Starting phenix.real_space_refine on Sun Dec 29 09:08:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk7_32561/12_2024/7wk7_32561.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk7_32561/12_2024/7wk7_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_32561/12_2024/7wk7_32561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk7_32561/12_2024/7wk7_32561.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk7_32561/12_2024/7wk7_32561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk7_32561/12_2024/7wk7_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-5532/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: 6.46, per 1000 atoms: 0.63 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: 2.63 Conformation dependent library (CDL) restraints added in 1.1 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: 1.10 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: 3.15 Time building geometry restraints manager: 2.96 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.390 Find NCS groups from input model: 0.310 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 31.110 ------------------------------------------------------------------------------- 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 : 0.940 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: 0.2674 time to fit residues: 164.7669 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 : 1.074 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.6943 (m-30) cc_final: 0.6686 (t0) REVERT: A 195 LEU cc_start: 0.8369 (tp) cc_final: 0.8105 (tp) REVERT: A 236 LEU cc_start: 0.8543 (tp) cc_final: 0.8015 (tt) REVERT: A 245 LYS cc_start: 0.7825 (ttmm) cc_final: 0.7597 (ttmm) REVERT: A 247 TYR cc_start: 0.7590 (m-10) cc_final: 0.6719 (m-10) REVERT: A 263 ASN cc_start: 0.8227 (t0) cc_final: 0.7912 (t0) REVERT: A 288 LEU cc_start: 0.8812 (tp) cc_final: 0.8610 (tp) REVERT: A 369 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7728 (mmtt) REVERT: A 378 VAL cc_start: 0.8219 (t) cc_final: 0.7863 (p) REVERT: A 384 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6700 (mm-30) REVERT: A 385 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7748 (t80) REVERT: A 391 SER cc_start: 0.8596 (m) cc_final: 0.8209 (p) REVERT: A 394 PHE cc_start: 0.8367 (t80) cc_final: 0.7404 (t80) REVERT: A 398 PHE cc_start: 0.7711 (m-80) cc_final: 0.7272 (m-80) REVERT: A 432 MET cc_start: 0.7333 (tpt) cc_final: 0.6922 (tpt) REVERT: A 436 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8442 (m) REVERT: A 447 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8235 (mtpp) REVERT: A 473 LYS cc_start: 0.8610 (mtpt) cc_final: 0.7915 (mtpt) REVERT: A 546 LYS cc_start: 0.8299 (mttm) cc_final: 0.8091 (mtpp) REVERT: A 556 TYR cc_start: 0.8296 (p90) cc_final: 0.7784 (p90) REVERT: A 560 ASP cc_start: 0.7847 (m-30) cc_final: 0.6457 (m-30) REVERT: A 573 ASP cc_start: 0.7563 (t0) cc_final: 0.7335 (t0) REVERT: A 581 ARG cc_start: 0.7711 (mmt180) cc_final: 0.7488 (mtp85) REVERT: A 677 ARG cc_start: 0.7864 (ptm-80) cc_final: 0.7541 (ttt-90) REVERT: A 698 ASP cc_start: 0.7154 (t0) cc_final: 0.6823 (t0) REVERT: B 34 GLN cc_start: 0.8353 (mt0) cc_final: 0.8140 (mt0) REVERT: B 66 LYS cc_start: 0.8314 (tppt) cc_final: 0.8084 (tppt) REVERT: B 69 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8301 (mt) REVERT: B 100 LEU cc_start: 0.8899 (tp) cc_final: 0.8604 (tp) REVERT: B 195 LEU cc_start: 0.8374 (tp) cc_final: 0.7961 (tp) REVERT: B 213 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7137 (mtt180) REVERT: B 244 THR cc_start: 0.8178 (p) cc_final: 0.7660 (t) REVERT: B 259 GLU cc_start: 0.7934 (tt0) cc_final: 0.7517 (tt0) REVERT: B 276 LEU cc_start: 0.8610 (tp) cc_final: 0.8359 (tt) REVERT: B 287 GLU cc_start: 0.7735 (tp30) cc_final: 0.6779 (tp30) REVERT: B 309 ILE cc_start: 0.8352 (tp) cc_final: 0.8141 (pt) REVERT: B 355 SER cc_start: 0.8471 (m) cc_final: 0.8020 (p) REVERT: B 361 TYR cc_start: 0.8271 (t80) cc_final: 0.7890 (t80) REVERT: B 366 SER cc_start: 0.8382 (t) cc_final: 0.8152 (p) REVERT: B 367 VAL cc_start: 0.8603 (t) cc_final: 0.8277 (m) REVERT: B 370 VAL cc_start: 0.8969 (t) cc_final: 0.8744 (p) REVERT: B 391 SER cc_start: 0.8609 (m) cc_final: 0.8271 (p) REVERT: B 394 PHE cc_start: 0.8364 (t80) cc_final: 0.7277 (t80) REVERT: B 398 PHE cc_start: 0.7701 (m-80) cc_final: 0.7429 (m-10) REVERT: B 414 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6726 (tm-30) REVERT: B 432 MET cc_start: 0.7630 (tpt) cc_final: 0.7228 (tpt) REVERT: B 447 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8267 (mtpt) REVERT: B 473 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8185 (mtpt) REVERT: B 560 ASP cc_start: 0.7532 (m-30) cc_final: 0.7329 (m-30) REVERT: B 702 LYS cc_start: 0.8086 (tptp) cc_final: 0.7164 (ttmm) outliers start: 45 outliers final: 25 residues processed: 400 average time/residue: 0.2616 time to fit residues: 139.7698 Evaluate side-chains 389 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 361 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 129 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 135 HIS B 160 HIS B 382 ASN B 457 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3231 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= 0.239 Angle : 0.634 9.891 14142 Z= 0.327 Chirality : 0.043 0.178 1718 Planarity : 0.004 0.040 1760 Dihedral : 5.485 80.932 1433 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.46 % Allowed : 19.07 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.44 (0.23), residues: 1322 helix: -0.04 (0.17), residues: 856 sheet: -3.26 (0.76), residues: 36 loop : -2.55 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 74 HIS 0.013 0.001 HIS B 160 PHE 0.018 0.001 PHE B 272 TYR 0.014 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 388 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 338 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8050 (tpp-160) cc_final: 0.7642 (mpp-170) REVERT: A 87 ASP cc_start: 0.7079 (m-30) cc_final: 0.6859 (t0) REVERT: A 195 LEU cc_start: 0.8391 (tp) cc_final: 0.8064 (tp) REVERT: A 236 LEU cc_start: 0.8589 (tp) cc_final: 0.8147 (tt) REVERT: A 240 LEU cc_start: 0.8351 (mm) cc_final: 0.8131 (mp) REVERT: A 245 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7617 (ttmm) REVERT: A 247 TYR cc_start: 0.7633 (m-10) cc_final: 0.6785 (m-10) REVERT: A 251 LEU cc_start: 0.8645 (mm) cc_final: 0.8113 (mm) REVERT: A 353 SER cc_start: 0.8447 (m) cc_final: 0.8222 (t) REVERT: A 369 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7758 (mmtt) REVERT: A 384 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6815 (mm-30) REVERT: A 385 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7712 (t80) REVERT: A 391 SER cc_start: 0.8630 (m) cc_final: 0.8197 (p) REVERT: A 394 PHE cc_start: 0.8374 (t80) cc_final: 0.7499 (t80) REVERT: A 398 PHE cc_start: 0.7755 (m-80) cc_final: 0.7281 (m-80) REVERT: A 432 MET cc_start: 0.7315 (tpt) cc_final: 0.6945 (tpt) REVERT: A 436 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8442 (m) REVERT: A 447 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8224 (ttmt) REVERT: A 475 ASN cc_start: 0.6885 (m-40) cc_final: 0.6399 (m-40) REVERT: A 478 ASP cc_start: 0.7073 (m-30) cc_final: 0.6807 (m-30) REVERT: A 531 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7684 (mmmt) REVERT: A 546 LYS cc_start: 0.8314 (mttm) cc_final: 0.8092 (mtpp) REVERT: A 563 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8143 (mmmt) REVERT: A 573 ASP cc_start: 0.7652 (t0) cc_final: 0.7305 (t0) REVERT: A 677 ARG cc_start: 0.7966 (ptm-80) cc_final: 0.7357 (ttt90) REVERT: A 698 ASP cc_start: 0.7201 (t0) cc_final: 0.6803 (t0) REVERT: B 34 GLN cc_start: 0.8331 (mt0) cc_final: 0.8112 (mt0) REVERT: B 66 LYS cc_start: 0.8289 (tppt) cc_final: 0.8074 (tppt) REVERT: B 69 LEU cc_start: 0.8494 (mt) cc_final: 0.8271 (mt) REVERT: B 71 ILE cc_start: 0.8629 (tt) cc_final: 0.8381 (tp) REVERT: B 100 LEU cc_start: 0.8950 (tp) cc_final: 0.8749 (tp) REVERT: B 155 MET cc_start: 0.7542 (mpp) cc_final: 0.7146 (mpp) REVERT: B 195 LEU cc_start: 0.8356 (tp) cc_final: 0.7971 (tp) REVERT: B 244 THR cc_start: 0.8176 (p) cc_final: 0.7548 (t) REVERT: B 259 GLU cc_start: 0.7901 (tt0) cc_final: 0.7486 (tt0) REVERT: B 276 LEU cc_start: 0.8587 (tp) cc_final: 0.8368 (tt) REVERT: B 287 GLU cc_start: 0.7801 (tp30) cc_final: 0.6824 (tp30) REVERT: B 309 ILE cc_start: 0.8354 (tp) cc_final: 0.8120 (pt) REVERT: B 355 SER cc_start: 0.8472 (m) cc_final: 0.8010 (p) REVERT: B 361 TYR cc_start: 0.8355 (t80) cc_final: 0.8006 (t80) REVERT: B 366 SER cc_start: 0.8427 (t) cc_final: 0.8142 (p) REVERT: B 367 VAL cc_start: 0.8679 (t) cc_final: 0.8319 (m) REVERT: B 378 VAL cc_start: 0.8504 (t) cc_final: 0.8245 (m) REVERT: B 384 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7129 (mm-30) REVERT: B 391 SER cc_start: 0.8655 (m) cc_final: 0.8226 (p) REVERT: B 394 PHE cc_start: 0.8357 (t80) cc_final: 0.7215 (t80) REVERT: B 398 PHE cc_start: 0.7719 (m-80) cc_final: 0.7409 (m-80) REVERT: B 414 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6744 (tm-30) REVERT: B 432 MET cc_start: 0.7623 (tpt) cc_final: 0.7250 (tpt) REVERT: B 447 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8276 (mtpt) REVERT: B 459 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8453 (ttpp) REVERT: B 473 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8169 (mtpt) REVERT: B 476 LYS cc_start: 0.8292 (mtpp) cc_final: 0.8078 (mtpp) REVERT: B 478 ASP cc_start: 0.7230 (m-30) cc_final: 0.6997 (m-30) REVERT: B 531 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7663 (mmmt) REVERT: B 674 ARG cc_start: 0.7333 (mtt180) cc_final: 0.7110 (mtm-85) outliers start: 50 outliers final: 36 residues processed: 365 average time/residue: 0.2519 time to fit residues: 124.0312 Evaluate side-chains 352 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 313 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 580 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain 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 459 LYS 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 118 optimal weight: 0.7980 chunk 90 optimal weight: 0.0170 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.0030 chunk 80 optimal weight: 0.1980 chunk 120 optimal weight: 0.4980 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 34 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 overall best weight: 0.1626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 382 ASN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 33 GLN B 457 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10406 Z= 0.172 Angle : 0.604 9.563 14142 Z= 0.310 Chirality : 0.042 0.194 1718 Planarity : 0.004 0.037 1760 Dihedral : 5.530 82.093 1433 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.28 % Allowed : 20.77 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.01 (0.23), residues: 