Starting phenix.real_space_refine on Fri Mar 6 02:28:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o6a_0631/03_2026/6o6a_0631.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o6a_0631/03_2026/6o6a_0631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o6a_0631/03_2026/6o6a_0631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o6a_0631/03_2026/6o6a_0631.map" model { file = "/net/cci-nas-00/data/ceres_data/6o6a_0631/03_2026/6o6a_0631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o6a_0631/03_2026/6o6a_0631.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 S 128 5.16 5 Na 4 4.78 5 C 17848 2.51 5 N 4436 2.21 5 O 4804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27220 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6769 Classifications: {'peptide': 828} Link IDs: {'PTRANS': 20, 'TRANS': 807} Chain breaks: 9 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' NA': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 7.39, per 1000 atoms: 0.27 Number of scatterers: 27220 At special positions: 0 Unit cell: (129.198, 129.198, 148.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 Na 4 11.00 O 4804 8.00 N 4436 7.00 C 17848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6320 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 4 sheets defined 66.3% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.957A pdb=" N MET A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 167 removed outlier: 3.631A pdb=" N PHE A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.548A pdb=" N VAL A 186 " --> pdb=" O TYR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 279 removed outlier: 3.506A pdb=" N TYR A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 removed outlier: 3.923A pdb=" N LEU A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.238A pdb=" N ILE A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 358' Processing helix chain 'A' and resid 361 through 374 removed outlier: 3.542A pdb=" N SER A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 395 through 409 removed outlier: 4.082A pdb=" N PHE A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 405 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 4.065A pdb=" N GLN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.690A pdb=" N THR A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.520A pdb=" N LEU A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.741A pdb=" N ILE A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 551 through 562 removed outlier: 4.401A pdb=" N ILE A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 562 " --> pdb=" O TRP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 573 removed outlier: 3.740A pdb=" N GLU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 591 removed outlier: 3.571A pdb=" N ALA A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 626 removed outlier: 3.589A pdb=" N GLU A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 619 " --> pdb=" O ARG A 615 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.533A pdb=" N GLN A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 654 removed outlier: 3.522A pdb=" N ALA A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 662 through 674 Processing helix chain 'A' and resid 683 through 691 removed outlier: 4.133A pdb=" N ILE A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS A 689 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 removed outlier: 3.530A pdb=" N ILE A 696 " --> pdb=" O PHE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 Processing helix chain 'A' and resid 724 through 749 removed outlier: 3.670A pdb=" N ILE A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR A 736 " --> pdb=" O ASN A 732 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 772 removed outlier: 3.621A pdb=" N ILE A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 772 " --> pdb=" O VAL A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 789 through 808 removed outlier: 3.525A pdb=" N ILE A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 802 " --> pdb=" O PHE A 798 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 803 " --> pdb=" O TYR A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 842 removed outlier: 3.869A pdb=" N ILE A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 827 " --> pdb=" O CYS A 823 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 removed outlier: 4.020A pdb=" N ILE A 848 " --> pdb=" O PRO A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 877 Processing helix chain 'A' and resid 888 through 896 removed outlier: 3.595A pdb=" N VAL A 893 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE A 894 " --> pdb=" O PHE A 890 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR A 895 " --> pdb=" O ARG A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 969 removed outlier: 4.223A pdb=" N THR A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.776A pdb=" N TRP A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 985 " --> pdb=" O ASP A 981 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 992 " --> pdb=" O ARG A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.504A pdb=" N VAL A1006 " --> pdb=" O PHE A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1060 removed outlier: 3.626A pdb=" N GLU A1046 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET