Starting phenix.real_space_refine on Mon Dec 30 08:22:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgv_44524/12_2024/9bgv_44524.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgv_44524/12_2024/9bgv_44524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bgv_44524/12_2024/9bgv_44524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgv_44524/12_2024/9bgv_44524.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgv_44524/12_2024/9bgv_44524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgv_44524/12_2024/9bgv_44524.cif" } resolution = 3.65 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= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 66 5.16 5 C 7984 2.51 5 N 2192 2.21 5 O 2344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12588 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6251 Classifications: {'peptide': 787} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 751} Chain: "B" Number of atoms: 6251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6251 Classifications: {'peptide': 787} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 751} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.72, per 1000 atoms: 0.61 Number of scatterers: 12588 At special positions: 0 Unit cell: (87.9038, 102.554, 203.777, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 66 16.00 O 2344 8.00 N 2192 7.00 C 7984 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.8 seconds 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 15 sheets defined 46.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.983A pdb=" N GLN A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.610A pdb=" N MET A 67 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 133 through 153 removed outlier: 4.566A pdb=" N GLN A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 201 through 210 removed outlier: 3.993A pdb=" N GLN A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 Processing helix chain 'A' and resid 278 through 294 removed outlier: 3.556A pdb=" N GLU A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 381 removed outlier: 3.561A pdb=" N HIS A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 408 Processing helix chain 'A' and resid 421 through 429 removed outlier: 4.004A pdb=" N VAL A 425 " --> pdb=" O HIS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 448 Processing helix chain 'A' and resid 471 through 485 Processing helix chain 'A' and resid 514 through 531 removed outlier: 4.349A pdb=" N ALA A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 562 removed outlier: 3.693A pdb=" N LYS A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 Proline residue: A 604 - end of helix removed outlier: 3.569A pdb=" N GLY A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 632 removed outlier: 3.819A pdb=" N ILE A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 removed outlier: 4.097A pdb=" N GLN A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS A 663 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.798A pdb=" N ILE A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 695 " --> pdb=" O ARG A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 removed outlier: 3.859A pdb=" N VAL A 732 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 728 through 733' Processing helix chain 'A' and resid 740 through 756 removed outlier: 3.804A pdb=" N LEU A 744 " --> pdb=" O ARG A 740 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 776 removed outlier: 4.118A pdb=" N ILE A 776 " --> pdb=" O MET A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 793 No H-bonds generated for 'chain 'A' and resid 791 through 793' Processing helix chain 'A' and resid 794 through 802 removed outlier: 4.419A pdb=" N SER A 800 " --> pdb=" O PRO A 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 28 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.805A pdb=" N VAL B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 removed outlier: 4.132A pdb=" N GLY B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 152 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 256 through 274 Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.675A pdb=" N GLU B 284 " --> pdb=" O HIS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 382 removed outlier: 4.172A pdb=" N LEU B 369 " --> pdb=" O HIS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 408 removed outlier: 4.194A pdb=" N ASN B 400 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP B 404 " --> pdb=" O ASN B 400 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 429 Processing helix chain 'B' and resid 430 through 449 Processing helix chain 'B' and resid 471 through 485 removed outlier: 3.510A pdb=" N GLN B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 removed outlier: 3.595A pdb=" N LEU B 516 " --> pdb=" O ASN B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 563 removed outlier: 4.610A pdb=" N MET B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL B 546 " --> pdb=" O MET B 542 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 610 Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 611 through 633 removed outlier: 3.692A pdb=" N TRP B 630 " --> pdb=" O GLN B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 666 removed outlier: 3.689A pdb=" N VAL B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP B 665 " --> pdb=" O ALA B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 670 No H-bonds generated for 'chain 'B' and resid 668 through 670' Processing helix chain 'B' and resid 685 through 690 Processing helix chain 'B' and resid 691 through 699 removed outlier: 4.197A pdb=" N LEU B 695 " --> pdb=" O ARG B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 719 Processing helix chain 'B' and resid 728 through 733 removed outlier: 3.532A pdb=" N VAL B 732 " --> pdb=" O ASP B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 756 removed outlier: 3.700A pdb=" N LEU B 744 " --> pdb=" O ARG B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 777 Processing helix chain 'B' and resid 794 through 802 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.632A pdb=" N MET A 43 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 35 " --> pdb=" O MET A 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE A 45 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ALA A 33 " --> pdb=" O PHE A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 169 removed outlier: 