1322 helix: 0.24 (0.18), residues: 852 sheet: -2.93 (0.78), residues: 36 loop : -2.24 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 472 HIS 0.003 0.000 HIS A 656 PHE 0.012 0.001 PHE A 484 TYR 0.016 0.001 TYR B 105 ARG 0.010 0.001 ARG B 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 372 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 324 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8100 (tpp-160) cc_final: 0.7480 (mpp-170) REVERT: A 94 THR cc_start: 0.8292 (t) cc_final: 0.7910 (p) REVERT: A 194 LEU cc_start: 0.8716 (tp) cc_final: 0.8453 (mp) REVERT: A 195 LEU cc_start: 0.8367 (tp) cc_final: 0.8070 (tp) REVERT: A 236 LEU cc_start: 0.8550 (tp) cc_final: 0.8079 (tt) REVERT: A 245 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7654 (ttmm) REVERT: A 247 TYR cc_start: 0.7583 (m-10) cc_final: 0.6959 (m-10) REVERT: A 251 LEU cc_start: 0.8579 (mm) cc_final: 0.8274 (mm) REVERT: A 259 GLU cc_start: 0.7902 (tt0) cc_final: 0.7575 (tp30) REVERT: A 353 SER cc_start: 0.8440 (m) cc_final: 0.8128 (t) REVERT: A 369 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7720 (mmtt) REVERT: A 384 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6820 (mm-30) REVERT: A 385 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7644 (t80) REVERT: A 391 SER cc_start: 0.8624 (m) cc_final: 0.8184 (p) REVERT: A 394 PHE cc_start: 0.8370 (t80) cc_final: 0.7657 (t80) REVERT: A 398 PHE cc_start: 0.7673 (m-80) cc_final: 0.7357 (m-80) REVERT: A 432 MET cc_start: 0.7202 (tpt) cc_final: 0.6837 (tpt) REVERT: A 436 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8433 (m) REVERT: A 447 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8284 (mtpp) REVERT: A 475 ASN cc_start: 0.6799 (m-40) cc_final: 0.6291 (m-40) REVERT: A 478 ASP cc_start: 0.7110 (m-30) cc_final: 0.6882 (m-30) REVERT: A 531 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7700 (mmmt) REVERT: A 546 LYS cc_start: 0.8290 (mttm) cc_final: 0.8020 (mtpp) REVERT: A 560 ASP cc_start: 0.7775 (m-30) cc_final: 0.7518 (m-30) REVERT: A 563 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8181 (mmmt) REVERT: A 573 ASP cc_start: 0.7594 (t0) cc_final: 0.7259 (t0) REVERT: A 677 ARG cc_start: 0.7945 (ptm-80) cc_final: 0.7567 (ttt-90) REVERT: A 698 ASP cc_start: 0.7133 (t0) cc_final: 0.6765 (t0) REVERT: B 27 TYR cc_start: 0.7466 (m-10) cc_final: 0.7141 (m-10) REVERT: B 34 GLN cc_start: 0.8270 (mt0) cc_final: 0.8046 (mt0) REVERT: B 71 ILE cc_start: 0.8587 (tt) cc_final: 0.8257 (tp) REVERT: B 100 LEU cc_start: 0.9056 (tp) cc_final: 0.8830 (tp) REVERT: B 155 MET cc_start: 0.7497 (mpp) cc_final: 0.7237 (mpp) REVERT: B 195 LEU cc_start: 0.8342 (tp) cc_final: 0.7984 (tp) REVERT: B 244 THR cc_start: 0.8204 (p) cc_final: 0.8000 (t) REVERT: B 276 LEU cc_start: 0.8566 (tp) cc_final: 0.8357 (tt) REVERT: B 287 GLU cc_start: 0.7811 (tp30) cc_final: 0.6799 (tp30) REVERT: B 303 GLU cc_start: 0.7823 (mp0) cc_final: 0.7471 (mp0) REVERT: B 309 ILE cc_start: 0.8354 (tp) cc_final: 0.8095 (pt) REVERT: B 361 TYR cc_start: 0.8251 (t80) cc_final: 0.7923 (t80) REVERT: B 366 SER cc_start: 0.8305 (t) cc_final: 0.8090 (p) REVERT: B 373 THR cc_start: 0.8413 (m) cc_final: 0.8059 (t) REVERT: B 382 ASN cc_start: 0.8407 (m-40) cc_final: 0.8010 (t0) REVERT: B 391 SER cc_start: 0.8649 (m) cc_final: 0.8214 (p) REVERT: B 394 PHE cc_start: 0.8348 (t80) cc_final: 0.7269 (t80) REVERT: B 398 PHE cc_start: 0.7667 (m-80) cc_final: 0.7365 (m-80) REVERT: B 432 MET cc_start: 0.7476 (tpt) cc_final: 0.7113 (tpt) REVERT: B 447 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8234 (mtpt) REVERT: B 473 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8204 (mtpt) REVERT: B 475 ASN cc_start: 0.7252 (m-40) cc_final: 0.6836 (m-40) REVERT: B 478 ASP cc_start: 0.7259 (m-30) cc_final: 0.6948 (m-30) REVERT: B 531 LYS cc_start: 0.8230 (mmmt) cc_final: 0.7561 (mmmt) REVERT: B 674 ARG cc_start: 0.7285 (mtt180) cc_final: 0.7055 (mtm-85) REVERT: B 702 LYS cc_start: 0.7650 (tptp) cc_final: 0.7129 (tptm) REVERT: B 714 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7772 (mtm-85) outliers start: 48 outliers final: 33 residues processed: 352 average time/residue: 0.2897 time to fit residues: 135.9917 Evaluate side-chains 344 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 309 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 50 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 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 541 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 52 optimal weight: 0.4980 chunk 108 optimal weight: 0.0970 chunk 88 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.2134 ------------------------------------------------------------------------------- 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 382 ASN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 33 GLN B 457 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10406 Z= 0.182 Angle : 0.623 9.526 14142 Z= 0.315 Chirality : 0.042 0.172 1718 Planarity : 0.004 0.045 1760 Dihedral : 5.547 82.193 1433 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.28 % Allowed : 22.37 % Favored : 73.35 % 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: -0.82 (0.23), residues: 1322 helix: 0.36 (0.18), residues: 852 sheet: -2.43 (0.87), residues: 36 loop : -2.15 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 482 HIS 0.013 0.001 HIS A 656 PHE 0.012 0.001 PHE A 115 TYR 0.019 0.001 TYR B 105 ARG 