A1049 " --> pdb=" O TRP A1045 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1092 removed outlier: 3.613A pdb=" N LEU A1082 " --> pdb=" O LYS A1078 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A1087 " --> pdb=" O LYS A1083 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU A1088 " --> pdb=" O GLY A1084 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE A1089 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.957A pdb=" N MET B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.630A pdb=" N PHE B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.549A pdb=" N VAL B 186 " --> pdb=" O TYR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 removed outlier: 3.506A pdb=" N TYR B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 279 " --> pdb=" O TYR B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.923A pdb=" N LEU B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 353 through 358 removed outlier: 4.237A pdb=" N ILE B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 358' Processing helix chain 'B' and resid 361 through 374 removed outlier: 3.543A pdb=" N SER B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 395 through 409 removed outlier: 4.083A pdb=" N PHE B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS B 405 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 removed outlier: 4.066A pdb=" N GLN B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 449 through 459 removed outlier: 3.691A pdb=" N THR B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 480 through 491 removed outlier: 3.520A pdb=" N LEU B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 507 removed outlier: 3.740A pdb=" N ILE B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 Processing helix chain 'B' and resid 551 through 562 removed outlier: 4.402A pdb=" N ILE B 557 " --> pdb=" O GLN B 553 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 562 " --> pdb=" O TRP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 573 removed outlier: 3.740A pdb=" N GLU B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 591 removed outlier: 3.571A pdb=" N ALA B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 626 removed outlier: 3.589A pdb=" N GLU B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 615 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.533A pdb=" N GLN B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 654 removed outlier: 3.522A pdb=" N ALA B 651 " --> pdb=" O CYS B 647 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 662 through 674 Processing helix chain 'B' and resid 683 through 691 removed outlier: 4.133A pdb=" N ILE B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS B 689 " --> pdb=" O LYS B 685 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 691 " --> pdb=" O ILE B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.530A pdb=" N ILE B 696 " --> pdb=" O PHE B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 724 through 749 removed outlier: 3.671A pdb=" N ILE B 734 " --> pdb=" O SER B 730 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR B 736 " --> pdb=" O ASN B 732 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 742 " --> pdb=" O ALA B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 772 removed outlier: 3.621A pdb=" N ILE B 761 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 762 " --> pdb=" O LEU B 758 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 772 " --> pdb=" O VAL B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 777 Processing helix chain 'B' and resid 789 through 808 removed outlier: 3.525A pdb=" N ILE B 797 " --> pdb=" O ASP B 793 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 802 " --> pdb=" O PHE B 798 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY B 803 " --> pdb=" O TYR B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 842 removed outlier: 3.870A pdb=" N ILE B 821 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP B 825 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 827 " --> pdb=" O CYS B 823 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 removed outlier: 4.020A pdb=" N ILE B 848 " --> pdb=" O PRO B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 877 Processing helix chain 'B' and resid 888 through 896 removed outlier: 3.595A pdb=" N VAL B 893 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE B 894 " --> pdb=" O PHE B 890 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR B 895 " --> pdb=" O ARG B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 969 removed outlier: 4.223A pdb=" N THR B 957 " --> pdb=" O TYR B 953 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 963 " --> pdb=" O ILE B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 997 removed outlier: 3.777A pdb=" N TRP B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 985 " --> pdb=" O ASP B 981 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 992 " --> pdb=" O ARG B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1006 removed outlier: 3.504A pdb=" N VAL B1006 " --> pdb=" O PHE B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1060 removed outlier: 3.626A pdb=" N GLU B1046 " --> pdb=" O ILE B1042 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B1048 " --> pdb=" O ALA B1044 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET B1049 " --> pdb=" O TRP B1045 