6.386A pdb=" N VAL A 159 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS A 169 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A 157 " --> pdb=" O CYS A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 314 removed outlier: 6.911A pdb=" N LEU A 301 " --> pdb=" O TRP A 312 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER A 314 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A 299 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 339 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 331 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE A 341 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA A 329 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN A 343 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP A 327 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS A 345 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN A 325 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 454 through 459 removed outlier: 5.394A pdb=" N LEU A 455 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 466 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ARG A 457 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 464 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 504 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU A 501 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N GLN A 536 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 503 " --> pdb=" O GLN A 536 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 566 through 568 Processing sheet with id=AA6, first strand: chain 'A' and resid 640 through 641 removed outlier: 7.826A pdb=" N SER A 641 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 583 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN A 572 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 725 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLU A 762 " --> pdb=" O ILE A 725 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 673 through 676 removed outlier: 3.786A pdb=" N ILE A 676 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.024A pdb=" N LEU B 35 " --> pdb=" O MET B 43 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 45 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA B 33 " --> pdb=" O PHE B 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.024A pdb=" N LEU B 35 " --> pdb=" O MET B 43 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 45 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA B 33 " --> pdb=" O PHE B 45 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 158 through 160 removed outlier: 3.666A pdb=" N SER B 235 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 308 through 314 removed outlier: 6.651A pdb=" N LEU B 301 " --> pdb=" O TRP B 312 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER B 314 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 299 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA B 339 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 331 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE B 341 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA B 329 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLN B 343 " --> pdb=" O TRP B 327 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP B 327 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS B 345 " --> pdb=" O GLN B 325 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLN B 325 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 454 through 459 removed outlier: 7.001A pdb=" N GLN B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 500 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AB5, first strand: chain 'B' and resid 790 through 791 removed outlier: 4.563A pdb=" N GLY B 783 " --> pdb=" O PRO B 571 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL B 759 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLN B 782 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA B 761 " --> pdb=" O GLN B 782 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B 725 " --> pdb=" O VAL B 760 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLU B 762 " --> pdb=" O ILE B 725 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE B 727 " --> pdb=" O GLU B 762 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL B 764 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 704 " --> pdb=" O LYS B 726 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N SER B 703 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 674 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 675 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU B 580 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B 574 " --> pdb=" O LEU B 580 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 590 through 591 removed outlier: 3.625A pdb=" N ASP B 591 " --> pdb=" O GLY B 595 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1800 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: 4.93 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 5149 1.39 - 1.57: 7585 1.57 - 1.75: 0 1.75 - 1.92: 116 1.92 - 2.10: 8 Bond restraints: 12858 Sorted by residual: bond pdb=" N HIS A 77 " pdb=" CA HIS A 77 " ideal model delta sigma weight residual 1.462 1.486 -0.024 7.70e-03 1.69e+04 9.86e+00 bond pdb=" N GLU B 197 " pdb=" CA GLU B 197 " ideal model delta sigma weight residual 1.457 1.491 -0.035 1.40e-02 5.10e+03 6.14e+00 bond pdb=" N PHE B 198 " pdb=" CA PHE B 198 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.41e-02 5.03e+03 5.37e+00 bond pdb=" CA LEU A 210 " pdb=" C LEU A 210 " ideal model delta sigma weight residual 1.522 1.494 0.028 1.38e-02 5.25e+03 4.26e+00 bond pdb=" N ASP B 201 " pdb=" CA ASP B 201 " ideal model delta sigma weight residual 1.463 1.488 -0.024 1.31e-02 5.83e+03 3.47e+00 ... (remaining 12853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 16897 1.71 - 3.42: 467 3.42 - 5.14: 65 5.14 - 6.85: 13 6.85 - 8.56: 8 Bond angle restraints: 17450 Sorted by residual: angle pdb=" N VAL A 722 " pdb=" CA VAL A 722 " pdb=" C VAL A 722 " ideal model delta sigma weight residual 111.91 106.86 5.05 8.90e-01 1.26e+00 3.22e+01 angle pdb=" N GLY B 336 " pdb=" CA GLY B 336 " pdb=" C GLY B 336 " ideal model delta sigma weight residual 111.21 116.87 -5.66 1.04e+00 9.25e-01 2.96e+01 angle pdb=" C PRO B 199 " pdb=" CA PRO B 199 " pdb=" CB PRO B 199 " ideal model delta sigma weight residual 113.09 107.87 5.22 1.36e+00 5.41e-01 1.48e+01 angle pdb=" C PRO A 