0.010 0.001 ARG A 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 368 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 320 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8082 (tpp-160) cc_final: 0.7492 (mpp-170) REVERT: A 48 ASP cc_start: 0.8179 (t70) cc_final: 0.7877 (p0) REVERT: A 94 THR cc_start: 0.8381 (t) cc_final: 0.8030 (p) REVERT: A 194 LEU cc_start: 0.8713 (tp) cc_final: 0.8404 (mp) REVERT: A 195 LEU cc_start: 0.8370 (tp) cc_final: 0.8072 (tp) REVERT: A 236 LEU cc_start: 0.8568 (tp) cc_final: 0.8209 (tt) REVERT: A 237 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8274 (tttt) REVERT: A 247 TYR cc_start: 0.7565 (m-10) cc_final: 0.6976 (m-10) REVERT: A 251 LEU cc_start: 0.8483 (mm) cc_final: 0.8172 (mm) REVERT: A 318 ASN cc_start: 0.8072 (t0) cc_final: 0.7736 (t0) REVERT: A 353 SER cc_start: 0.8399 (m) cc_final: 0.8094 (t) REVERT: A 384 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6839 (mm-30) REVERT: A 385 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7645 (t80) REVERT: A 391 SER cc_start: 0.8616 (m) cc_final: 0.8208 (p) REVERT: A 394 PHE cc_start: 0.8369 (t80) cc_final: 0.7665 (t80) REVERT: A 398 PHE cc_start: 0.7664 (m-80) cc_final: 0.7367 (m-80) REVERT: A 414 GLU cc_start: 0.7439 (tm-30) cc_final: 0.6966 (tm-30) REVERT: A 432 MET cc_start: 0.7144 (tpt) cc_final: 0.6794 (tpt) REVERT: A 436 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8436 (m) REVERT: A 447 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8336 (mtpt) REVERT: A 478 ASP cc_start: 0.7234 (m-30) cc_final: 0.6961 (m-30) REVERT: A 531 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7675 (mmmt) REVERT: A 560 ASP cc_start: 0.7733 (m-30) cc_final: 0.7491 (m-30) REVERT: A 563 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8260 (mmmt) REVERT: A 573 ASP cc_start: 0.7579 (t0) cc_final: 0.7251 (t0) REVERT: A 677 ARG cc_start: 0.7942 (ptm-80) cc_final: 0.7417 (ttt90) REVERT: A 698 ASP cc_start: 0.7134 (t0) cc_final: 0.6754 (t0) REVERT: A 704 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7262 (tm-30) REVERT: B 71 ILE cc_start: 0.8590 (tt) cc_final: 0.8372 (tp) REVERT: B 155 MET cc_start: 0.7491 (mpp) cc_final: 0.7287 (mpp) REVERT: B 195 LEU cc_start: 0.8333 (tp) cc_final: 0.7972 (tp) REVERT: B 276 LEU cc_start: 0.8588 (tp) cc_final: 0.8384 (tt) REVERT: B 287 GLU cc_start: 0.7819 (tp30) cc_final: 0.6818 (tp30) REVERT: B 361 TYR cc_start: 0.8324 (t80) cc_final: 0.7993 (t80) REVERT: B 366 SER cc_start: 0.8342 (t) cc_final: 0.8117 (p) REVERT: B 373 THR cc_start: 0.8386 (m) cc_final: 0.8050 (t) REVERT: B 382 ASN cc_start: 0.8485 (m-40) cc_final: 0.8045 (t0) REVERT: B 391 SER cc_start: 0.8672 (m) cc_final: 0.8227 (p) REVERT: B 394 PHE cc_start: 0.8344 (t80) cc_final: 0.7899 (t80) REVERT: B 432 MET cc_start: 0.7438 (tpt) cc_final: 0.7087 (tpt) REVERT: B 447 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8252 (mtpt) REVERT: B 459 LYS cc_start: 0.8660 (ttpp) cc_final: 0.8454 (ttpp) REVERT: B 473 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8215 (mtpt) REVERT: B 475 ASN cc_start: 0.7271 (m-40) cc_final: 0.6826 (m-40) REVERT: B 478 ASP cc_start: 0.7318 (m-30) cc_final: 0.6957 (m-30) REVERT: B 531 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7528 (mmmt) REVERT: B 674 ARG cc_start: 0.7274 (mtt180) cc_final: 0.7050 (mtm-85) REVERT: B 681 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8101 (ttmm) REVERT: B 682 GLU cc_start: 0.7671 (tt0) cc_final: 0.7345 (mt-10) REVERT: B 702 LYS cc_start: 0.7617 (tptp) cc_final: 0.7031 (tptt) REVERT: B 714 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7756 (mtm-85) outliers start: 48 outliers final: 36 residues processed: 350 average time/residue: 0.2590 time to fit residues: 121.5058 Evaluate side-chains 348 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 229 PHE 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 541 GLU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain A residue 671 VAL 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 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 668 LEU Chi-restraints excluded: chain B residue 681 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 31 optimal weight: 0.2980 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 656 HIS B 34 GLN B 135 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10406 Z= 0.220 Angle : 0.640 9.973 14142 Z= 0.324 Chirality : 0.043 0.173 1718 Planarity : 0.004 0.044 1760 Dihedral : 5.510 81.765 1431 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.10 % Allowed : 23.44 % Favored : 72.46 % 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: -0.66 (0.24), residues: 1322 helix: 0.48 (0.18), residues: 852 sheet: -1.99 (0.93), residues: 36 loop : -2.11 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 74 HIS 0.017 0.001 HIS A 656 PHE 0.025 0.001 PHE B 484 TYR 0.021 0.001 TYR B 105 ARG 0.011 0.001 ARG A 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 350 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8102 (tpp-160) cc_final: 0.7430 (mpp-170) REVERT: A 48 ASP cc_start: 0.8197 (t70) cc_final: 0.7873 (p0) REVERT: A 94 THR cc_start: 0.8348 (t) cc_final: 0.7900 (p) REVERT: A 195 LEU cc_start: 0.8394 (tp) cc_final: 0.8101 (tp) REVERT: A 236 LEU cc_start: 0.8543 (tp) cc_final: 0.8178 (tt) REVERT: A 251 LEU cc_start: 0.8470 (mm) cc_final: 0.8166 (mm) REVERT: A 318 ASN cc_start: 0.8129 (t0) cc_final: 0.7801 (t0) REVERT: A 353 SER