: A 573 ASP cc_start: 0.7972 (t0) cc_final: 0.7618 (t0) REVERT: A 677 ARG cc_start: 0.8280 (ptm-80) cc_final: 0.7719 (ttt90) REVERT: A 698 ASP cc_start: 0.7686 (t0) cc_final: 0.7302 (t0) REVERT: B 34 GLN cc_start: 0.8381 (mt0) cc_final: 0.8165 (mt0) REVERT: B 66 LYS cc_start: 0.8368 (tppt) cc_final: 0.8142 (tppt) REVERT: B 69 LEU cc_start: 0.8586 (mt) cc_final: 0.8353 (mt) REVERT: B 71 ILE cc_start: 0.8635 (tt) cc_final: 0.8399 (tp) REVERT: B 155 MET cc_start: 0.8226 (mpp) cc_final: 0.7844 (mpp) REVERT: B 181 ARG cc_start: 0.8513 (tmm-80) cc_final: 0.8258 (ttt-90) REVERT: B 195 LEU cc_start: 0.8633 (tp) cc_final: 0.8263 (tp) REVERT: B 213 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7849 (mtt180) REVERT: B 244 THR cc_start: 0.8407 (p) cc_final: 0.7791 (t) REVERT: B 259 GLU cc_start: 0.8466 (tt0) cc_final: 0.8096 (tt0) REVERT: B 276 LEU cc_start: 0.8703 (tp) cc_final: 0.8491 (tt) REVERT: B 287 GLU cc_start: 0.8061 (tp30) cc_final: 0.7094 (tp30) REVERT: B 309 ILE cc_start: 0.8429 (tp) cc_final: 0.8205 (pt) REVERT: B 318 ASN cc_start: 0.8347 (t0) cc_final: 0.8132 (t0) REVERT: B 361 TYR cc_start: 0.8585 (t80) cc_final: 0.8260 (t80) REVERT: B 366 SER cc_start: 0.8611 (t) cc_final: 0.8337 (p) REVERT: B 367 VAL cc_start: 0.8867 (t) cc_final: 0.8523 (m) REVERT: B 378 VAL cc_start: 0.8548 (t) cc_final: 0.8279 (m) REVERT: B 384 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7442 (mm-30) REVERT: B 391 SER cc_start: 0.8674 (m) cc_final: 0.8269 (p) REVERT: B 394 PHE cc_start: 0.8463 (t80) cc_final: 0.7401 (t80) REVERT: B 398 PHE cc_start: 0.7993 (m-80) cc_final: 0.7692 (m-80) REVERT: B 414 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7013 (tm-30) REVERT: B 432 MET cc_start: 0.8039 (tpt) cc_final: 0.7664 (tpt) REVERT: B 447 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8464 (mtpt) REVERT: B 473 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8264 (mtpt) REVERT: B 476 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8155 (mtpp) REVERT: B 531 LYS cc_start: 0.8441 (mmmt) cc_final: 0.7827 (mmmt) outliers start: 50 outliers final: 36 residues processed: 374 average time/residue: 0.2750 time to fit residues: 135.8698 Evaluate side-chains 359 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 320 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 276 LEU 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 A residue 703 MET 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 382 ASN 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 131 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 475 ASN A 656 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.119927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100694 restraints weight = 17844.768| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.91 r_work: 0.3207 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10406 Z= 0.248 Angle : 0.629 9.743 14142 Z= 0.326 Chirality : 0.044 0.266 1718 Planarity : 0.004 0.042 1760 Dihedral : 5.578 81.301 1433 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.55 % Allowed : 20.32 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.23), residues: 1322 helix: 0.19 (0.18), residues: 852 sheet: -2.98 (0.80), residues: 36 loop : -2.31 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 472 HIS 0.003 0.001 HIS A 656 PHE 0.012 0.001 PHE A 115 TYR 0.019 0.001 TYR B 105 ARG 0.009 0.000 ARG A 38 *********************** 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 386 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 335 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7271 (m-30) cc_final: 0.6993 (t0) REVERT: A 94 THR cc_start: 0.8471 (t) cc_final: 0.8098 (p) REVERT: A 195 LEU cc_start: 0.8635 (tp) cc_final: 0.8359 (tp) REVERT: A 236 LEU cc_start: 0.8744 (tp) cc_final: 0.8323 (tt) REVERT: A 245 LYS cc_start: 0.8264 (ttmm) cc_final: 0.7849 (ttmm) REVERT: A 247 TYR cc_start: 0.8165 (m-10) cc_final: 0.7478 (m-10) REVERT: A 251 LEU cc_start: 0.8816 (mm) cc_final: 0.8528 (mm) REVERT: A 276 LEU cc_start: 0.8713 (tp) cc_final: 0.8353 (tt) REVERT: A 369 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7913 (mmtt) REVERT: A 384 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7262 (mm-30) REVERT: A 385 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7842 (t80) REVERT: A 391 SER cc_start: 0.8721 (m) cc_final: 0.8317 (p) REVERT: A 394 PHE cc_start: 0.8576 (t80) cc_final: 0.7916 (t80) REVERT: A 398 PHE cc_start: 0.8065 (m-80) cc_final: 0.7696 (m-80) REVERT: A 414 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 432 MET cc_start: 0.7931 (tpt) cc_final: 0.7548 (tpt) REVERT: A 436 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8498 (m) REVERT: A 447 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8445 (ttmt) REVERT: A 470 ARG cc_start: 0.8003 (tpp80) cc_final: 0.7764 (tpp80) REVERT: A 475 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7372 (m-40) REVERT: A 531 