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN B1058 " --> pdb=" O LEU B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1092 removed outlier: 3.612A pdb=" N LEU B1082 " --> pdb=" O LYS B1078 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B1083 " --> pdb=" O LEU B1079 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B1087 " --> pdb=" O LYS B1083 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLU B1088 " --> pdb=" O GLY B1084 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE B1089 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B1090 " --> pdb=" O LEU B1086 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B1091 " --> pdb=" O LYS B1087 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.957A pdb=" N MET C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 167 removed outlier: 3.631A pdb=" N PHE C 156 " --> pdb=" O MET C 152 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.548A pdb=" N VAL C 186 " --> pdb=" O TYR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 279 removed outlier: 3.506A pdb=" N TYR C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 279 " --> pdb=" O TYR C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 removed outlier: 3.923A pdb=" N LEU C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 333 Processing helix chain 'C' and resid 353 through 358 removed outlier: 4.237A pdb=" N ILE C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 358' Processing helix chain 'C' and resid 361 through 374 removed outlier: 3.542A pdb=" N SER C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 370 " --> pdb=" O GLU C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 395 through 409 removed outlier: 4.083A pdb=" N PHE C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 405 " --> pdb=" O PHE C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 4.066A pdb=" N GLN C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 Processing helix chain 'C' and resid 449 through 459 removed outlier: 3.690A pdb=" N THR C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 458 " --> pdb=" O PHE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 471 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 480 through 491 removed outlier: 3.519A pdb=" N LEU C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN C 490 " --> pdb=" O GLU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 507 removed outlier: 3.741A pdb=" N ILE C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 Processing helix chain 'C' and resid 551 through 562 removed outlier: 4.401A pdb=" N ILE C 557 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN C 562 " --> pdb=" O TRP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 removed outlier: 3.741A pdb=" N GLU C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 591 removed outlier: 3.571A pdb=" N ALA C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU C 583 " --> pdb=" O THR C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 626 removed outlier: 3.589A pdb=" N GLU C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 615 " --> pdb=" O GLU C 611 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 618 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 619 " --> pdb=" O ARG C 615 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 636 removed outlier: 3.532A pdb=" N GLN C 633 " --> pdb=" O ASP C 629 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 654 removed outlier: 3.523A pdb=" N ALA C 651 " --> pdb=" O CYS C 647 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 654 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 662 through 674 Processing helix chain 'C' and resid 683 through 691 removed outlier: 4.133A pdb=" N ILE C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS C 689 " --> pdb=" O LYS C 685 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 691 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 696 removed outlier: 3.530A pdb=" N ILE C 696 " --> pdb=" O PHE C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 722 Processing helix chain 'C' and resid 724 through 749 removed outlier: 3.670A pdb=" N ILE C 734 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR C 736 " --> pdb=" O ASN C 732 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 742 " --> pdb=" O ALA C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 772 removed outlier: 3.622A pdb=" N ILE C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 772 " --> pdb=" O VAL C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 777 Processing helix chain 'C' and resid 789 through 808 removed outlier: 3.525A pdb=" N ILE C 797 " --> pdb=" O ASP C 793 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C 802 " --> pdb=" O PHE C 798 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 803 " --> pdb=" O TYR C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 842 removed outlier: 3.869A pdb=" N ILE C 821 " --> pdb=" O SER C 817 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP C 825 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C 827 " --> pdb=" O CYS C 823 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 848 removed outlier: 4.021A pdb=" N ILE C 848 " --> pdb=" O PRO C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 877 Processing helix chain 'C' and resid 888 through 896 removed outlier: 3.594A pdb=" N VAL C 893 " --> pdb=" O ILE C 889 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE C 894 " --> pdb=" O PHE C 890 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR C 895 " --> pdb=" O ARG C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 969 removed outlier: 4.223A pdb=" N THR C 957 " --> pdb=" O TYR C 953 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 963 " --> pdb=" O ILE C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.776A pdb=" N TRP C 984 " --> pdb=" O ASN C 980 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 985 " --> pdb=" O ASP C 981 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 992 " --> pdb=" O ARG C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1006 removed outlier: 3.503A pdb=" N VAL C1006 " --> pdb=" O PHE C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1060 removed outlier: 3.627A pdb=" N GLU C1046 " --> pdb=" O ILE C1042 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL C1048 " --> pdb=" O ALA C1044 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C1049 " --> pdb=" O TRP C1045 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C1058 " --> pdb=" O LEU C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1072 through 1092 removed outlier: 3.612A pdb=" N LEU C1082 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS C1083 " --> pdb=" O LEU C1079 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C1087 " --> pdb=" O LYS C1083 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU C1088 " --> pdb=" O GLY C1084 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE C1089 " --> pdb=" O LEU C1085 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER C1090 " --> pdb=" O LEU C1086 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C1091 " --> pdb=" O LYS C1087 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.957A pdb=" N MET D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 167 removed outlier: 3.630A pdb=" N PHE D 156 " --> pdb=" O MET D 152 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE D 160 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 190 removed outlier: 3.548A pdb=" N VAL D 186 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 279 removed outlier: 3.505A pdb=" N TYR D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 279 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 removed outlier: 3.923A pdb=" N LEU D 304 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 353 through 358 removed outlier: 4.238A pdb=" N ILE D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 353 through 358' Processing helix chain 'D' and resid 361 through 374 removed outlier: 3.542A pdb=" N SER D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE D 369 " --> pdb=" O THR D 365 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 370 " --> pdb=" O GLU D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 380 No H-bonds generated for 'chain 'D' and resid 378 through 380' Processing helix chain 'D' and resid 395 through 409 removed outlier: 4.082A pdb=" N PHE D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS D 405 " --> pdb=" O PHE D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 removed outlier: 4.065A pdb=" N GLN D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 437 Processing helix chain 'D' and resid 449 through 459 removed outlier: 3.690A pdb=" N THR D 455 " --> pdb=" O ASP D 451 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 458 " --> pdb=" O PHE D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 480 through 491 removed outlier: 3.520A pdb=" N LEU D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN D 490 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 507 removed outlier: 3.742A pdb=" N ILE D 502 " --> pdb=" O LYS D 498 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 507 " --> pdb=" O ALA D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 Processing helix chain 'D' and resid 551 through 562 removed outlier: 4.401A pdb=" N ILE D 557 " --> pdb=" O GLN D 553 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN D 562 " --> pdb=" O TRP D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 573 removed outlier: 3.741A pdb=" N GLU D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 591 removed outlier: 3.571A pdb=" N ALA D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 626 removed outlier: 3.589A pdb=" N GLU D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 615 " --> pdb=" O GLU D 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 618 " --> pdb=" O THR D 614 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 619 " --> pdb=" O ARG D 615 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.534A pdb=" N GLN D 633 " --> pdb=" O ASP D 629 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 654 removed outlier: 3.522A pdb=" N ALA D 651 " --> pdb=" O CYS D 647 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 Processing helix chain 'D' and resid 662 through 674 Processing helix chain 'D' and resid 683 through 691 removed outlier: 4.134A pdb=" N ILE D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 691 " --> pdb=" O ILE D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 696 removed outlier: 3.530A pdb=" N ILE D 696 " --> pdb=" O PHE D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 722 Processing helix chain 'D' and resid 724 through 749 removed outlier: 