cc_start: 0.8426 (m) cc_final: 0.8137 (t) REVERT: A 384 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6906 (mm-30) REVERT: A 385 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7618 (t80) REVERT: A 391 SER cc_start: 0.8646 (m) cc_final: 0.8213 (p) REVERT: A 394 PHE cc_start: 0.8388 (t80) cc_final: 0.8184 (t80) REVERT: A 414 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7030 (tm-30) REVERT: A 432 MET cc_start: 0.7193 (tpt) cc_final: 0.6825 (tpt) REVERT: A 436 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8439 (m) REVERT: A 447 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8368 (mtpt) REVERT: A 475 ASN cc_start: 0.6958 (m-40) cc_final: 0.6571 (m-40) REVERT: A 478 ASP cc_start: 0.7327 (m-30) cc_final: 0.7087 (m-30) REVERT: A 531 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7665 (mmmt) REVERT: A 560 ASP cc_start: 0.7758 (m-30) cc_final: 0.7525 (m-30) REVERT: A 567 ASN cc_start: 0.7976 (m-40) cc_final: 0.7760 (m-40) REVERT: A 573 ASP cc_start: 0.7594 (t0) cc_final: 0.6965 (t70) REVERT: A 677 ARG cc_start: 0.8023 (ptm-80) cc_final: 0.7640 (ttt-90) REVERT: A 697 ASP cc_start: 0.7359 (m-30) cc_final: 0.6807 (m-30) REVERT: A 698 ASP cc_start: 0.7160 (t0) cc_final: 0.6789 (t0) REVERT: A 704 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7269 (tm-30) REVERT: B 71 ILE cc_start: 0.8616 (tt) cc_final: 0.8292 (tp) REVERT: B 155 MET cc_start: 0.7546 (mpp) cc_final: 0.7313 (mpp) REVERT: B 195 LEU cc_start: 0.8367 (tp) cc_final: 0.7994 (tp) REVERT: B 263 ASN cc_start: 0.8076 (m-40) cc_final: 0.7782 (t0) REVERT: B 276 LEU cc_start: 0.8599 (tp) cc_final: 0.8383 (tt) REVERT: B 287 GLU cc_start: 0.7837 (tp30) cc_final: 0.6809 (tp30) REVERT: B 366 SER cc_start: 0.8355 (t) cc_final: 0.8132 (p) REVERT: B 373 THR cc_start: 0.8312 (m) cc_final: 0.8023 (t) REVERT: B 377 TYR cc_start: 0.8027 (p90) cc_final: 0.7500 (p90) REVERT: B 382 ASN cc_start: 0.8515 (m-40) cc_final: 0.8088 (t0) REVERT: B 391 SER cc_start: 0.8688 (m) cc_final: 0.8232 (p) REVERT: B 394 PHE cc_start: 0.8407 (t80) cc_final: 0.7987 (t80) REVERT: B 432 MET cc_start: 0.7443 (tpt) cc_final: 0.7084 (tpt) REVERT: B 447 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8256 (mtpt) REVERT: B 459 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8486 (ttpp) REVERT: B 473 LYS cc_start: 0.8443 (mtpt) cc_final: 0.8213 (mtpt) REVERT: B 478 ASP cc_start: 0.7440 (m-30) cc_final: 0.7167 (m-30) REVERT: B 531 LYS cc_start: 0.8211 (mmmt) cc_final: 0.7516 (mmmt) REVERT: B 674 ARG cc_start: 0.7345 (mtt180) cc_final: 0.7116 (mtm-85) REVERT: B 681 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8140 (ttmm) REVERT: B 682 GLU cc_start: 0.7699 (tt0) cc_final: 0.7406 (mt-10) REVERT: B 702 LYS cc_start: 0.7482 (tptp) cc_final: 0.7239 (tptm) REVERT: B 714 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7770 (mtm-85) outliers start: 46 outliers final: 33 residues processed: 334 average time/residue: 0.2678 time to fit residues: 120.3673 Evaluate side-chains 339 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 302 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 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 543 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 671 VAL 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 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 459 LYS Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.0370 chunk 72 optimal weight: 0.2980 chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 382 ASN A 457 ASN A 656 HIS B 34 GLN B 262 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3975 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= 0.211 Angle : 0.637 9.619 14142 Z= 0.321 Chirality : 0.043 0.172 1718 Planarity : 0.004 0.037 1760 Dihedral : 5.564 82.849 1431 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.46 % Allowed : 23.80 % Favored : 71.75 % 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: -0.58 (0.24), residues: 1322 helix: 0.51 (0.18), residues: 860 sheet: -1.67 (0.95), residues: 36 loop : -2.09 (0.30), residues: 426 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 0.021 0.001 PHE B 484 TYR 0.021 0.001 TYR B 105 ARG 0.009 0.001 ARG B 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 355 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 305 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8085 (tpp-160) cc_final: 0.7479 (mpp-170) REVERT: A 48 ASP cc_start: 0.8218 (t70) cc_final: 0.7888 (p0) REVERT: A 195 LEU cc_start: 0.8384 (tp) cc_final: 0.8052 (tp) REVERT: A 236 LEU cc_start: 0.8587 (tp) cc_final: 0.8137 (tt) REVERT: A 318 ASN cc_start: 0.8222 (t0) cc_final: 0.7928 (t0) REVERT: A 353 SER cc_start: 0.8422 (m) cc_final: 0.8144 (t) REVERT: A 384 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6910 (mm-30) REVERT: A 385 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7584 (t80) REVERT: A 391 SER cc_start: 0.8676 (m) cc_final: 0.8255 (p) REVERT: A 394 PHE cc_start: 0.8429 (t80) cc_final: 0.7919 (t80) REVERT: A 398 PHE cc_start: 0.7795 (m-80) cc_final: 0.7092 (m-10) REVERT: A 414 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7052 (tm-30) REVERT: A 432 MET cc_start: 0.7155 (tpt) cc_final: 0.6785 (tpt) REVERT: A 531 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7933 (mmmm) REVERT: A 560 ASP cc_start: 0.7728 (m-30) cc_final: 0.7497 (m-30) REVERT: A 563 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8239 (mmmt) REVERT: A 573 