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8148 (mmmm) REVERT: A 563 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8348 (mmmt) REVERT: A 573 ASP cc_start: 0.7971 (t0) cc_final: 0.7581 (t0) REVERT: A 581 ARG cc_start: 0.8061 (mmt180) cc_final: 0.7730 (mtp85) REVERT: A 677 ARG cc_start: 0.8366 (ptm-80) cc_final: 0.7839 (ttt90) REVERT: A 698 ASP cc_start: 0.7731 (t0) cc_final: 0.7366 (t0) REVERT: B 34 GLN cc_start: 0.8392 (mt0) cc_final: 0.8185 (mt0) REVERT: B 69 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8244 (mt) REVERT: B 71 ILE cc_start: 0.8670 (tt) cc_final: 0.8307 (tp) REVERT: B 155 MET cc_start: 0.8281 (mpp) cc_final: 0.7933 (mpp) REVERT: B 195 LEU cc_start: 0.8611 (tp) cc_final: 0.8236 (tp) REVERT: B 207 GLN cc_start: 0.8283 (mm110) cc_final: 0.7967 (mm-40) REVERT: B 213 ARG cc_start: 0.8228 (mtt180) cc_final: 0.7937 (ttp-170) REVERT: B 244 THR cc_start: 0.8442 (p) cc_final: 0.8153 (t) REVERT: B 287 GLU cc_start: 0.8180 (tp30) cc_final: 0.7181 (tp30) REVERT: B 309 ILE cc_start: 0.8468 (tp) cc_final: 0.8202 (pt) REVERT: B 329 LYS cc_start: 0.8329 (pttt) cc_final: 0.8108 (pttt) REVERT: B 361 TYR cc_start: 0.8587 (t80) cc_final: 0.8220 (t80) REVERT: B 366 SER cc_start: 0.8504 (t) cc_final: 0.8297 (p) REVERT: B 367 VAL cc_start: 0.8700 (t) cc_final: 0.8461 (m) REVERT: B 373 THR cc_start: 0.8471 (m) cc_final: 0.8101 (t) REVERT: B 378 VAL cc_start: 0.8561 (t) cc_final: 0.8271 (p) REVERT: B 382 ASN cc_start: 0.8435 (m-40) cc_final: 0.8004 (t0) REVERT: B 391 SER cc_start: 0.8746 (m) cc_final: 0.8342 (p) REVERT: B 394 PHE cc_start: 0.8537 (t80) cc_final: 0.7532 (t80) REVERT: B 398 PHE cc_start: 0.8042 (m-80) cc_final: 0.7677 (m-80) REVERT: B 432 MET cc_start: 0.8080 (tpt) cc_final: 0.7677 (tpt) REVERT: B 447 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8471 (mtpt) REVERT: B 459 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8556 (ttpp) REVERT: B 473 LYS cc_start: 0.8562 (mtpt) cc_final: 0.8343 (mtpt) REVERT: B 531 LYS cc_start: 0.8464 (mmmt) cc_final: 0.7740 (mmmt) REVERT: B 681 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8341 (ttmm) REVERT: B 714 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.8133 (mtm-85) outliers start: 51 outliers final: 35 residues processed: 366 average time/residue: 0.2876 time to fit residues: 139.1815 Evaluate side-chains 362 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 322 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 163 VAL Chi-restraints excluded: chain A residue 202 VAL 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 B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR 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 379 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 57 optimal weight: 0.0270 chunk 64 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 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 = 0.3639 r_free = 0.3639 target = 0.120565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.101435 restraints weight = 17682.253| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.82 r_work: 0.3223 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3686 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= 0.212 Angle : 0.639 9.764 14142 Z= 0.324 Chirality : 0.043 0.198 1718 Planarity : 0.004 0.046 1760 Dihedral : 5.611 82.244 1433 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.63 % Allowed : 21.93 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.23), residues: 1322 helix: 0.35 (0.18), residues: 850 sheet: -2.52 (0.86), residues: 36 loop : -2.22 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 482 HIS 0.014 0.001 HIS A 656 PHE 0.013 0.001 PHE A 115 TYR 0.019 0.001 TYR B 105 ARG 0.012 0.001 ARG B 38 *********************** 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 380 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 328 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8228 (tpp-160) cc_final: 0.7489 (mpp-170) REVERT: A 87 ASP cc_start: 0.7244 (m-30) cc_final: 0.6939 (t0) REVERT: A 94 THR cc_start: 0.8408 (t) cc_final: 0.8052 (p) REVERT: A 195 LEU cc_start: 0.8680 (tp) cc_final: 0.8417 (tp) REVERT: A 236 LEU cc_start: 0.8784 (tp) cc_final: 0.8437 (tt) REVERT: A 245 LYS cc_start: 0.8267 (ttmm) cc_final: 0.7886 (ttmm) REVERT: A 247 TYR cc_start: 0.8153 (m-10) cc_final: 0.7586 (m-10) REVERT: A 251 LEU cc_start: 0.8683 (mm) cc_final: 0.8367 (mm) REVERT: A 384 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7167 (mm-30) REVERT: A 385 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7788 (t80) REVERT: A 391 SER cc_start: 0.8663 (m) cc_final: 0.8306 (p) REVERT: A 414 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 432 MET cc_start: 0.7791 (tpt) cc_final: 0.7432 (tpt) REVERT: A 436 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8525 (m) REVERT: A 447 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8466 (mtpt) REVERT: A 470 ARG cc_start: 0.8012 (tpp80) cc_final: 0.7765 (tpp80) REVERT: A 475 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.7332 (m-40) REVERT: A 478 ASP cc_start: 0.7470 (m-30) cc_final: 0.7242 (m-30) REVERT: A 531 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8175 (mmmm) REVERT: A 560 ASP cc_start: 0.8362 (m-30) cc_final: 0.7200 (m-30) REVERT: A 563 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8435 (mmmt) REVERT: A 573 ASP cc_start: 0.7971 (t0) cc_final: 0.7640 (t0) REVERT: A 581 ARG cc_start: 0.8051 (mmt180) cc_final: 0.7713 (mtp85) REVERT: A 677 ARG cc_start: 0.8324 (ptm-80) cc_final: 0.7841 (ttt90) REVERT: A 698 ASP cc_start: 0.7653 (t0) cc_final: 0.7292 (t0) REVERT: A 704 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7817 (tm-30) REVERT: B 71 ILE cc_start: 0.8637 (tt) cc_final: 0.8301 (tp) REVERT: B 155 MET cc_start: 0.8280 (mpp) cc_final: 0.7983 (mpp) REVERT: B 181 ARG cc_start: 0.8493 (tmm-80) cc_final: 0.8204 (ttt-90) REVERT: B 195 LEU cc_start: 0.8642 (tp) cc_final: 0.8283 (tp) REVERT: B 213 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7792 (mtt180) REVERT: B 287 GLU cc_start: 0.8122 (tp30) cc_final: 0.7151 (tp30) REVERT: B 318 ASN cc_start: 0.8206 (t0) cc_final: 0.7943 (t0) REVERT: B 324 ASN cc_start: 0.8401 (t0) cc_final: 0.8045 (t0) REVERT: B 329 LYS cc_start: 0.8254 (pttt) cc_final: 0.7967 (ptmm) REVERT: B 366 SER cc_start: 0.8532 (t) cc_final: 0.8324 (p) REVERT: B 367 VAL cc_start: 0.8750 (t) cc_final: 0.8523 (m) REVERT: B 373 THR cc_start: 0.8425 (m) cc_final: 0.8113 (t) REVERT: B 378 VAL cc_start: 0.8524 (t) cc_final: 0.8231 (p) REVERT: B 391 SER cc_start: 0.8719 (m) cc_final: 0.8289 (p) REVERT: B 394 PHE cc_start: 0.8497 (t80) cc_final: 0.8087 (t80) REVERT: B 432 MET cc_start: 0.7976 (tpt) cc_final: 0.7601 (tpt) REVERT: B 473 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8130 (mtpp) REVERT: B 554 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7929 (pt) REVERT: B 563 LYS cc_start: 0.8781 (mmmm) cc_final: 0.8398 (mmmm) REVERT: B 567 ASN cc_start: 0.8272 (m-40) cc_final: 0.8020 (m110) REVERT: B 580 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7807 (mmmt) REVERT: B 677 ARG cc_start: 0.8567 (tpt-90) cc_final: 0.8236 (tpt-90) REVERT: B 681 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8231 (mttp) REVERT: B 714 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.8107 (mtm-85) outliers start: 52 outliers final: 37 residues processed: 361 average time/residue: 0.2692 time to fit residues: 130.3267 Evaluate side-chains 348 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 473 LYS Chi-restraints excluded: chain A residue 475 ASN 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 727 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 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 251 LEU Chi-restraints excluded: chain B residue 255 TYR 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 541 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 554 ILE 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 21 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 34 GLN A 135 HIS A 382 ASN A 457 ASN A 475 ASN A 656 HIS B 34 GLN B 135 HIS B 241 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100457 restraints weight = 17987.826| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.89 r_work: 0.3189 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10406 Z= 0.269 Angle : 0.645 9.923 14142 Z= 0.332 Chirality : 0.045 0.185 1718 Planarity : 0.004 0.045 1760 Dihedral : 5.633 82.216 1431 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.08 % Allowed : 22.37 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1322 helix: 0.41 (0.18), residues: 850 sheet: -2.21 (0.91), residues: 36 loop : -2.19 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 472 HIS 0.014 0.001 HIS A 656 PHE 0.020 0.001 PHE B 272 TYR 0.017 0.002 TYR B 105 ARG 0.009 0.000 ARG B 38 *********************** 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 383 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 326 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8205 (t70) cc_final: 0.7873 (p0) REVERT: A 87 ASP cc_start: 0.7394 (m-30) cc_final: 0.7120 (t0) REVERT: A 94 THR cc_start: 0.8461 (t) cc_final: 0.8101 (p) REVERT: A 195 LEU cc_start: 0.8606 (tp) cc_final: 0.8354 (tp) REVERT: A 236 LEU cc_start: 0.8778 (tp) cc_final: 0.8430 (tt) REVERT: A 245 LYS cc_start: 0.8321 (ttmm) cc_final: 0.7913 (ttmm) REVERT: A 247 TYR cc_start: 0.8150 (m-10) cc_final: 0.7543 (m-10) REVERT: A 251 LEU cc_start: 0.8704 (mm) cc_final: 0.8396 (mm) REVERT: A 276 LEU cc_start: 0.8730 (tp) cc_final: 0.8358 (tp) REVERT: A 369 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7935 (mmtt) REVERT: A 384 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7349 (mm-30) REVERT: A 385 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7739 (t80) REVERT: A 391 SER cc_start: 0.8759 (m) cc_final: 0.8367 (p) REVERT: A 394 PHE