540 " pdb=" N ALA A 541 " pdb=" CA ALA A 541 " ideal model delta sigma weight residual 122.46 115.67 6.79 1.80e+00 3.09e-01 1.42e+01 angle pdb=" CA ASP B 201 " pdb=" C ASP B 201 " pdb=" O ASP B 201 " ideal model delta sigma weight residual 122.37 118.23 4.14 1.15e+00 7.56e-01 1.30e+01 ... (remaining 17445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6955 17.73 - 35.45: 663 35.45 - 53.18: 106 53.18 - 70.91: 27 70.91 - 88.63: 17 Dihedral angle restraints: 7768 sinusoidal: 3196 harmonic: 4572 Sorted by residual: dihedral pdb=" CA PRO B 199 " pdb=" C PRO B 199 " pdb=" N ALA B 200 " pdb=" CA ALA B 200 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA HIS A 152 " pdb=" C HIS A 152 " pdb=" N LEU A 153 " pdb=" CA LEU A 153 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLN A 536 " pdb=" C GLN A 536 " pdb=" N PHE A 537 " pdb=" CA PHE A 537 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 7765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1183 0.035 - 0.069: 479 0.069 - 0.104: 199 0.104 - 0.139: 64 0.139 - 0.173: 5 Chirality restraints: 1930 Sorted by residual: chirality pdb=" CB VAL B 718 " pdb=" CA VAL B 718 " pdb=" CG1 VAL B 718 " pdb=" CG2 VAL B 718 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CB ILE B 503 " pdb=" CA ILE B 503 " pdb=" CG1 ILE B 503 " pdb=" CG2 ILE B 503 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA ASN B 756 " pdb=" N ASN B 756 " pdb=" C ASN B 756 " pdb=" CB ASN B 756 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 1927 not shown) Planarity restraints: 2270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 392 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 393 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 393 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 393 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 161 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO B 162 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 161 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO A 162 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " -0.022 5.00e-02 4.00e+02 ... (remaining 2267 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 69 2.49 - 3.09: 9171 3.09 - 3.70: 19374 3.70 - 4.30: 26440 4.30 - 4.90: 43835 Nonbonded interactions: 98889 Sorted by model distance: nonbonded pdb=" CE1 PHE B 198 " pdb=" CB ALA B 200 " model vdw 1.891 3.760 nonbonded pdb=" CZ PHE B 198 " pdb=" CB ALA B 200 " model vdw 1.960 3.760 nonbonded pdb=" NE2 GLN A 142 " pdb=" OE1 GLN B 168 " model vdw 2.158 3.120 nonbonded pdb=" OG1 THR A 226 " pdb=" OE1 GLU A 228 " model vdw 2.199 3.040 nonbonded pdb=" OG SER B 297 " pdb=" O LYS B 345 " model vdw 2.203 3.040 ... (remaining 98884 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 group one per residue 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: 1.410 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.420 Find NCS groups from input model: 0.380 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 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 : 0.005 0.098 12858 Z= 0.296 Angle : 0.692 8.560 17450 Z= 0.385 Chirality : 0.046 0.173 1930 Planarity : 0.005 0.048 2270 Dihedral : 14.633 88.633 4800 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.07 % Allowed : 2.05 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.54 (0.22), residues: 1570 helix: 0.66 (0.21), residues: 656 sheet: -0.67 (0.28), residues: 308 loop : -1.23 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 589 HIS 0.004 0.001 HIS A 521 PHE 0.018 0.002 PHE B 602 TYR 0.020 0.002 TYR A 507 ARG 0.006 0.000 ARG B 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.3936 (tpt) cc_final: 0.3577 (tpt) REVERT: A 95 MET cc_start: 0.3926 (mtp) cc_final: 0.3674 (mtp) REVERT: A 185 SER cc_start: 0.7496 (t) cc_final: 0.7229 (p) REVERT: A 279 PHE cc_start: 0.7197 (t80) cc_final: 0.6641 (t80) REVERT: A 282 MET cc_start: 0.8093 (tpp) cc_final: 0.7272 (ttm) REVERT: A 364 GLN cc_start: 0.7732 (pp30) cc_final: 0.7059 (tm-30) REVERT: A 452 ASP cc_start: 0.7166 (t70) cc_final: 0.6829 (t0) REVERT: A 457 ARG cc_start: 0.5662 (ttt-90) cc_final: 0.4641 (ttt-90) REVERT: A 524 MET cc_start: 0.7178 (tmm) cc_final: 0.6810 (tmm) REVERT: A 557 LYS cc_start: 0.8437 (ttmm) cc_final: 0.8189 (ttmm) REVERT: A 571 PRO cc_start: 0.8100 (Cg_endo) cc_final: 0.7869 (Cg_exo) REVERT: A 596 HIS cc_start: 0.4704 (t70) cc_final: 0.4450 (t70) REVERT: A 687 GLU cc_start: 0.6108 (pm20) cc_final: 0.5806 (pm20) REVERT: A 729 LYS cc_start: 0.7147 (tptp) cc_final: 0.6398 (tptt) REVERT: A 745 LEU cc_start: 0.8142 (mt) cc_final: 0.7848 (mt) REVERT: A 762 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6601 (tm-30) REVERT: A 778 CYS cc_start: 0.7713 (t) cc_final: 0.7463 (t) REVERT: A 794 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6874 (mt-10) REVERT: B 98 GLU cc_start: 0.8123 (pm20) cc_final: 0.7914 (pm20) REVERT: B 177 PHE cc_start: 0.7605 (m-80) cc_final: 0.7398 (m-80) REVERT: B 279 PHE cc_start: 0.7435 (t80) cc_final: 0.7138 (t80) REVERT: B 282 MET cc_start: 0.5374 (tpt) cc_final: 0.5110 (tpt) REVERT: B 298 HIS cc_start: 0.7041 (t-90) cc_final: 0.6658 (t-90) REVERT: B 345 LYS cc_start: 0.7875 (ptpp) cc_final: 0.7076 (ptpp) REVERT: B 448 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7655 (ttmm) REVERT: B 449 LEU cc_start: 0.7849 (pp) cc_final: 0.7604 (tp) REVERT: B 480 ASP cc_start: 0.6985 (m-30) cc_final: 0.6470 (m-30) REVERT: B 493 ASP cc_start: 0.6854 (t0) cc_final: 0.6551 (t0) REVERT: B 495 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7477 (ttmm) REVERT: B 529 LYS cc_start: 0.8113 (tmtt) cc_final: 0.7644 (tmtt) REVERT: B 590 HIS cc_start: 0.6636 (t70) cc_final: 0.6393 (t70) REVERT: B 614 ASN cc_start: 0.7347 (m-40) cc_final: 0.6977 (m-40) REVERT: B 716 ARG cc_start: 0.7086 (mmm160) cc_final: 0.6701 (mmm160) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.3146 time to fit residues: 138.3499 Evaluate side-chains 286 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 562 ASN A 670 HIS B 474 ASN B 521 HIS B 564 GLN B 626 GLN B 670 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 12858 Z= 0.284 Angle : 0.691 12.907 17450 Z= 0.347 Chirality : 0.047 0.180 1930 Planarity : 0.005 0.074 2270 Dihedral : 6.329 70.960 1712 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.76 % Allowed : 13.12 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.45 (0.22), residues: 1570 helix: 0.67 (0.21), residues: 654 sheet: -0.57 (0.28), residues: 323 loop : -1.13 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 589 HIS 0.012 0.001 HIS B 77 PHE 0.029 0.002 PHE B 602 TYR 0.016 0.002 TYR A 507 ARG 0.008 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 303 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.3896 (mtp) cc_final: 0.3632 (mtp) REVERT: A 163 GLU cc_start: 0.7312 (mp0) cc_final: 0.7074 (mp0) REVERT: A 279 PHE cc_start: 0.7232 (t80) cc_final: 0.6473 (t80) REVERT: A 282 MET cc_start: 0.8238 (tpp) cc_final: 0.7856 (ttm) REVERT: A 345 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7886 (mttt) REVERT: A 364 GLN cc_start: 0.7737 (pp30) cc_final: 0.7111 (tm-30) REVERT: A 389 MET cc_start: 0.6938 (ttp) cc_final: 0.6585 (ttm) REVERT: A 452 ASP cc_start: 0.7196 (t70) cc_final: 0.6849 (t0) REVERT: A 502 SER cc_start: 0.7360 (t) cc_final: 0.7136 (t) REVERT: A 525 ASP cc_start: 0.6142 (t70) cc_final: 0.5803 (t0) REVERT: A 665 TRP cc_start: 0.5939 (m-90) cc_final: 0.5725 (m-90) REVERT: A 678 GLU cc_start: 0.7370 (pm20) cc_final: 0.7166 (pp20) REVERT: A 716 ARG cc_start: 0.7034 (tpp-160) cc_final: 0.6746 (mmm160) REVERT: A 745 LEU cc_start: 0.8032 (mt) cc_final: 0.7778 (mt) REVERT: A 751 ILE cc_start: 0.5686 (OUTLIER) cc_final: 0.5364 (mp) REVERT: A 778 CYS cc_start: 0.7830 (t) cc_final: 0.7552 (t) REVERT: A 794 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6910 (mt-10) REVERT: B 98 GLU cc_start: 0.8272 (pm20) cc_final: 0.7964 (pm20) REVERT: B 112 ARG cc_start: 0.7657 (mtp85) cc_final: 0.7374 (mtp85) REVERT: B 139 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7419 (tp-100) REVERT: B 141 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7470 (mm-30) REVERT: B 177 PHE cc_start: 0.7562 (m-80) cc_final: 0.7180 (m-10) REVERT: B 260 ARG cc_start: 0.7430 (ttm170) cc_final: 0.7206 (tpp80) REVERT: B 279 PHE cc_start: 0.7516 (t80) cc_final: 0.7269 (t80) REVERT: B 282 MET cc_start: 0.5319 (tpt) cc_final: 0.5094 (tpt) REVERT: B 298 HIS cc_start: 0.7117 (t-90) cc_final: 0.6741 (t-90) REVERT: B 311 HIS cc_start: 0.6701 (t-90) cc_final: 0.6441 (t-90) REVERT: B 345 LYS cc_start: 0.7937 (ptpp) cc_final: 0.7086 (ptpp) REVERT: B 493 ASP cc_start: 0.6674 (t0) cc_final: 0.6355 (t0) REVERT: B 495 LYS cc_start: 0.7784 (ttmm) cc_final: 0.7389 (ttmm) REVERT: B 529 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7616 (tmtt) REVERT: B 590 HIS cc_start: 0.6620 (t70) cc_final: 0.6404 (t70) REVERT: B 614 ASN cc_start: 0.7538 (m-40) cc_final: 0.7134 (m-40) REVERT: B 689 PHE cc_start: 0.7596 (t80) cc_final: 0.7158 (t80) REVERT: B 716 ARG cc_start: 0.7086 (mmm160) cc_final: 0.6707 (mmm160) REVERT: B 726 LYS cc_start: 0.8263 (mttt) cc_final: 0.7803 (ttmt) outliers start: 24 outliers final: 11 residues processed: 308 average time/residue: 0.3286 time to fit residues: 138.2889 Evaluate side-chains 290 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 277 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 744 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 117 optimal weight: 0.0040 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN B 564 GLN B 626 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 12858 Z= 0.257 Angle : 0.664 11.513 17450 Z= 0.334 Chirality : 0.046 0.180 1930 Planarity : 0.005 0.059 2270 Dihedral : 6.303 73.569 1712 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.27 % Allowed : 15.32 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.51 (0.22), residues: 1570 helix: 0.57 (0.20), residues: 669 sheet: -0.50 (0.28), residues: 321 loop : -1.21 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 231 HIS 0.007 0.001 HIS B 77 PHE 0.058 0.002 PHE A 445 TYR 0.028 0.002 TYR B 80 ARG 0.006 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.3547 (tpt) cc_final: 0.3336 (tpt) REVERT: A 95 MET cc_start: 0.3847 (mtp) cc_final: 0.3585 (mtp) REVERT: A 163 GLU cc_start: 0.7270 (mp0) cc_final: 0.7047 (mp0) REVERT: A 279 PHE cc_start: 0.7162 (t80) cc_final: 0.6411 (t80) REVERT: A 282 MET cc_start: 0.8174 (tpp) cc_final: 0.7823 (ttm) REVERT: A 364 GLN cc_start: 0.7712 (pp30) cc_final: 0.7157 (tm-30) REVERT: A 452 ASP cc_start: 0.7169 (t70) cc_final: 0.6805 (t0) REVERT: A 457 ARG cc_start: 0.5832 (ttm-80) cc_final: 0.5596 (ttm-80) REVERT: A 502 SER cc_start: 0.7460 (t) cc_final: 0.7253 (t) REVERT: A 525 ASP cc_start: 0.6130 (t70) cc_final: 0.5797 (t0) REVERT: A 611 GLU cc_start: 0.6645 (mp0) cc_final: 0.6298 (mp0) REVERT: A 665 TRP cc_start: 0.5926 (m-90) cc_final: 0.5712 (m-90) REVERT: A 751 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.5327 (mp) REVERT: A 776 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7843 (pt) REVERT: A 778 CYS cc_start: 0.7756 (t) cc_final: 0.6533 (m) REVERT: A 794 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6881 (mt-10) REVERT: B 77 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7283 (m-70) REVERT: B 98 GLU cc_start: 0.8312 (pm20) cc_final: 0.8004 (pm20) REVERT: B 141 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7417 (mm-30) REVERT: B 177 PHE cc_start: 0.7559 (m-80) cc_final: 0.7195 (m-10) REVERT: B 187 MET cc_start: 0.5820 (ttt) cc_final: 0.5557 (tmm) REVERT: B 201 ASP cc_start: 0.6892 (p0) cc_final: 0.6343 (p0) REVERT: B 260 ARG cc_start: 0.7410 (ttm170) cc_final: 0.7188 (tpp80) REVERT: B 279 PHE cc_start: 0.7499 (t80) cc_final: 0.7256 (t80) REVERT: B 282 MET cc_start: 0.5331 (tpt) cc_final: 0.5118 (tpt) REVERT: B 298 HIS cc_start: 0.7138 (t-90) cc_final: 0.6754 (t-90) REVERT: B 345 LYS cc_start: 0.7918 (ptpp) cc_final: 0.7074 (ptpp) REVERT: B 357 GLU cc_start: 0.7458 (tp30) cc_final: 0.6927 (tp30) REVERT: B 407 ASP cc_start: 0.6690 (p0) cc_final: 0.6329 (p0) REVERT: B 495 LYS cc_start: 0.7768 (ttmm) cc_final: 0.7412 (ttmm) REVERT: B 529 LYS cc_start: 0.8151 (tmtt) cc_final: 0.7615 (tmtt) REVERT: B 590 HIS cc_start: 0.6608 (t70) cc_final: 0.6373 (t70) REVERT: B 614 ASN cc_start: 0.7658 (m-40) cc_final: 0.6770 (m110) REVERT: B 689 PHE cc_start: 0.7726 (t80) cc_final: 0.7455 (t80) REVERT: B 726 LYS cc_start: 0.8301 (mttt) cc_final: 0.7783 (ttmt) outliers start: 31 outliers final: 18 residues processed: 309 average time/residue: 0.3045 time to fit residues: 129.2861 Evaluate side-chains 305 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 284 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 744 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 12858 Z= 0.358 Angle : 0.709 11.160 17450 