ASP cc_start: 0.7534 (t0) cc_final: 0.6903 (t70) REVERT: A 677 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7707 (ttt-90) REVERT: A 697 ASP cc_start: 0.7355 (m-30) cc_final: 0.6752 (m-30) REVERT: A 698 ASP cc_start: 0.7167 (t0) cc_final: 0.6791 (t0) REVERT: A 704 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7277 (tm-30) REVERT: B 66 LYS cc_start: 0.8093 (tppt) cc_final: 0.7807 (tppt) REVERT: B 71 ILE cc_start: 0.8610 (tt) cc_final: 0.8263 (tp) REVERT: B 155 MET cc_start: 0.7537 (mpp) cc_final: 0.7316 (mpp) REVERT: B 195 LEU cc_start: 0.8365 (tp) cc_final: 0.8005 (tp) REVERT: B 237 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8568 (ttmt) REVERT: B 286 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8408 (mtmm) REVERT: B 287 GLU cc_start: 0.7857 (tp30) cc_final: 0.6870 (tp30) REVERT: B 366 SER cc_start: 0.8353 (t) cc_final: 0.8133 (p) REVERT: B 373 THR cc_start: 0.8279 (m) cc_final: 0.8011 (t) REVERT: B 382 ASN cc_start: 0.8526 (m-40) cc_final: 0.8082 (t0) REVERT: B 391 SER cc_start: 0.8701 (m) cc_final: 0.8235 (p) REVERT: B 394 PHE cc_start: 0.8384 (t80) cc_final: 0.7982 (t80) REVERT: B 432 MET cc_start: 0.7422 (tpt) cc_final: 0.7051 (tpt) REVERT: B 447 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8234 (mtpt) REVERT: B 459 LYS cc_start: 0.8690 (ttpp) cc_final: 0.8476 (ttpp) REVERT: B 473 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8205 (mtpt) REVERT: B 478 ASP cc_start: 0.7525 (m-30) cc_final: 0.7144 (m-30) REVERT: B 531 LYS cc_start: 0.8246 (mmmt) cc_final: 0.7511 (mmmt) REVERT: B 674 ARG cc_start: 0.7331 (mtt180) cc_final: 0.7111 (mtm-85) REVERT: B 681 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8120 (ttmm) REVERT: B 702 LYS cc_start: 0.7460 (tptp) cc_final: 0.7243 (tptm) outliers start: 50 outliers final: 36 residues processed: 336 average time/residue: 0.2660 time to fit residues: 119.4283 Evaluate side-chains 343 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 304 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 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 457 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 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 135 HIS 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 244 THR Chi-restraints excluded: chain B residue 246 ASN 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 540 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain B residue 697 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 382 ASN A 457 ASN A 656 HIS A 728 HIS B 34 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10406 Z= 0.268 Angle : 0.673 9.748 14142 Z= 0.340 Chirality : 0.045 0.229 1718 Planarity : 0.004 0.050 1760 Dihedral : 5.645 81.751 1431 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.46 % Allowed : 23.62 % Favored : 71.93 % 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: 0.52 (0.18), residues: 858 sheet: -1.45 (0.97), residues: 36 loop : -1.99 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.015 0.001 HIS A 656 PHE 0.021 0.001 PHE B 272 TYR 0.020 0.002 TYR B 105 ARG 0.013 0.001 ARG B 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 363 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 313 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8244 (t70) cc_final: 0.7904 (p0) REVERT: A 195 LEU cc_start: 0.8409 (tp) cc_final: 0.8146 (tp) REVERT: A 236 LEU cc_start: 0.8592 (tp) cc_final: 0.8184 (tt) REVERT: A 384 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6995 (mm-30) REVERT: A 385 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7553 (t80) REVERT: A 391 SER cc_start: 0.8715 (m) cc_final: 0.8288 (p) REVERT: A 394 PHE cc_start: 0.8460 (t80) cc_final: 0.7914 (t80) REVERT: A 398 PHE cc_start: 0.7838 (m-80) cc_final: 0.7244 (m-10) REVERT: A 414 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7106 (tm-30) REVERT: A 432 MET cc_start: 0.7207 (tpt) cc_final: 0.6842 (tpt) REVERT: A 447 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8450 (mmmm) REVERT: A 560 ASP cc_start: 0.7693 (m-30) cc_final: 0.7486 (m-30) REVERT: A 563 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8241 (mmmt) REVERT: A 573 ASP cc_start: 0.7603 (t0) cc_final: 0.7096 (t0) REVERT: A 677 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7714 (ttt-90) REVERT: A 697 ASP cc_start: 0.7396 (m-30) cc_final: 0.6793 (m-30) REVERT: A 698 ASP cc_start: 0.7188 (t0) cc_final: 0.6839 (t0) REVERT: A 704 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7354 (tm-30) REVERT: B 66 LYS cc_start: 0.8103 (tppt) cc_final: 0.7827 (tppt) REVERT: B 71 ILE cc_start: 0.8685 (tt) cc_final: 0.8356 (tp) REVERT: B 155 MET cc_start: 0.7538 (mpp) cc_final: 0.7289 (mpp) REVERT: B 193 THR cc_start: 0.8648 (m) cc_final: 0.8293 (p) REVERT: B 195 LEU cc_start: 0.8382 (tp) cc_final: 0.8024 (tp) REVERT: B 207 GLN cc_start: 0.7999 (mm110) cc_final: 0.7688 (mm-40) REVERT: B 286 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8396 (mtmm) REVERT: B 287 GLU cc_start: 0.7888 (tp30) cc_final: 0.6915 (tp30) REVERT: B 366 SER cc_start: 0.8385 (t) cc_final: 0.8138 (p) REVERT: B 373 THR cc_start: 0.8275 (m) cc_final: 0.8021 (t) REVERT: B 378 VAL cc_start: 0.8479 (t) cc_final: 0.8189 (p) REVERT: B 382 ASN cc_start: 0.8578 (m-40) cc_final: 0.8102 (t0) REVERT: B 391 SER cc_start: 0.8751 (m) cc_final: 0.8267 (p) REVERT: B 394 PHE cc_start: 0.8402 (t80) cc_final: 0.8034 (t80) REVERT: B 432 MET cc_start: 0.7451 (tpt) cc_final: 