cc_start: 0.8564 (t80) cc_final: 0.8065 (t80) REVERT: A 398 PHE cc_start: 0.8127 (m-80) cc_final: 0.7482 (m-10) REVERT: A 414 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7456 (tm-30) REVERT: A 432 MET cc_start: 0.7836 (tpt) cc_final: 0.7456 (tpt) REVERT: A 436 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8530 (m) REVERT: A 447 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8445 (mtpt) REVERT: A 470 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7789 (tpp80) REVERT: A 475 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7502 (m-40) REVERT: A 531 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8122 (mmmm) REVERT: A 573 ASP cc_start: 0.8029 (t0) cc_final: 0.7642 (t0) REVERT: A 581 ARG cc_start: 0.8034 (mmt180) cc_final: 0.7666 (mtp85) REVERT: A 677 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7783 (ttt90) REVERT: A 698 ASP cc_start: 0.7683 (t0) cc_final: 0.7314 (t0) REVERT: A 704 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 71 ILE cc_start: 0.8685 (tt) cc_final: 0.8346 (tp) REVERT: B 155 MET cc_start: 0.8264 (mpp) cc_final: 0.7937 (mpp) REVERT: B 195 LEU cc_start: 0.8601 (tp) cc_final: 0.8252 (tp) REVERT: B 213 ARG cc_start: 0.8201 (mtt180) cc_final: 0.7965 (ttp-170) REVERT: B 286 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8409 (mtmm) REVERT: B 287 GLU cc_start: 0.8188 (tp30) cc_final: 0.7184 (tp30) REVERT: B 366 SER cc_start: 0.8484 (t) cc_final: 0.8281 (p) REVERT: B 373 THR cc_start: 0.8374 (m) cc_final: 0.8101 (t) REVERT: B 378 VAL cc_start: 0.8557 (t) cc_final: 0.8249 (p) REVERT: B 391 SER cc_start: 0.8784 (m) cc_final: 0.8355 (p) REVERT: B 394 PHE cc_start: 0.8595 (t80) cc_final: 0.8177 (t80) REVERT: B 432 MET cc_start: 0.8013 (tpt) cc_final: 0.7615 (tpt) REVERT: B 459 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8546 (ttpp) REVERT: B 473 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8377 (mtpt) REVERT: B 554 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7921 (pt) REVERT: B 677 ARG cc_start: 0.8578 (tpt-90) cc_final: 0.8304 (tpt-90) REVERT: B 681 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8281 (ttmm) REVERT: B 714 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8145 (mtm-85) outliers start: 57 outliers final: 36 residues processed: 361 average time/residue: 0.2801 time to fit residues: 133.7889 Evaluate side-chains 360 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 202 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 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 727 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 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 259 GLU Chi-restraints excluded: chain B residue 283 MET 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 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 54 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 113 optimal weight: 0.0040 chunk 117 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 chunk 99 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 overall best weight: 0.3950 ------------------------------------------------------------------------------- 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 241 ASN ** B 519 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 = 0.3657 r_free = 0.3657 target = 0.120951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.101602 restraints weight = 18161.190| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.93 r_work: 0.3214 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10406 Z= 0.211 Angle : 0.654 10.394 14142 Z= 0.331 Chirality : 0.044 0.178 1718 Planarity : 0.004 0.041 1760 Dihedral : 5.637 82.549 1431 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1322 helix: 0.47 (0.18), residues: 850 sheet: -1.90 (0.94), residues: 36 loop : -2.13 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.014 0.001 HIS A 656 PHE 0.016 0.001 PHE A 394 TYR 0.015 0.001 TYR B 105 ARG 0.012 0.001 ARG A 38 *********************** 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 372 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 318 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8244 (tpp-160) cc_final: 0.7485 (mpp-170) REVERT: A 38 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7871 (ttp-110) REVERT: A 48 ASP cc_start: 0.8235 (t70) cc_final: 0.7880 (p0) REVERT: A 87 ASP cc_start: 0.7426 (m-30) cc_final: 0.7145 (t70) REVERT: A 94 THR cc_start: 0.8481 (t) cc_final: 0.8089 (p) REVERT: A 195 LEU cc_start: 0.8567 (tp) cc_final: 0.8317 (tp) REVERT: A 213 ARG cc_start: 0.8339 (mtm180) cc_final: 0.8129 (ttm170) REVERT: A 236 LEU cc_start: 0.8751 (tp) cc_final: 0.8364 (tt) REVERT: A 245 LYS cc_start: 0.8322 (ttmm) cc_final: 0.7933 (ttmm) REVERT: A 247 TYR cc_start: 0.8178 (m-10) cc_final: 0.7578 (m-10) REVERT: A 276 LEU cc_start: 0.8713 (tp) cc_final: 0.8341 (tp) REVERT: A 369 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7929 (mmtt) REVERT: A 378 