3.671A pdb=" N ILE D 734 " --> pdb=" O SER D 730 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR D 736 " --> pdb=" O ASN D 732 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 742 " --> pdb=" O ALA D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 772 removed outlier: 3.621A pdb=" N ILE D 761 " --> pdb=" O ALA D 757 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 762 " --> pdb=" O LEU D 758 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 772 " --> pdb=" O VAL D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 777 Processing helix chain 'D' and resid 789 through 808 removed outlier: 3.525A pdb=" N ILE D 797 " --> pdb=" O ASP D 793 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 802 " --> pdb=" O PHE D 798 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 803 " --> pdb=" O TYR D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 842 removed outlier: 3.869A pdb=" N ILE D 821 " --> pdb=" O SER D 817 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP D 825 " --> pdb=" O ILE D 821 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 827 " --> pdb=" O CYS D 823 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN D 842 " --> pdb=" O THR D 838 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 848 removed outlier: 4.020A pdb=" N ILE D 848 " --> pdb=" O PRO D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 877 Processing helix chain 'D' and resid 888 through 896 removed outlier: 3.594A pdb=" N VAL D 893 " --> pdb=" O ILE D 889 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE D 894 " --> pdb=" O PHE D 890 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR D 895 " --> pdb=" O ARG D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 969 removed outlier: 4.223A pdb=" N THR D 957 " --> pdb=" O TYR D 953 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN D 963 " --> pdb=" O ILE D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 997 removed outlier: 3.776A pdb=" N TRP D 984 " --> pdb=" O ASN D 980 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D 985 " --> pdb=" O ASP D 981 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 992 " --> pdb=" O ARG D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1006 removed outlier: 3.503A pdb=" N VAL D1006 " --> pdb=" O PHE D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1060 removed outlier: 3.626A pdb=" N GLU D1046 " --> pdb=" O ILE D1042 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL D1048 " --> pdb=" O ALA D1044 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET D1049 " --> pdb=" O TRP D1045 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN D1058 " --> pdb=" O LEU D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1072 through 1092 removed outlier: 3.613A pdb=" N LEU D1082 " --> pdb=" O LYS D1078 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D1083 " --> pdb=" O LEU D1079 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D1085 " --> pdb=" O ASP D1081 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS D1087 " --> pdb=" O LYS D1083 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU D1088 " --> pdb=" O GLY D1084 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE D1089 " --> pdb=" O LEU D1085 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D1091 " --> pdb=" O LYS D1087 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 250 through 252 removed outlier: 6.514A pdb=" N ALA A 202 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU A 252 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY A 204 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE A 170 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 205 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR A 172 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 135 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE A 295 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE A 137 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 317 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 321 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 318 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 385 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 320 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 250 through 252 removed outlier: 6.514A pdb=" N ALA B 202 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU B 252 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY B 204 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE B 170 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 205 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N THR B 172 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU B 135 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE B 295 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE B 137 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B 317 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU B 321 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 318 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE B 385 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 320 " --> pdb=" O ILE B 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 250 through 252 removed outlier: 6.514A pdb=" N ALA C 202 " --> pdb=" O HIS C 250 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU C 252 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY C 204 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE C 170 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE C 205 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR C 172 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU C 135 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE C 295 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE C 137 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS C 317 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C 321 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL C 318 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE C 385 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 320 " --> pdb=" O ILE C 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 250 through 252 removed outlier: 6.514A pdb=" N ALA D 202 " --> pdb=" O HIS D 250 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU D 252 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY D 204 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE D 170 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE D 205 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR D 172 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU D 135 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE D 295 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE D 137 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS D 317 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU D 321 " --> pdb=" O ALA D 296 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 318 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE D 385 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 320 " --> pdb=" O ILE D 385 " (cutoff:3.500A) 1238 hydrogen bonds defined for protein. 3678 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: 6.04 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4304 1.31 - 1.44: 7821 1.44 - 1.56: 15483 1.56 - 1.69: 36 1.69 - 1.82: 212 Bond restraints: 27856 Sorted by residual: bond pdb=" CAI Y01 D1301 " pdb=" CAZ Y01 D1301 " ideal model delta sigma weight residual 1.332 1.695 -0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" CAI Y01 B1301 " pdb=" CAZ Y01 B1301 " ideal model delta sigma weight residual 1.332 1.695 -0.363 2.00e-02 2.50e+03 3.29e+02 bond pdb=" CAI Y01 A1301 " pdb=" CAZ Y01 A1301 " ideal model delta sigma weight residual 1.332 1.695 -0.363 2.00e-02 2.50e+03 3.29e+02 bond pdb=" CAI Y01 C1301 " pdb=" CAZ Y01 C1301 " ideal model delta sigma weight residual 1.332 1.695 -0.363 2.00e-02 2.50e+03 3.29e+02 bond pdb=" CBB Y01 C1301 " pdb=" CBE Y01 C1301 " ideal model delta sigma weight residual 1.535 1.376 0.159 2.00e-02 2.50e+03 6.35e+01 ... (remaining 27851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 37110 3.25 - 6.51: 510 6.51 - 9.76: 72 9.76 - 13.01: 4 13.01 - 16.27: 12 Bond angle restraints: 37708 Sorted by residual: angle pdb=" C THR C 681 " pdb=" N LYS C 682 " pdb=" CA LYS C 682 " ideal model delta sigma weight residual 121.54 132.97 -11.43 1.91e+00 2.74e-01 3.58e+01 angle pdb=" C THR A 681 " pdb=" N LYS A 682 " pdb=" CA LYS A 682 " ideal model delta sigma weight residual 121.54 132.96 -11.42 1.91e+00 2.74e-01 3.58e+01 angle pdb=" C THR B 681 " pdb=" N LYS B 682 " pdb=" CA LYS B 682 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" C THR D 681 " pdb=" N LYS D 682 " pdb=" CA LYS D 682 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" N PHE B1003 " pdb=" CA PHE B1003 " pdb=" C PHE B1003 " ideal model delta sigma weight residual 113.16 121.63 -8.47 1.42e+00 4.96e-01 3.56e+01 ... (remaining 37703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 14608 17.85 - 35.70: 1577 35.70 - 53.56: 307 53.56 - 71.41: 52 71.41 - 89.26: 32 Dihedral angle restraints: 16576 sinusoidal: 6860 harmonic: 9716 Sorted by residual: dihedral pdb=" CA ILE A 315 " pdb=" C ILE A 315 " pdb=" N PRO A 316 " pdb=" CA PRO A 316 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ILE B 315 " pdb=" C ILE B 315 " pdb=" N PRO B 316 " pdb=" CA PRO B 316 " ideal model delta harmonic sigma weight residual 180.00 153.94 26.06 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ILE C 315 " pdb=" C ILE C 315 " pdb=" N PRO C 316 " pdb=" CA PRO C 316 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 16573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3993 0.098 - 0.195: 235 0.195 - 0.293: 8 0.293 - 0.391: 4 0.391 - 0.489: 8 Chirality restraints: 4248 Sorted by residual: chirality pdb=" CBF Y01 A1301 " pdb=" CAS Y01 A1301 " pdb=" CBD Y01 A1301 " pdb=" CBH Y01 A1301 " both_signs ideal model delta sigma weight residual False -2.45 -2.93 0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" CBF Y01 C1301 " pdb=" CAS Y01 C1301 " pdb=" CBD Y01 C1301 " pdb=" CBH Y01 C1301 " both_signs ideal model delta sigma weight residual False -2.45 -2.93 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CBF Y01 B1301 " pdb=" CAS Y01 B1301 " pdb=" CBD Y01 B1301 " pdb=" CBH Y01 B1301 " both_signs ideal model delta sigma weight residual False -2.45 -2.93 0.49 2.00e-01 2.50e+01 5.93e+00 ... (remaining 4245 not shown) Planarity restraints: 4632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 958 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" CG ASN C 958 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN C 958 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 958 