0.7075 (tpt) REVERT: B 447 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8267 (mtpt) REVERT: B 459 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8503 (ttpp) REVERT: B 473 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8246 (mtpt) REVERT: B 531 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7552 (mmmt) REVERT: B 677 ARG cc_start: 0.8138 (tpt-90) cc_final: 0.7840 (tpt-90) REVERT: B 681 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8123 (ttmm) outliers start: 50 outliers final: 33 residues processed: 343 average time/residue: 0.2913 time to fit residues: 130.4106 Evaluate side-chains 342 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 305 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 457 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 682 GLU 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 135 HIS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 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 459 LYS 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 697 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.0270 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 135 HIS A 160 HIS A 382 ASN A 457 ASN A 656 HIS ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10406 Z= 0.257 Angle : 0.684 11.685 14142 Z= 0.344 Chirality : 0.045 0.217 1718 Planarity : 0.004 0.049 1760 Dihedral : 5.699 82.287 1431 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.92 % Allowed : 24.69 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.24), residues: 1322 helix: 0.52 (0.18), residues: 858 sheet: -1.38 (0.98), residues: 36 loop : -1.92 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 472 HIS 0.013 0.001 HIS A 656 PHE 0.015 0.001 PHE B 484 TYR 0.019 0.001 TYR B 105 ARG 0.014 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 363 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 319 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8247 (t70) cc_final: 0.7880 (p0) REVERT: A 195 LEU cc_start: 0.8317 (tp) cc_final: 0.8091 (tp) REVERT: A 236 LEU cc_start: 0.8605 (tp) cc_final: 0.8224 (tt) REVERT: A 276 LEU cc_start: 0.8656 (tp) cc_final: 0.8306 (tp) REVERT: A 378 VAL cc_start: 0.8265 (t) cc_final: 0.7998 (p) REVERT: A 391 SER cc_start: 0.8708 (m) cc_final: 0.8326 (p) REVERT: A 394 PHE cc_start: 0.8467 (t80) cc_final: 0.7794 (t80) REVERT: A 398 PHE cc_start: 0.7829 (m-80) cc_final: 0.7274 (m-80) REVERT: A 414 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 432 MET cc_start: 0.7191 (tpt) cc_final: 0.6806 (tpt) REVERT: A 447 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8436 (mmmm) REVERT: A 521 LEU cc_start: 0.8674 (mp) cc_final: 0.8465 (mp) REVERT: A 560 ASP cc_start: 0.7651 (m-30) cc_final: 0.7440 (m-30) REVERT: A 573 ASP cc_start: 0.7605 (t0) cc_final: 0.7322 (t0) REVERT: A 587 ARG cc_start: 0.7090 (mmm-85) cc_final: 0.6864 (tpt170) REVERT: A 677 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7719 (ttt-90) REVERT: A 698 ASP cc_start: 0.7168 (t0) cc_final: 0.6837 (t0) REVERT: A 704 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7358 (tm-30) REVERT: B 66 LYS cc_start: 0.8101 (tppt) cc_final: 0.7838 (tppt) REVERT: B 71 ILE cc_start: 0.8672 (tt) cc_final: 0.8320 (tp) REVERT: B 155 MET cc_start: 0.7533 (mpp) cc_final: 0.7282 (mpp) REVERT: B 193 THR cc_start: 0.8635 (m) cc_final: 0.8282 (p) REVERT: B 195 LEU cc_start: 0.8384 (tp) cc_final: 0.8019 (tp) REVERT: B 207 GLN cc_start: 0.8024 (mm110) cc_final: 0.7695 (mm-40) REVERT: B 286 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8420 (mtmm) REVERT: B 287 GLU cc_start: 0.7896 (tp30) cc_final: 0.6925 (tp30) REVERT: B 366 SER cc_start: 0.8393 (t) cc_final: 0.8138 (p) REVERT: B 373 THR cc_start: 0.8231 (m) cc_final: 0.7998 (t) REVERT: B 378 VAL cc_start: 0.8486 (t) cc_final: 0.8189 (p) REVERT: B 382 ASN cc_start: 0.8553 (m-40) cc_final: 0.8138 (t0) REVERT: B 391 SER cc_start: 0.8750 (m) cc_final: 0.8256 (p) REVERT: B 394 PHE cc_start: 0.8399 (t80) cc_final: 0.8030 (t80) REVERT: B 432 MET cc_start: 0.7474 (tpt) cc_final: 0.7078 (tpt) REVERT: B 447 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8264 (mtpt) REVERT: B 473 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8256 (mtpt) REVERT: B 478 ASP cc_start: 0.7467 (m-30) cc_final: 0.7173 (m-30) REVERT: B 677 ARG cc_start: 0.8091 (tpt-90) cc_final: 0.7790 (tpt-90) REVERT: B 681 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8093 (ttmm) outliers start: 44 outliers final: 32 residues processed: 349 average time/residue: 0.2886 time to fit residues: 132.0357 Evaluate side-chains 342 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 308 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 229 PHE 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 382 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 682 GLU 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 113 VAL 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 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 668 LEU Chi-restraints excluded: chain B residue 681 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.0770 chunk 87 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 0.0570 chunk 64 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 32 optimal weight: 0.0970 overall best weight: 0.2454 ------------------------------------------------------------------------------- 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 457 