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7760 (p) REVERT: A 384 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7356 (mm-30) REVERT: A 385 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7729 (t80) REVERT: A 391 SER cc_start: 0.8766 (m) cc_final: 0.8370 (p) REVERT: A 394 PHE cc_start: 0.8590 (t80) cc_final: 0.8128 (t80) REVERT: A 398 PHE cc_start: 0.8114 (m-80) cc_final: 0.7591 (m-10) REVERT: A 414 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 432 MET cc_start: 0.7777 (tpt) cc_final: 0.7400 (tpt) REVERT: A 447 LYS cc_start: 0.8848 (mtpt) cc_final: 0.8429 (mtpt) REVERT: A 470 ARG cc_start: 0.8052 (tpp80) cc_final: 0.7797 (tpp80) REVERT: A 475 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7512 (m-40) REVERT: A 531 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8131 (mmmm) REVERT: A 563 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8406 (mmmt) REVERT: A 573 ASP cc_start: 0.7934 (t0) cc_final: 0.7573 (t0) REVERT: A 581 ARG cc_start: 0.8008 (mmt180) cc_final: 0.7636 (mtp85) REVERT: A 677 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7755 (ttt90) REVERT: A 698 ASP cc_start: 0.7668 (t0) cc_final: 0.7305 (t0) REVERT: B 71 ILE cc_start: 0.8661 (tt) cc_final: 0.8311 (tp) REVERT: B 155 MET cc_start: 0.8303 (mpp) cc_final: 0.7988 (mpp) REVERT: B 195 LEU cc_start: 0.8578 (tp) cc_final: 0.8233 (tp) REVERT: B 213 ARG cc_start: 0.8179 (mtt180) cc_final: 0.7899 (mtt180) REVERT: B 241 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8622 (t0) REVERT: B 286 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8392 (mtmm) REVERT: B 287 GLU cc_start: 0.8195 (tp30) cc_final: 0.7196 (tp30) REVERT: B 329 LYS cc_start: 0.8388 (pttt) cc_final: 0.8177 (pttt) REVERT: B 366 SER cc_start: 0.8503 (t) cc_final: 0.8290 (p) REVERT: B 373 THR cc_start: 0.8345 (m) cc_final: 0.8086 (t) REVERT: B 378 VAL cc_start: 0.8536 (t) cc_final: 0.8236 (p) REVERT: B 391 SER cc_start: 0.8786 (m) cc_final: 0.8359 (p) REVERT: B 394 PHE cc_start: 0.8578 (t80) cc_final: 0.8168 (t80) REVERT: B 432 MET cc_start: 0.7951 (tpt) cc_final: 0.7571 (tpt) REVERT: B 459 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8534 (ttpp) REVERT: B 473 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8384 (mtpt) REVERT: B 531 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8261 (mmmm) REVERT: B 554 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7924 (pt) REVERT: B 677 ARG cc_start: 0.8561 (tpt-90) cc_final: 0.8287 (tpt-90) REVERT: B 681 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8252 (ttmm) REVERT: B 702 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7764 (ttmm) REVERT: B 714 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.8117 (mtm-85) outliers start: 54 outliers final: 36 residues processed: 349 average time/residue: 0.2825 time to fit residues: 129.4997 Evaluate side-chains 356 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 313 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 378 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 541 GLU 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 671 VAL Chi-restraints excluded: chain A residue 677 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 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 259 GLU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 0.2980 chunk 131 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 9 optimal weight: 0.0020 chunk 64 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 241 ASN ** B 519 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 = 0.3644 r_free = 0.3644 target = 0.119909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100799 restraints weight = 18039.222| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.91 r_work: 0.3203 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10406 Z= 0.244 Angle : 0.662 9.744 14142 Z= 0.336 Chirality : 0.045 0.191 1718 Planarity : 0.004 0.044 1760 Dihedral : 5.672 82.153 1431 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.17 % Allowed : 23.98 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1322 helix: 0.43 (0.18), residues: 858 sheet: -1.77 (0.94), residues: 36 loop : -2.07 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 74 HIS 0.015 0.001 HIS A 656 PHE 0.015 0.001 PHE A 394 TYR 0.015 0.001 TYR B 578 ARG 0.011 0.001 ARG A 38 *********************** 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 376 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 318 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8071 (ttm110) cc_final: 0.7841 (ttp-110) REVERT: A 48 ASP cc_start: 0.8250 (t70) cc_final: 0.7893 (p0) REVERT: A 87 ASP cc_start: 0.7456 (m-30) cc_final: 0.7169 (t70) REVERT: A 94 THR cc_start: 0.8506 (t) cc_final: 0.8163 (p) REVERT: A 195 LEU cc_start: 0.8576 (tp) cc_final: 0.8290 (tp) REVERT: A 236 LEU cc_start: 0.8764 (tp) cc_final: 0.8374 (tt) REVERT: A 245 LYS cc_start: 0.8316 (ttmm) cc_final: 0.7933 (ttmm) REVERT: A 247 TYR cc_start: 0.8182 (m-10) cc_final: 0.7569 (m-10) REVERT: A 276 LEU cc_start: 0.8724 (tp) cc_final: 0.8350 (tp) REVERT: A 378 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7784 (p) REVERT: A 384 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7391 (mm-30) REVERT: A 385 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7709 (t80) REVERT: A 391 SER cc_start: 0.8758 (m) cc_final: 0.8395 (p) REVERT: A 394 PHE cc_start: 0.8604 (t80) cc_final: 0.8216 (t80) REVERT: A 398 PHE cc_start: 0.8129 (m-80) cc_final: 0.7695 (m-10) REVERT: A 414 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 432 MET cc_start: 0.7814 (tpt) cc_final: 0.7434 (tpt) REVERT: A 447 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8615 (mtpt) REVERT: A 470 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7823 (tpp80) REVERT: A 563 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8463 (mmmt) REVERT: A 573 ASP cc_start: 0.7928 (t0) cc_final: 0.7579 (t0) REVERT: A 581 ARG cc_start: 0.8016 (mmt180) cc_final: 0.7642 (mtp85) REVERT: A 677 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7821 (ttt90) REVERT: A 698 ASP cc_start: 0.7655 (t0) cc_final: 0.7277 (t0) REVERT: B 71 ILE cc_start: 0.8696 (tt) cc_final: 0.8361 (tp) REVERT: B 155 MET cc_start: 0.8263 (mpp) cc_final: 0.7934 (mpp) REVERT: B 195 LEU cc_start: 0.8608 (tp) cc_final: 0.8248 (tp) REVERT: B 213 ARG cc_start: 0.8179 (mtt180) cc_final: 0.7955 (ttp-170) REVERT: B 260 ILE cc_start: 0.8674 (tt) cc_final: 0.8372 (pt) REVERT: B 286 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8395 (mtmm) REVERT: B 287 GLU cc_start: 0.8212 (tp30) cc_final: 0.7218 (tp30) REVERT: B 366 SER cc_start: 0.8520 (t) cc_final: 0.8295 (p) REVERT: B 373 THR cc_start: 0.8323 (m) cc_final: 0.8073 (t) REVERT: B 377 TYR cc_start: 0.8065 (p90) cc_final: 0.7396 (p90) REVERT: B 378 VAL cc_start: 0.8539 (t) cc_final: 0.8067 (p) REVERT: B 391 SER cc_start: 0.8786 (m) cc_final: 0.8345 (p) REVERT: B 394 PHE cc_start: 0.8589 (t80) cc_final: 0.8204 (t80) REVERT: B 432 MET cc_start: 0.7943 (tpt) cc_final: 0.7564 (tpt) REVERT: B 459 LYS cc_start: 0.8805 (ttpp) cc_final: 0.8538 (ttpp) REVERT: B 473 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8385 (mtpt) REVERT: B 531 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8307 (mmmm) REVERT: B 554 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7957 (pt) REVERT: B 677 ARG cc_start: 0.8559 (tpt-90) cc_final: 0.8307 (tpt-90) REVERT: B 681 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8250 (ttmm) REVERT: B 702 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7724 (ttmm) REVERT: B 714 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.8125 (mtm-85) outliers start: 58 outliers final: 38 residues processed: 356 average time/residue: 0.2797 time to fit residues: 130.9946 Evaluate side-chains 356 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 313 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 117 LEU 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 202 VAL 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 378 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 473 LYS 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 671 VAL 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 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 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 259 GLU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 73 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 110 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.0270 chunk 46 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 34 GLN ** 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 = 0.3652 r_free = 0.3652 target = 0.120396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101364 restraints weight = 18130.404| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.91 r_work: 0.3211 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10406 Z= 0.220 Angle : 0.669 11.487 14142 Z= 0.337 Chirality : 0.044 0.191 1718 Planarity : 0.004 0.042 1760 Dihedral : 5.686 83.043 1431 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.90 % Allowed : 24.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1322 helix: 0.56 (0.18), residues: 852 sheet: -1.60 (0.96), residues: 36 loop : -2.10 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 472 HIS 0.014 0.001 HIS A 656 PHE 0.014 0.001 PHE A 394 TYR 0.014 0.001 TYR B 105 ARG 0.011 0.001 ARG A 38 *********************** 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 375 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 320 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8257 (tpp-160) cc_final: 0.7499 (mpp-170) REVERT: A 48 ASP cc_start: 0.8242 (t70) cc_final: 0.7884 (p0) REVERT: A 94 THR cc_start: 0.8474 (t) cc_final: 0.8084 (p) REVERT: A 195 LEU cc_start: 0.8576 (tp) cc_final: 0.8326 (tp) REVERT: A 236 LEU cc_start: 0.8769 (tp) cc_final: 0.8375 (tt) REVERT: A 245 LYS cc_start: 0.8285 (ttmm) cc_final: 0.7941 (ttmm) REVERT: A 247 TYR cc_start: 0.8149 (m-10) cc_final: 0.7540 (m-10) REVERT: A 276 LEU cc_start: 0.8733 (tp) cc_final: 0.8358 (tp) REVERT: A 303 GLU cc_start: 0.8065 (mp0) cc_final: 0.7754 (mp0) REVERT: A 378 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7827 (p) REVERT: A 384 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7383 (mm-30) REVERT: A 391 SER cc_start: 0.8757 (m) cc_final: 0.8397 (p) REVERT: A 394 PHE cc_start: 0.8606 (t80) cc_final: 0.8215 (t80) REVERT: A 398 PHE cc_start: 0.8091 (m-80) cc_final: 0.7687 (m-10) REVERT: A 414 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 432 MET cc_start: 0.7747 (tpt) cc_final: 0.7367 (tpt) REVERT: A 447 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8434 (mtpt) REVERT: A 470 ARG cc_start: 0.8055 (tpp80) cc_final: 0.7811 (tpp80) REVERT: A 563 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8497 (mmmt) REVERT: A 573 ASP cc_start: 0.7895 (t0) cc_final: 0.7584 (t0) REVERT: A 581 ARG cc_start: 0.8000 (mmt180) cc_final: 0.7630 (mtp85) REVERT: A 587 ARG cc_start: 0.7378 (mmm-85) cc_final: 0.6962 (tpt170) REVERT: A 677 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7689 (ttt90) REVERT: A 698 ASP cc_start: 0.7613 (t0) cc_final: 0.7278 (t0) REVERT: B 71 ILE cc_start: 0.8673 (tt) cc_final: 0.8342 (tp) REVERT: B 155 MET cc_start: 0.8247 (mpp) cc_final: 0.7933 (mpp) REVERT: B 181 ARG cc_start: 0.8554 (tmm-80) cc_final: 0.8181 (ttt-90) REVERT: B 195 LEU cc_start: 0.8618 (tp) cc_final: 0.8278 (tp) REVERT: B 260 ILE cc_start: 0.8638 (tt) cc_final: 0.8362 (pt) REVERT: B 286 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8467 (mtmm) REVERT: B 287 GLU cc_start: 0.8198 (tp30) cc_final: 0.7230 (tp30) REVERT: B 366 SER cc_start: 0.8519 (t) cc_final: 0.8289 (p) REVERT: B 373 THR cc_start: 0.8284 (m) cc_final: 0.8048 (t) REVERT: B 378 VAL cc_start: 0.8539 (t) cc_final: 0.8248 (p) REVERT: B 391 SER cc_start: 0.8788 (m) cc_final: 0.8344 (p) REVERT: B 394 PHE cc_start: 0.8553 (t80) cc_final: 0.8182 (t80) REVERT: B 432 MET cc_start: 0.7874 (tpt) cc_final: 0.7486 (tpt) REVERT: B 459 LYS cc_start: 0.8807 (ttpp) cc_final: 0.8527 (ttpp) REVERT: B 473 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8404 (mtpt) REVERT: B 554 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7977 (pt) REVERT: B 677 ARG cc_start: 0.8547 (tpt-90) cc_final: 0.8291 (tpt-90) REVERT: B 681 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8244 (ttmm) REVERT: B 702 LYS cc_start: 0.7910 (ttmm) cc_final: 0.7693 (ttmm) REVERT: B 714 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8146 (mtm-85) outliers start: 55 outliers final: 41 residues processed: 356 average time/residue: 0.2802 time to fit residues: 131.1860 Evaluate side-chains 361 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 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 378 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 541 GLU 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 671 VAL 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 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 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 259 GLU Chi-restraints excluded: chain B residue 298 VAL 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 554 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 697 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 110 optimal weight: 0.9990 chunk 102 optimal weight: 0.2980 chunk 76 optimal weight: 0.6980 chunk 64 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 34 GLN ** 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 = 0.3658 r_free = 0.3658 target = 0.120878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.101969 restraints weight = 18054.770| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.91 r_work: 0.3218 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4290 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= 0.217 Angle : 0.683 10.260 14142 Z= 0.343 Chirality : 0.044 0.192 1718 Planarity : 0.004 0.052 1760 Dihedral : 5.558 82.705 1429 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.19 % Allowed : 25.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.24), residues: 1322 helix: 0.59 (0.18), residues: 850 sheet: -1.47 (0.97), residues: 36 loop : -2.12 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 472 HIS 0.013 0.001 HIS A 656 PHE 0.014 0.001 PHE A 115 TYR 0.014 0.001 TYR B 105 ARG 0.015 0.001 ARG A 38 ********************** 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 367 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 320 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8269 (tpp-160) cc_final: 0.7503 (mpp-170) REVERT: A 48 ASP cc_start: 0.8263 (t70) cc_final: 0.7877 (p0) REVERT: A 87 ASP cc_start: 0.7451 (m-30) cc_final: 0.7076 (t0) REVERT: A 195 LEU cc_start: 0.8545 (tp) cc_final: 0.8300 (tp) REVERT: A 236 LEU cc_start: 