Z= 0.361 Chirality : 0.047 0.181 1930 Planarity : 0.005 0.076 2270 Dihedral : 6.412 73.347 1712 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.45 % Allowed : 17.01 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.88 (0.21), residues: 1570 helix: 0.25 (0.20), residues: 681 sheet: -0.76 (0.27), residues: 331 loop : -1.36 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 231 HIS 0.007 0.001 HIS A 365 PHE 0.065 0.003 PHE A 445 TYR 0.031 0.002 TYR B 80 ARG 0.007 0.001 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 294 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.3873 (mtp) cc_final: 0.3641 (mtp) REVERT: A 279 PHE cc_start: 0.7243 (t80) cc_final: 0.6452 (t80) REVERT: A 282 MET cc_start: 0.8167 (tpp) cc_final: 0.7755 (ttm) REVERT: A 364 GLN cc_start: 0.7761 (pp30) cc_final: 0.7280 (tm-30) REVERT: A 382 GLN cc_start: 0.7016 (mm110) cc_final: 0.6793 (tm-30) REVERT: A 452 ASP cc_start: 0.7161 (t70) cc_final: 0.6807 (t0) REVERT: A 495 LYS cc_start: 0.8194 (mttm) cc_final: 0.7878 (mttm) REVERT: A 502 SER cc_start: 0.7645 (t) cc_final: 0.7368 (t) REVERT: A 525 ASP cc_start: 0.6119 (t70) cc_final: 0.5787 (t0) REVERT: A 596 HIS cc_start: 0.4696 (t70) cc_final: 0.4376 (t70) REVERT: A 665 TRP cc_start: 0.5987 (m-90) cc_final: 0.5781 (m-90) REVERT: A 745 LEU cc_start: 0.8025 (mt) cc_final: 0.7749 (mp) REVERT: A 746 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6549 (tm-30) REVERT: A 751 ILE cc_start: 0.5223 (OUTLIER) cc_final: 0.4686 (mm) REVERT: A 776 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7837 (pt) REVERT: A 778 CYS cc_start: 0.7864 (t) cc_final: 0.6572 (m) REVERT: A 794 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6931 (mt-10) REVERT: B 77 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.7297 (m-70) REVERT: B 98 GLU cc_start: 0.8321 (pm20) cc_final: 0.8018 (pm20) REVERT: B 112 ARG cc_start: 0.7703 (mtp85) cc_final: 0.7416 (mtp85) REVERT: B 118 VAL cc_start: 0.4204 (OUTLIER) cc_final: 0.3933 (t) REVERT: B 141 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7486 (mm-30) REVERT: B 177 PHE cc_start: 0.7429 (m-80) cc_final: 0.7096 (m-10) REVERT: B 187 MET cc_start: 0.5790 (ttt) cc_final: 0.5432 (tmm) REVERT: B 220 PHE cc_start: 0.7725 (m-10) cc_final: 0.7208 (m-80) REVERT: B 260 ARG cc_start: 0.7314 (ttm170) cc_final: 0.7087 (tpp80) REVERT: B 279 PHE cc_start: 0.7436 (t80) cc_final: 0.7128 (t80) REVERT: B 282 MET cc_start: 0.5405 (tpt) cc_final: 0.5199 (tpt) REVERT: B 298 HIS cc_start: 0.7133 (t-90) cc_final: 0.6712 (t-90) REVERT: B 345 LYS cc_start: 0.7914 (ptpp) cc_final: 0.7079 (ptpp) REVERT: B 357 GLU cc_start: 0.7363 (tp30) cc_final: 0.6913 (tp30) REVERT: B 371 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7470 (mm) REVERT: B 372 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6707 (tm-30) REVERT: B 495 LYS cc_start: 0.7816 (ttmm) cc_final: 0.7439 (ttmm) REVERT: B 529 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7609 (tmtt) REVERT: B 590 HIS cc_start: 0.6585 (t70) cc_final: 0.6328 (t70) REVERT: B 614 ASN cc_start: 0.7785 (m-40) cc_final: 0.7508 (m110) REVERT: B 689 PHE cc_start: 0.7690 (t80) cc_final: 0.7187 (t80) REVERT: B 726 LYS cc_start: 0.8277 (mttt) cc_final: 0.7820 (ttmt) outliers start: 47 outliers final: 23 residues processed: 321 average time/residue: 0.3016 time to fit residues: 133.6371 Evaluate side-chains 314 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 286 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 744 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.8980 chunk 85 optimal weight: 0.0050 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 135 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 12858 Z= 0.230 Angle : 0.666 10.788 17450 Z= 0.336 Chirality : 0.046 0.228 1930 Planarity : 0.005 0.067 2270 Dihedral : 6.249 72.034 1712 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.30 % Allowed : 18.77 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.57 (0.21), residues: 1570 helix: 0.60 (0.20), residues: 667 sheet: -0.57 (0.28), residues: 315 loop : -1.32 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 618 HIS 0.007 0.001 HIS B 77 PHE 0.026 0.002 PHE B 602 TYR 0.030 0.001 TYR B 80 ARG 0.008 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 286 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.3871 (mtp) cc_final: 0.3600 (mtp) REVERT: A 158 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8147 (pt) REVERT: A 163 GLU cc_start: 0.7238 (mp0) cc_final: 0.7033 (mp0) REVERT: A 279 PHE cc_start: 0.7095 (t80) cc_final: 0.6319 (t80) REVERT: A 282 MET cc_start: 0.8168 (tpp) cc_final: 0.7772 (ttm) REVERT: A 364 GLN cc_start: 0.7705 (pp30) cc_final: 0.7206 (tm-30) REVERT: A 452 ASP cc_start: 0.7097 (t70) cc_final: 0.6839 (t0) REVERT: A 495 LYS cc_start: 0.8147 (mttm) cc_final: 0.7831 (mttm) REVERT: A 502 SER cc_start: 0.7583 (t) cc_final: 0.7324 (t) REVERT: A 525 ASP cc_start: 0.6095 (t70) cc_final: 0.5755 (t0) REVERT: A 596 HIS cc_start: 0.4617 (t70) cc_final: 0.4306 (t70) REVERT: A 598 PRO cc_start: 0.8003 (Cg_exo) cc_final: 0.7696 (Cg_endo) REVERT: A 630 TRP cc_start: 0.7830 (m-10) cc_final: 0.7367 (m-10) REVERT: A 665 TRP cc_start: 0.5945 (m-90) cc_final: 0.5738 (m-90) REVERT: A 734 ARG cc_start: 0.6786 (ttm110) cc_final: 0.6555 (ttm110) REVERT: A 745 LEU cc_start: 0.8002 (mt) cc_final: 0.7746 (mp) REVERT: A 751 ILE cc_start: 0.5043 (OUTLIER) cc_final: 0.4709 (mp) REVERT: A 776 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.7934 (pt) REVERT: A 778 CYS cc_start: 0.7825 (t) cc_final: 0.6529 (m) REVERT: B 77 HIS cc_start: 0.8120 (OUTLIER) cc_final: 0.7299 (m-70) REVERT: B 98 GLU cc_start: 0.8313 (pm20) cc_final: 0.7997 (pm20) REVERT: B 118 VAL cc_start: 0.4089 (OUTLIER) cc_final: 0.3811 (t) REVERT: B 141 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 177 PHE cc_start: 0.7419 (m-80) cc_final: 0.7084 (m-10) REVERT: B 187 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.5346 (tmm) REVERT: B 220 PHE cc_start: 0.7624 (m-10) cc_final: 0.7100 (m-80) REVERT: B 260 ARG cc_start: 0.7398 (ttm170) cc_final: 0.7178 (tpp80) REVERT: B 279 PHE cc_start: 0.7490 (t80) cc_final: 0.7237 (t80) REVERT: B 298 HIS cc_start: 0.7132 (t-90) cc_final: 0.6668 (t-90) REVERT: B 345 LYS cc_start: 0.7874 (ptpp) cc_final: 0.7048 (ptpp) REVERT: B 371 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7471 (mm) REVERT: B 417 ILE cc_start: 0.8010 (tp) cc_final: 0.7730 (tp) REVERT: B 468 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5921 (mm) REVERT: B 495 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7451 (ttmm) REVERT: B 529 LYS cc_start: 0.8146 (tmtt) cc_final: 0.7599 (tmtt) REVERT: B 590 HIS cc_start: 0.6587 (t70) cc_final: 0.6373 (t70) REVERT: B 614 ASN cc_start: 0.7606 (m-40) cc_final: 0.7306 (m110) outliers start: 45 outliers final: 26 residues processed: 310 average time/residue: 0.3014 time to fit residues: 128.7206 Evaluate side-chains 316 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 744 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9980 chunk 135 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN B 564 GLN B 614 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 12858 Z= 0.269 Angle : 0.679 10.472 17450 Z= 0.344 Chirality : 0.046 0.184 1930 Planarity : 0.005 0.057 2270 Dihedral : 6.247 72.023 1712 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.74 % Allowed : 19.65 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.64 (0.21), residues: 1570 helix: 0.59 (0.20), residues: 666 sheet: -0.69 (0.28), residues: 331 loop : -1.37 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 618 HIS 0.007 0.001 HIS B 77 PHE 0.061 0.002 PHE A 445 TYR 0.030 0.002 TYR B 80 ARG 0.009 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 293 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.3849 (mtp) cc_final: 0.3621 (mtp) REVERT: A 132 ASP cc_start: 0.6585 (p0) cc_final: 0.6253 (p0) REVERT: A 160 LEU cc_start: 0.7088 (mp) cc_final: 0.6799 (mp) REVERT: A 163 GLU cc_start: 0.7271 (mp0) cc_final: 0.7021 (mp0) REVERT: A 279 PHE cc_start: 0.7132 (t80) cc_final: 0.6353 (t80) REVERT: A 282 MET cc_start: 0.8158 (tpp) cc_final: 0.7793 (ttm) REVERT: A 364 GLN cc_start: 0.7756 (pp30) cc_final: 0.7257 (tm-30) REVERT: A 452 ASP cc_start: 0.7109 (t70) cc_final: 0.6855 (t0) REVERT: A 495 LYS cc_start: 0.8148 (mttm) cc_final: 0.7829 (mttm) REVERT: A 502 SER cc_start: 0.7631 (t) cc_final: 0.7352 (t) REVERT: A 525 ASP cc_start: 0.6086 (t70) cc_final: 0.5760 (t0) REVERT: A 596 HIS cc_start: 0.4853 (t70) cc_final: 0.4385 (t70) REVERT: A 598 PRO cc_start: 0.8026 (Cg_exo) cc_final: 0.7723 (Cg_endo) REVERT: A 665 TRP cc_start: 0.5963 (m-90) cc_final: 0.5756 (m-90) REVERT: A 745 LEU cc_start: 0.7962 (mt) cc_final: 0.7713 (mp) REVERT: A 751 ILE cc_start: 0.4739 (OUTLIER) cc_final: 0.4451 (mp) REVERT: A 776 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8085 (pt) REVERT: A 778 CYS cc_start: 0.7756 (t) cc_final: 0.6631 (m) REVERT: B 77 HIS cc_start: 0.8120 (OUTLIER) cc_final: 0.7386 (m-70) REVERT: B 112 ARG cc_start: 0.7606 (mtp85) cc_final: 0.7295 (mtp85) REVERT: B 118 VAL cc_start: 0.4090 (OUTLIER) cc_final: 0.3809 (t) REVERT: B 141 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7478 (mm-30) REVERT: B 177 PHE cc_start: 0.7302 (m-80) cc_final: 0.7045 (m-10) REVERT: B 187 MET cc_start: 0.5765 (OUTLIER) cc_final: 0.5470 (tmm) REVERT: B 220 PHE cc_start: 0.7631 (m-10) cc_final: 0.7149 (m-80) REVERT: B 260 ARG cc_start: 0.7277 (ttm170) cc_final: 0.6996 (tpp80) REVERT: B 263 ARG cc_start: 0.6907 (mtp-110) cc_final: 0.6594 (mmm-85) REVERT: B 279 PHE cc_start: 0.7557 (t80) cc_final: 0.7333 (t80) REVERT: B 298 HIS cc_start: 0.7099 (t-90) cc_final: 0.6655 (t-90) REVERT: B 345 LYS cc_start: 0.7881 (ptpp) cc_final: 0.7040 (ptpp) REVERT: B 371 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7495 (mm) REVERT: B 417 ILE cc_start: 0.8025 (tp) cc_final: 0.7760 (tp) REVERT: B 468 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5952 (mm) REVERT: B 495 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7424 (ttmm) REVERT: B 529 LYS cc_start: 0.8158 (tmtt) cc_final: 0.7603 (tmtt) REVERT: B 614 ASN cc_start: 0.7540 (m110) cc_final: 0.7197 (m110) REVERT: B 675 GLU cc_start: 0.6742 (mp0) cc_final: 0.6272 (mm-30) outliers start: 51 outliers final: 33 residues processed: 319 average time/residue: 0.3053 time to fit residues: 133.4197 Evaluate side-chains 335 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 295 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 744 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 69 optimal weight: 0.0570 chunk 93 optimal weight: 0.6980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN B 168 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 12858 Z= 0.248 Angle : 0.695 10.441 17450 Z= 0.351 Chirality : 0.046 0.193 1930 Planarity : 0.005 0.051 2270 Dihedral : 6.200 72.071 1712 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.89 % Allowed : 20.67 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.64 (0.21), residues: 1570 helix: 0.58 (0.20), residues: 674 sheet: -0.69 (0.28), residues: 319 loop : -1.37 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 231 HIS 0.007 0.001 HIS B 77 PHE 0.026 0.002 PHE A 445 TYR 0.030 0.002 TYR B 80 ARG 0.012 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.3866 (mtp) cc_final: 0.3610 (mtp) REVERT: A 131 ARG cc_start: 0.6392 (tpp80) cc_final: 0.6115 (tpp80) REVERT: A 163 GLU cc_start: 0.7240 (mp0) cc_final: 0.7031 (mp0) REVERT: A 279 PHE cc_start: 0.7084 (t80) cc_final: 0.6301 (t80) REVERT: A 282 MET cc_start: 0.8127 (tpp) cc_final: 0.7788 (ttm) REVERT: A 364 GLN cc_start: 0.7749 (pp30) cc_final: 0.7253 (tm-30) REVERT: A 382 GLN cc_start: 0.7124 (tm-30) cc_final: 0.6889 (tm-30) REVERT: A 452 ASP cc_start: 0.7099 (t70) cc_final: 0.6877 (t0) REVERT: A 495 LYS cc_start: 0.8145 (mttm) cc_final: 0.7820 (mttm) REVERT: A 502 SER cc_start: 0.7607 (t) cc_final: 0.7327 (t) REVERT: A 525 ASP cc_start: 0.6084 (t70) cc_final: 0.5742 (t0) REVERT: A 596 HIS cc_start: 0.4810 (t70) cc_final: 0.4348 (t70) REVERT: A 598 PRO cc_start: 0.7994 (Cg_exo) cc_final: 0.7690 (Cg_endo) REVERT: A 665 TRP cc_start: 0.6151 (m-90) cc_final: 0.5893 (m-90) REVERT: A 745 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7732 (mp) REVERT: A 776 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8038 (pt) REVERT: A 778 CYS cc_start: 0.7804 (t) cc_final: 0.6603 (m) REVERT: B 77 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7315 (m-70) REVERT: B 112 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7159 (mtp85) REVERT: B 118 VAL cc_start: 0.4067 (OUTLIER) cc_final: 0.3778 (t) REVERT: B 141 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7517 (mm-30) REVERT: B 177 PHE cc_start: 0.7332 (m-80) cc_final: 0.7082 (m-10) REVERT: B 187 MET cc_start: 0.5732 (OUTLIER) cc_final: 0.5444 (tmm) REVERT: B 201 ASP cc_start: 0.6876 (p0) cc_final: 0.6237 (p0) REVERT: B 220 PHE cc_start: 0.7621 (m-10) cc_final: 0.7124 (m-80) REVERT: B 260 ARG cc_start: 0.7393 (ttm170) cc_final: 0.7181 (tpp80) REVERT: B 279 PHE cc_start: 0.7475 (t80) cc_final: 0.7232 (t80) REVERT: B 298 HIS cc_start: 0.7089 (t-90) cc_final: 0.6637 (t-90) REVERT: B 345 LYS cc_start: 0.7877 (ptpp) cc_final: 0.7027 (ptpp) REVERT: B 371 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7501 (mm) REVERT: B 372 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6692 (tm-30) REVERT: B 417 ILE cc_start: 0.8029 (tp) cc_final: 0.7750 (tp) REVERT: B 468 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.6008 (mm) REVERT: B 495 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7402 (ttmm) REVERT: B 529 LYS cc_start: 0.8161 (tmtt) cc_final: 0.7595 (tmtt) REVERT: B 590 HIS cc_start: 0.6942 (t-90) cc_final: 0.6527 (t70) REVERT: B 591 ASP cc_start: 0.7076 (t70) cc_final: 0.6813 (p0) REVERT: B 614 ASN cc_start: 0.7495 (m110) cc_final: 0.7155 (m-40) REVERT: B 675 GLU cc_start: 0.6675 (mp0) cc_final: 0.6261 (mm-30) REVERT: B 744 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7986 (tp) outliers start: 53 outliers final: 34 residues processed: 327 average time/residue: 0.3070 time to fit residues: 137.5559 Evaluate side-chains 331 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 289 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 663 HIS Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 744 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 102 optimal weight: 0.1980 chunk 74 optimal weight: 0.0060 chunk 14 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 136 optimal weight: 0.0980 chunk 144 optimal weight: 0.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN B 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12858 Z= 0.231 Angle : 0.691 10.416 17450 Z= 0.348 Chirality : 0.046 0.268 1930 Planarity : 0.005 0.047 2270 Dihedral : 6.162 73.184 1712 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.59 % Allowed : 21.77 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.21), residues: 1570 helix: 0.63 (0.20), residues: 673 sheet: -0.66 (0.28), residues: 325 loop : -1.34 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 231 HIS 0.007 0.001 HIS B 77 PHE 0.058 0.002 PHE A 445 TYR 0.030 0.001 TYR B 80 ARG 0.008 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 296 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.2461 (tpt) cc_final: 0.1829 (tpt) REVERT: A 95 MET cc_start: 0.3863 (mtp) cc_final: 0.3637 (mtp) REVERT: A 158 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8109 (pt) REVERT: A 279 PHE cc_start: 0.6986 (t80) cc_final: 0.6196 (t80) REVERT: A 282 MET cc_start: 0.7981 (tpp) cc_final: 0.7603 (ttm) REVERT: A 364 GLN cc_start: 0.7706 (pp30) cc_final: 0.7182 (tm-30) REVERT: A 452 ASP cc_start: 0.7072 (t70) cc_final: 0.6856 (t0) REVERT: A 495 LYS cc_start: 0.8138 (mttm) cc_final: 0.7822 (mttm) REVERT: A 525 ASP cc_start: 0.6055 (t70) cc_final: 0.5711 (t0) REVERT: A 596 HIS cc_start: 0.4816 (t70) cc_final: 0.4404 (t70) REVERT: A 598 PRO cc_start: 0.7950 (Cg_exo) cc_final: 0.7655 (Cg_endo) REVERT: A 665 TRP cc_start: 0.6157 (m-90) cc_final: 0.5852 (m-90) REVERT: A 745 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7742 (mp) REVERT: A 776 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8042 (pt) REVERT: A 778 CYS cc_start: 0.7765 (t) cc_final: 0.6664 (m) REVERT: A 794 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6373 (tm-30) REVERT: B 77 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7333 (m-70) REVERT: B 112 ARG cc_start: 0.7470 (mtp85) cc_final: 0.7147 (mtp85) REVERT: B 118 VAL cc_start: 0.4229 (OUTLIER) cc_final: 0.3938 (t) REVERT: B 175 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7075 (mt-10) REVERT: B 177 PHE cc_start: 0.7318 (m-80) cc_final: 0.7086 (m-10) REVERT: B 187 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.5401 (tmm) REVERT: B 220 PHE cc_start: 0.7582 (m-10) cc_final: 0.7136 (m-80) REVERT: B 279 PHE cc_start: 0.7515 (t80) cc_final: 0.7294 (t80) REVERT: B 298 HIS cc_start: 0.7088 (t-90) cc_final: 0.6626 (t-90) REVERT: B 345 LYS cc_start: 0.7864 (ptpp) cc_final: 0.7015 (ptpp) REVERT: B 371 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7494 (mm) REVERT: B 417 ILE cc_start: 0.8040 (tp) cc_final: 0.7760 (tp) REVERT: B 468 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5988 (mm) REVERT: B 495 LYS cc_start: 0.7744 (ttmm) cc_final: 0.7397 (ttmm) REVERT: B 529 LYS cc_start: 0.8151 (tmtt) cc_final: 0.7597 (tmtt) REVERT: B 614 ASN cc_start: 0.7469 (m110) cc_final: 0.7209 (m110) REVERT: B 675 GLU cc_start: 0.6649 (mp0) cc_final: 0.6233 (mm-30) outliers start: 49 outliers final: 29 residues processed: 322 average time/residue: 0.3262 time to fit residues: 144.1989 Evaluate side-chains 322 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 663 HIS Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 729 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 139 optimal weight: 0.1980 chunk 92 optimal weight: 0.0010 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 12858 Z= 0.242 Angle : 0.706 10.295 17450 Z= 0.358 Chirality : 0.046 0.237 1930 Planarity : 0.005 0.060 2270 Dihedral : 6.179 74.035 1712 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.45 % Allowed : 22.43 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.57 (0.21), residues: 1570 helix: 0.66 (0.20), residues: 673 sheet: -0.69 (0.28), residues: 325 loop : -1.33 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 618 HIS 0.007 0.001 HIS B 77 PHE 0.025 0.002 PHE B 602 TYR 0.030 0.001 TYR B 80 ARG 0.015 0.001 ARG B 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 284 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.2744 (tpt) cc_final: 0.2446 (tpt) REVERT: A 95 MET cc_start: 0.3895 (mtp) cc_final: 0.3636 (mtp) REVERT: A 158 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8109 (pt) REVERT: A 210 LEU cc_start: 0.7926 (mp) cc_final: 0.7589 (tt) REVERT: A 279 PHE cc_start: 0.6996 (t80) cc_final: 0.6211 (t80) REVERT: A 282 MET cc_start: 0.8027 (tpp) cc_final: 0.7643 (ttm) REVERT: A 364 GLN cc_start: 0.7697 (pp30) cc_final: 0.7179 (tm-30) REVERT: A 452 ASP cc_start: 0.7082 (t70) cc_final: 0.6870 (t0) REVERT: A 495 LYS cc_start: 0.8131 (mttm) cc_final: 0.7852 (mttm) REVERT: A 525 ASP cc_start: 0.6070 (t70) cc_final: 