ASN A 656 HIS ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10406 Z= 0.201 Angle : 0.688 11.539 14142 Z= 0.342 Chirality : 0.044 0.190 1718 Planarity : 0.004 0.049 1760 Dihedral : 5.586 83.019 1429 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.30 % Allowed : 25.85 % 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: -0.35 (0.24), residues: 1322 helix: 0.68 (0.18), residues: 850 sheet: -1.37 (0.99), residues: 36 loop : -1.93 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.013 0.001 HIS A 656 PHE 0.021 0.001 PHE B 484 TYR 0.017 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 364 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 327 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8132 (tpp-160) cc_final: 0.7499 (mpp-170) REVERT: A 48 ASP cc_start: 0.8236 (t70) cc_final: 0.7876 (p0) REVERT: A 195 LEU cc_start: 0.8309 (tp) cc_final: 0.8083 (tp) REVERT: A 236 LEU cc_start: 0.8613 (tp) cc_final: 0.8205 (tt) REVERT: A 303 GLU cc_start: 0.7610 (mp0) cc_final: 0.7329 (mp0) REVERT: A 378 VAL cc_start: 0.8258 (t) cc_final: 0.8009 (p) REVERT: A 385 PHE cc_start: 0.8391 (t80) cc_final: 0.8089 (m-80) REVERT: A 391 SER cc_start: 0.8711 (m) cc_final: 0.8313 (p) REVERT: A 394 PHE cc_start: 0.8465 (t80) cc_final: 0.7962 (t80) REVERT: A 398 PHE cc_start: 0.7753 (m-80) cc_final: 0.7320 (m-10) REVERT: A 414 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 432 MET cc_start: 0.7097 (tpt) cc_final: 0.6727 (tpt) REVERT: A 447 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8399 (mmmm) REVERT: A 521 LEU cc_start: 0.8544 (mp) cc_final: 0.8324 (mt) REVERT: A 560 ASP cc_start: 0.7627 (m-30) cc_final: 0.7409 (m-30) REVERT: A 563 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8219 (mmmt) REVERT: A 573 ASP cc_start: 0.7542 (t0) cc_final: 0.7267 (t0) REVERT: A 677 ARG cc_start: 0.8072 (ptm-80) cc_final: 0.7711 (ttt-90) REVERT: A 698 ASP cc_start: 0.7124 (t0) cc_final: 0.6779 (t0) REVERT: A 704 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7312 (tm-30) REVERT: B 66 LYS cc_start: 0.8029 (tppt) cc_final: 0.7788 (tppt) REVERT: B 71 ILE cc_start: 0.8592 (tt) cc_final: 0.8252 (tp) REVERT: B 155 MET cc_start: 0.7456 (mpp) cc_final: 0.7214 (mpp) REVERT: B 195 LEU cc_start: 0.8370 (tp) cc_final: 0.8017 (tp) REVERT: B 207 GLN cc_start: 0.7955 (mm110) cc_final: 0.7681 (mm-40) REVERT: B 286 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8426 (mtmm) REVERT: B 287 GLU cc_start: 0.7871 (tp30) cc_final: 0.6901 (tp30) REVERT: B 318 ASN cc_start: 0.8304 (t0) cc_final: 0.7566 (t0) REVERT: B 324 ASN cc_start: 0.8384 (t0) cc_final: 0.7997 (t0) REVERT: B 366 SER cc_start: 0.8361 (t) cc_final: 0.8121 (p) REVERT: B 373 THR cc_start: 0.8202 (m) cc_final: 0.7988 (t) REVERT: B 378 VAL cc_start: 0.8422 (t) cc_final: 0.8138 (p) REVERT: B 391 SER cc_start: 0.8728 (m) cc_final: 0.8242 (p) REVERT: B 394 PHE cc_start: 0.8381 (t80) cc_final: 0.8020 (t80) REVERT: B 432 MET cc_start: 0.7364 (tpt) cc_final: 0.6975 (tpt) REVERT: B 447 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8220 (mtpt) REVERT: B 473 LYS cc_start: 0.8467 (mtpt) cc_final: 0.8226 (mtpt) REVERT: B 478 ASP cc_start: 0.7388 (m-30) cc_final: 0.7080 (m-30) REVERT: B 521 LEU cc_start: 0.8725 (mp) cc_final: 0.8500 (mp) REVERT: B 567 ASN cc_start: 0.7927 (m-40) cc_final: 0.7694 (m110) REVERT: B 677 ARG cc_start: 0.8108 (tpt-90) cc_final: 0.7815 (tpt-90) REVERT: B 681 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8079 (ttmm) REVERT: B 702 LYS cc_start: 0.8048 (tptm) cc_final: 0.7843 (tptp) outliers start: 37 outliers final: 33 residues processed: 352 average time/residue: 0.2991 time to fit residues: 140.3471 Evaluate side-chains 335 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 301 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 229 PHE 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 457 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 682 GLU 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 279 ILE 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 543 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 0.0770 chunk 104 optimal weight: 0.0980 chunk 43 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.0040 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 0.0030 overall best weight: 0.1160 ------------------------------------------------------------------------------- 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 457 ASN A 656 HIS B 241 ASN ** 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 = 0.3698 r_free = 0.3698 target = 0.123436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104504 restraints weight = 17871.271| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.91 r_work: 0.3272 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10406 Z= 0.192 Angle : 0.691 11.596 14142 Z= 0.346 Chirality : 0.043 0.179 1718 Planarity : 0.005 0.052 1760 Dihedral : 5.578 82.970 1429 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.01 % Allowed : 25.40 % 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: -0.31 (0.24), residues: 1322 helix: 0.71 (0.18), residues: 850 sheet: -1.26 (1.00), residues: 36 loop : -1.93 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 472 HIS 0.013 0.001 HIS A 656 PHE 0.018 0.001 PHE B 484 TYR 0.021 0.001 TYR B 578 ARG 0.015 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3085.80 seconds wall clock time: 57 minutes 1.31 seconds (3421.31 seconds total)