0.8789 (tp) cc_final: 0.8402 (tt) REVERT: A 245 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7937 (ttmm) REVERT: A 247 TYR cc_start: 0.8160 (m-10) cc_final: 0.7565 (m-10) REVERT: A 276 LEU cc_start: 0.8712 (tp) cc_final: 0.8336 (tp) REVERT: A 303 GLU cc_start: 0.8055 (mp0) cc_final: 0.7755 (mp0) REVERT: A 378 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7814 (p) REVERT: A 385 PHE cc_start: 0.8529 (t80) cc_final: 0.8200 (m-80) REVERT: A 391 SER cc_start: 0.8775 (m) cc_final: 0.8423 (p) REVERT: A 394 PHE cc_start: 0.8635 (t80) cc_final: 0.8198 (t80) REVERT: A 398 PHE cc_start: 0.8103 (m-80) cc_final: 0.7678 (m-10) REVERT: A 414 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 432 MET cc_start: 0.7743 (tpt) cc_final: 0.7357 (tpt) REVERT: A 447 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8452 (mtpt) REVERT: A 470 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7816 (tpp80) REVERT: A 560 ASP cc_start: 0.8243 (m-30) cc_final: 0.7334 (m-30) REVERT: A 563 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8456 (mmmt) REVERT: A 573 ASP cc_start: 0.7867 (t0) cc_final: 0.7575 (t0) REVERT: A 581 ARG cc_start: 0.8010 (mmt180) cc_final: 0.7639 (mtp85) REVERT: A 677 ARG cc_start: 0.8210 (ptm-80) cc_final: 0.7751 (tpt-90) REVERT: A 698 ASP cc_start: 0.7579 (t0) cc_final: 0.7271 (t0) REVERT: B 71 ILE cc_start: 0.8667 (tt) cc_final: 0.8332 (tp) REVERT: B 155 MET cc_start: 0.8283 (mpp) cc_final: 0.7997 (mpp) REVERT: B 181 ARG cc_start: 0.8583 (tmm-80) cc_final: 0.8203 (ttt-90) REVERT: B 195 LEU cc_start: 0.8609 (tp) cc_final: 0.8271 (tp) REVERT: B 213 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7592 (ttt180) REVERT: B 260 ILE cc_start: 0.8613 (tt) cc_final: 0.8355 (pt) REVERT: B 286 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8478 (mtmm) REVERT: B 287 GLU cc_start: 0.8208 (tp30) cc_final: 0.7229 (tp30) REVERT: B 366 SER cc_start: 0.8527 (t) cc_final: 0.8289 (p) REVERT: B 373 THR cc_start: 0.8259 (m) cc_final: 0.8040 (t) REVERT: B 378 VAL cc_start: 0.8536 (t) cc_final: 0.8244 (p) REVERT: B 384 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7725 (mm-30) REVERT: B 391 SER cc_start: 0.8798 (m) cc_final: 0.8347 (p) REVERT: B 394 PHE cc_start: 0.8561 (t80) cc_final: 0.8190 (t80) REVERT: B 432 MET cc_start: 0.7838 (tpt) cc_final: 0.7453 (tpt) REVERT: B 459 LYS cc_start: 0.8789 (ttpp) cc_final: 0.8497 (ttpp) REVERT: B 473 LYS cc_start: 0.8623 (mtpt) cc_final: 0.8402 (mtpt) REVERT: B 573 ASP cc_start: 0.7188 (t70) cc_final: 0.6500 (p0) REVERT: B 677 ARG cc_start: 0.8528 (tpt-90) cc_final: 0.8264 (tpt-90) REVERT: B 681 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8234 (ttmm) REVERT: B 702 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7705 (ttmm) REVERT: B 714 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.8150 (mtm-85) outliers start: 47 outliers final: 40 residues processed: 351 average time/residue: 0.2879 time to fit residues: 132.9559 Evaluate side-chains 358 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 316 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 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 378 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 541 GLU 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 682 GLU Chi-restraints excluded: chain A residue 727 LEU 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 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 259 GLU Chi-restraints excluded: chain B residue 298 VAL 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 554 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain B residue 682 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 86 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 52 optimal weight: 0.0010 chunk 43 optimal weight: 0.0060 chunk 49 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 overall best weight: 0.2802 ------------------------------------------------------------------------------- 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 34 GLN 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 = 0.121675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102776 restraints weight = 17878.009| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.90 r_work: 0.3237 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10406 Z= 0.199 Angle : 0.681 11.074 14142 Z= 0.340 Chirality : 0.043 0.190 1718 Planarity : 0.004 0.051 1760 Dihedral : 5.548 83.041 1429 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.83 % Allowed : 25.58 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1322 helix: 0.62 (0.18), residues: 854 sheet: -1.49 (1.00), residues: 36 loop : -2.07 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 472 HIS 0.022 0.002 HIS A 656 PHE 0.013 0.001 PHE A 394 TYR 0.014 0.001 TYR B 105 ARG 0.014 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4780.93 seconds wall clock time: 85 minutes 48.88 seconds (5148.88 seconds total)