0.5725 (t0) REVERT: A 557 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8141 (mtpp) REVERT: A 596 HIS cc_start: 0.4780 (t70) cc_final: 0.4377 (t70) REVERT: A 598 PRO cc_start: 0.7942 (Cg_exo) cc_final: 0.7648 (Cg_endo) REVERT: A 665 TRP cc_start: 0.6163 (m-90) cc_final: 0.5856 (m-90) REVERT: A 745 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7683 (mp) REVERT: A 776 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8033 (pt) REVERT: A 778 CYS cc_start: 0.7757 (t) cc_final: 0.6653 (m) REVERT: A 794 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6496 (tm-30) REVERT: B 77 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7349 (m-70) REVERT: B 112 ARG cc_start: 0.7479 (mtp85) cc_final: 0.7129 (mtp85) REVERT: B 118 VAL cc_start: 0.3929 (OUTLIER) cc_final: 0.3611 (t) REVERT: B 177 PHE cc_start: 0.7331 (m-80) cc_final: 0.7100 (m-10) REVERT: B 187 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.5330 (tmm) REVERT: B 220 PHE cc_start: 0.7595 (m-10) cc_final: 0.7194 (m-80) REVERT: B 279 PHE cc_start: 0.7514 (t80) cc_final: 0.7290 (t80) REVERT: B 298 HIS cc_start: 0.7084 (t-90) cc_final: 0.6631 (t-90) REVERT: B 345 LYS cc_start: 0.7868 (ptpp) cc_final: 0.7026 (ptpp) REVERT: B 371 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7500 (mm) REVERT: B 372 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6742 (tm-30) REVERT: B 417 ILE cc_start: 0.8057 (tp) cc_final: 0.7746 (tp) REVERT: B 468 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5933 (mm) REVERT: B 495 LYS cc_start: 0.7749 (ttmm) cc_final: 0.7396 (ttmm) REVERT: B 529 LYS cc_start: 0.8165 (tmtt) cc_final: 0.7581 (tmtt) REVERT: B 590 HIS cc_start: 0.6783 (t-90) cc_final: 0.6462 (t70) REVERT: B 614 ASN cc_start: 0.7473 (m110) cc_final: 0.7237 (m110) REVERT: B 675 GLU cc_start: 0.6626 (mp0) cc_final: 0.6222 (mm-30) outliers start: 47 outliers final: 29 residues processed: 306 average time/residue: 0.3149 time to fit residues: 132.0040 Evaluate side-chains 319 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 729 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 155 optimal weight: 0.0970 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 12858 Z= 0.294 Angle : 0.745 10.300 17450 Z= 0.380 Chirality : 0.047 0.243 1930 Planarity : 0.005 0.059 2270 Dihedral : 6.292 74.590 1712 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.01 % Allowed : 23.39 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.69 (0.21), residues: 1570 helix: 0.54 (0.20), residues: 674 sheet: -0.78 (0.28), residues: 319 loop : -1.36 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 618 HIS 0.008 0.001 HIS B 590 PHE 0.025 0.002 PHE B 602 TYR 0.030 0.002 TYR B 80 ARG 0.015 0.001 ARG B 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.3888 (mtp) cc_final: 0.3668 (mtp) REVERT: A 158 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8195 (pt) REVERT: A 279 PHE cc_start: 0.7140 (t80) cc_final: 0.6297 (t80) REVERT: A 282 MET cc_start: 0.8149 (tpp) cc_final: 0.7770 (ttm) REVERT: A 364 GLN cc_start: 0.7741 (pp30) cc_final: 0.7251 (tm-30) REVERT: A 452 ASP cc_start: 0.7107 (t70) cc_final: 0.6894 (t0) REVERT: A 495 LYS cc_start: 0.8270 (mttm) cc_final: 0.7919 (mttm) REVERT: A 525 ASP cc_start: 0.6106 (t70) cc_final: 0.5749 (t0) REVERT: A 542 MET cc_start: 0.5341 (ptt) cc_final: 0.4801 (ptt) REVERT: A 557 LYS cc_start: 0.8505 (mtpp) cc_final: 0.8149 (mtpp) REVERT: A 596 HIS cc_start: 0.4794 (t70) cc_final: 0.4393 (t70) REVERT: A 598 PRO cc_start: 0.8010 (Cg_exo) cc_final: 0.7716 (Cg_endo) REVERT: A 665 TRP cc_start: 0.6191 (m-90) cc_final: 0.5882 (m-90) REVERT: A 745 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7692 (mp) REVERT: A 776 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8045 (pt) REVERT: A 778 CYS cc_start: 0.7795 (t) cc_final: 0.6654 (m) REVERT: A 794 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6292 (tm-30) REVERT: B 77 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7380 (m-70) REVERT: B 112 ARG cc_start: 0.7471 (mtp85) cc_final: 0.7144 (mtp85) REVERT: B 118 VAL cc_start: 0.3966 (OUTLIER) cc_final: 0.3653 (t) REVERT: B 177 PHE cc_start: 0.7369 (m-80) cc_final: 0.7147 (m-10) REVERT: B 187 MET cc_start: 0.5770 (OUTLIER) cc_final: 0.5460 (tmm) REVERT: B 220 PHE cc_start: 0.7513 (m-10) cc_final: 0.7140 (m-80) REVERT: B 279 PHE cc_start: 0.7545 (t80) cc_final: 0.7299 (t80) REVERT: B 298 HIS cc_start: 0.7075 (t-90) cc_final: 0.6612 (t-90) REVERT: B 345 LYS cc_start: 0.7872 (ptpp) cc_final: 0.7046 (ptpp) REVERT: B 371 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7424 (mm) REVERT: B 372 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6742 (tm-30) REVERT: B 417 ILE cc_start: 0.8116 (tp) cc_final: 0.7804 (tp) REVERT: B 468 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5905 (mm) REVERT: B 495 LYS cc_start: 0.7774 (ttmm) cc_final: 0.7443 (ttmm) REVERT: B 529 LYS cc_start: 0.8160 (tmtt) cc_final: 0.7696 (tmtt) REVERT: B 590 HIS cc_start: 0.6827 (t-90) cc_final: 0.6485 (t70) REVERT: B 614 ASN cc_start: 0.7538 (m110) cc_final: 0.7015 (m110) REVERT: B 675 GLU cc_start: 0.6634 (mp0) cc_final: 0.6234 (mm-30) REVERT: B 689 PHE cc_start: 0.7906 (t80) cc_final: 0.7671 (t80) outliers start: 41 outliers final: 29 residues processed: 301 average time/residue: 0.3155 time to fit residues: 130.1396 Evaluate side-chains 317 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 729 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.177891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.147559 restraints weight = 20554.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.152298 restraints weight = 11366.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.155487 restraints weight = 7417.463| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 12858 Z= 0.289 Angle : 0.763 11.063 17450 Z= 0.386 Chirality : 0.047 0.221 1930 Planarity : 0.005 0.054 2270 Dihedral : 6.278 74.073 1712 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.23 % Allowed : 23.24 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1570 helix: 0.59 (0.20), residues: 673 sheet: -0.79 (0.28), residues: 319 loop : -1.37 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 231 HIS 0.007 0.001 HIS B 77 PHE 0.024 0.002 PHE B 602 TYR 0.030 0.002 TYR B 80 ARG 0.014 0.001 ARG B 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3171.61 seconds wall clock time: 58 minutes 47.74 seconds (3527.74 seconds total)