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 958 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.05e+00 pdb=" CG ASN A 958 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 958 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 958 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 958 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" CG ASN D 958 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN D 958 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN D 958 " 0.015 2.00e-02 2.50e+03 ... (remaining 4629 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 189 2.57 - 3.15: 20936 3.15 - 3.73: 41751 3.73 - 4.32: 59092 4.32 - 4.90: 93736 Nonbonded interactions: 215704 Sorted by model distance: nonbonded pdb=" O THR B 575 " pdb=" NZ LYS B1050 " model vdw 1.986 3.120 nonbonded pdb=" O THR C 575 " pdb=" NZ LYS C1050 " model vdw 1.986 3.120 nonbonded pdb=" O THR A 575 " pdb=" NZ LYS A1050 " model vdw 1.987 3.120 nonbonded pdb=" O THR D 575 " pdb=" NZ LYS D1050 " model vdw 1.987 3.120 nonbonded pdb=" SG CYS C 578 " pdb=" NZ LYS C1050 " model vdw 2.179 3.480 ... (remaining 215699 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.810 Find NCS groups from input model: 0.260 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.008 0.363 27856 Z= 0.397 Angle : 0.988 16.268 37708 Z= 0.523 Chirality : 0.056 0.489 4248 Planarity : 0.006 0.062 4632 Dihedral : 15.679 89.262 10256 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.33 (0.09), residues: 3232 helix: -4.42 (0.05), residues: 2100 sheet: -3.11 (0.32), residues: 144 loop : -3.19 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 485 TYR 0.016 0.001 TYR C 121 PHE 0.033 0.002 PHE C 700 TRP 0.015 0.002 TRP D 984 HIS 0.004 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00818 (27856) covalent geometry : angle 0.98822 (37708) hydrogen bonds : bond 0.30405 ( 1238) hydrogen bonds : angle 10.11159 ( 3678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1039 time to evaluate : 1.064 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.9150 (tt) cc_final: 0.8876 (tt) REVERT: A 460 ASP cc_start: 0.7889 (t0) cc_final: 0.7542 (t70) REVERT: A 604 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7818 (mm-30) REVERT: A 655 ARG cc_start: 0.8730 (mtp85) cc_final: 0.8500 (ttm110) REVERT: A 682 LYS cc_start: 0.9312 (mmmm) cc_final: 0.8871 (mmmm) REVERT: A 731 TRP cc_start: 0.8215 (t-100) cc_final: 0.7941 (t-100) REVERT: A 856 ASP cc_start: 0.8473 (m-30) cc_final: 0.8264 (m-30) REVERT: A 868 MET cc_start: 0.8710 (mmm) cc_final: 0.8470 (mmm) REVERT: A 896 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7544 (mt-10) REVERT: A 963 ASN cc_start: 0.8546 (m-40) cc_final: 0.8304 (m-40) REVERT: A 980 ASN cc_start: 0.8233 (t0) cc_final: 0.7884 (m110) REVERT: A 990 PHE cc_start: 0.8353 (t80) cc_final: 0.8081 (t80) REVERT: A 1068 MET cc_start: 0.4998 (pmm) cc_final: 0.4741 (pmm) REVERT: A 1070 HIS cc_start: 0.7498 (p-80) cc_final: 0.7261 (p-80) REVERT: B 121 TYR cc_start: 0.6659 (t80) cc_final: 0.5982 (t80) REVERT: B 366 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8424 (mm-30) REVERT: B 453 MET cc_start: 0.8958 (tpp) cc_final: 0.8695 (tpp) REVERT: B 463 LYS cc_start: 0.9007 (mttm) cc_final: 0.8476 (mtmm) REVERT: B 626 ASN cc_start: 0.8067 (m-40) cc_final: 0.6996 (m-40) REVERT: B 655 ARG cc_start: 0.8812 (mtp85) cc_final: 0.8513 (ttm110) REVERT: B 731 TRP cc_start: 0.8290 (t-100) cc_final: 0.8041 (t-100) REVERT: B 736 TYR cc_start: 0.9082 (t80) cc_final: 0.8851 (t80) REVERT: B 867 TRP cc_start: 0.9169 (t60) cc_final: 0.8921 (t60) REVERT: B 980 ASN cc_start: 0.8328 (t0) cc_final: 0.7843 (m110) REVERT: B 985 LYS cc_start: 0.9348 (mttm) cc_final: 0.9080 (mttt) REVERT: B 1068 MET cc_start: 0.4914 (pmm) cc_final: 0.4712 (pmm) REVERT: B 1070 HIS cc_start: 0.7500 (p-80) cc_final: 0.7082 (p-80) REVERT: C 135 LEU cc_start: 0.9192 (tt) cc_final: 0.8901 (tt) REVERT: C 164 GLN cc_start: 0.8510 (tp40) cc_final: 0.7906 (tp40) REVERT: C 245 ASP cc_start: 0.8731 (t0) cc_final: 0.8280 (t0) REVERT: C 271 GLN cc_start: 0.6410 (tm-30) cc_final: 0.6026 (tm-30) REVERT: C 460 ASP cc_start: 0.8199 (t0) cc_final: 0.7970 (t70) REVERT: C 736 TYR cc_start: 0.9037 (t80) cc_final: 0.8796 (t80) REVERT: C 775 ARG cc_start: 0.6865 (mmm160) cc_final: 0.6505 (ptp-170) REVERT: C 856 ASP cc_start: 0.8306 (m-30) cc_final: 0.8077 (m-30) REVERT: C 867 TRP cc_start: 0.9140 (t60) cc_final: 0.8866 (t60) REVERT: C 963 ASN cc_start: 0.8424 (m-40) cc_final: 0.8177 (m-40) REVERT: C 980 ASN cc_start: 0.8364 (t0) cc_final: 0.7981 (m110) REVERT: C 985 LYS cc_start: 0.9306 (mttm) cc_final: 0.9037 (mttt) REVERT: C 990 PHE cc_start: 0.8308 (t80) cc_final: 0.7984 (t80) REVERT: C 1051 GLU cc_start: 0.8953 (tp30) cc_final: 0.8642 (tp30) REVERT: C 1068 MET cc_start: 0.5503 (pmm) cc_final: 0.5295 (pmm) REVERT: C 1081 ASP cc_start: 0.8662 (t0) cc_final: 0.8452 (t70) REVERT: D 164 GLN cc_start: 0.8351 (tp40) cc_final: 0.7907 (tp40) REVERT: D 271 GLN cc_start: 0.5920 (tm-30) cc_final: 0.5608 (tm-30) REVERT: D 346 LYS cc_start: 0.6317 (mptt) cc_final: 0.5432 (tppt) REVERT: D 365 THR cc_start: 0.5144 (m) cc_final: 0.4749 (m) REVERT: D 366 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8326 (mm-30) REVERT: D 463 LYS cc_start: 0.8989 (mttm) cc_final: 0.8603 (mtmm) REVERT: D 479 LEU cc_start: 0.9231 (mt) cc_final: 0.8922 (mt) REVERT: D 484 LEU cc_start: 0.9353 (mt) cc_final: 0.9119 (mm) REVERT: D 625 SER cc_start: 0.8794 (m) cc_final: 0.8520 (p) REVERT: D 633 GLN cc_start: 0.8407 (mt0) cc_final: 0.7808 (mp10) REVERT: D 655 ARG cc_start: 0.8729 (mtp85) cc_final: 0.8433 (ttm110) REVERT: D 740 LEU cc_start: 0.9198 (mt) cc_final: 0.8940 (mt) REVERT: D 868 MET cc_start: 0.8385 (mmm) cc_final: 0.7909 (mmm) REVERT: D 980 ASN cc_start: 0.7986 (t0) cc_final: 0.7398 (m-40) REVERT: D 1071 ARG cc_start: 0.8320 (mtt90) cc_final: 0.8007 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 1039 average time/residue: 0.1754 time to fit residues: 286.4082 Evaluate side-chains 806 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 806 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS A 248 HIS ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN A 429 GLN A 474 ASN A 550 HIS A 563 ASN A 597 ASN A 662 GLN A 790 ASN A1052 ASN A1074 GLN B 127 HIS B 248 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 429 GLN B 474 ASN B 550 HIS B 563 ASN B 597 ASN B 626 ASN B1052 ASN C 127 HIS C 248 HIS C 397 ASN C 412 HIS C 418 ASN C 429 GLN ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 563 ASN C 662 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1052 ASN D 127 HIS D 248 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 418 ASN D 429 GLN D 474 ASN D 550 HIS D 563 ASN D 597 ASN D 662 GLN D 790 ASN D 958 ASN D 963 ASN D1052 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.172024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.139873 restraints weight = 42150.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.144385 restraints weight = 23019.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.147301 restraints weight = 15994.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.149176 restraints weight = 12742.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150292 restraints weight = 11003.211| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27856 Z= 0.144 Angle : 0.666 11.707 37708 Z= 0.346 Chirality : 0.043 0.235 4248 Planarity : 0.005 0.050 4632 Dihedral : 6.667 48.849 3836 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.37 % Allowed : 15.87 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.12), residues: 3232 helix: -2.50 (0.08), residues: 2184 sheet: -2.94 (0.34), residues: 144 loop : -3.08 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 655 TYR 0.016 0.001 TYR A 121 PHE 0.024 0.001 PHE D 969 TRP 0.018 0.001 TRP C 984 HIS 0.012 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00322 (27856) covalent geometry : angle 0.66595 (37708) hydrogen bonds : bond 0.04074 ( 1238) hydrogen bonds : angle 5.05906 ( 3678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 970 time to evaluate : 0.811 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.9263 (tt) cc_final: 0.8999 (tt) REVERT: A 250 HIS cc_start: 0.8800 (m-70) cc_final: 0.8438 (m-70) REVERT: A 271 GLN cc_start: 0.6114 (tm-30) cc_final: 0.5865 (tm-30) REVERT: A 425 LEU cc_start: 0.9172 (tp) cc_final: 0.8933 (tp) REVERT: A 469 LEU cc_start: 0.9585 (mp) cc_final: 0.9052 (mp) REVERT: A 509 ASP cc_start: 0.8535 (t0) cc_final: 0.8118 (t0) REVERT: A 626 ASN cc_start: 0.8374 (m-40) cc_final: 0.7078 (m-40) REVERT: A 731 TRP cc_start: 0.8394 (t-100) cc_final: 0.8073 (t-100) REVERT: A 736 TYR cc_start: 0.8761 (t80) cc_final: 0.8275 (t80) REVERT: A 769 LEU cc_start: 0.8470 (tt) cc_final: 0.8216 (tt) REVERT: A 825 ASP cc_start: 0.8605 (t0) cc_final: 0.8297 (t0) REVERT: A 829 PHE cc_start: 0.9216 (m-10) cc_final: 0.8834 (m-10) REVERT: A 856 ASP cc_start: 0.8689 (m-30) cc_final: 0.8459 (m-30) REVERT: A 896 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 953 TYR cc_start: 0.7350 (t80) cc_final: 0.7004 (t80) REVERT: A 980 ASN cc_start: 0.8240 (t0) cc_final: 0.8008 (t0) REVERT: A 1074 GLN cc_start: 0.8284 (mt0) cc_final: 0.7949 (mp10) REVERT: A 1081 ASP cc_start: 0.8711 (t70) cc_final: 0.8405 (t0) REVERT: B 250 HIS cc_start: 0.8777 (m-70) cc_final: 0.8484 (m-70) REVERT: B 655 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8385 (ttm110) REVERT: B 745 TYR cc_start: 0.7421 (t80) cc_final: 0.7057 (t80) REVERT: B 769 LEU cc_start: 0.8347 (tt) cc_final: 0.8128 (tt) REVERT: B 953 TYR cc_start: 0.7312 (t80) cc_final: 0.6884 (t80) REVERT: B 980 ASN cc_start: 0.8276 (t0) cc_final: 0.8042 (t0) REVERT: B 1074 GLN cc_start: 0.8179 (mt0) cc_final: 0.7804 (mp10) REVERT: B 1081 ASP cc_start: 0.8705 (t70) cc_final: 0.8436 (t0) REVERT: C 122 ASP cc_start: 0.5727 (p0) cc_final: 0.5268 (t70) REVERT: C 271 GLN cc_start: 0.6423 (tm-30) cc_final: 0.6205 (tm-30) REVERT: C 460 ASP cc_start: 0.8201 (t0) cc_final: 0.7871 (t70) REVERT: C 587 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8695 (ttmm) REVERT: C 682 LYS cc_start: 0.9102 (mmmm) cc_final: 0.8672 (mmmm) REVERT: C 736 TYR cc_start: 0.8870 (t80) cc_final: 0.8102 (t80) REVERT: C 775 ARG cc_start: 0.6801 (mmm160) cc_final: 0.6526 (ptp90) REVERT: C 829 PHE cc_start: 0.9160 (m-10) cc_final: 0.8663 (m-10) REVERT: C 953 TYR cc_start: 0.7292 (t80) cc_final: 0.6855 (t80) REVERT: C 980 ASN cc_start: 0.8254 (t0) cc_final: 0.8051 (t0) REVERT: C 1081 ASP cc_start: 0.8664 (t0) cc_final: 0.8429 (t0) REVERT: D 164 GLN cc_start: 0.8450 (tp40) cc_final: 0.7836 (tp40) REVERT: D 290 ILE cc_start: 0.8923 (mm) cc_final: 0.8530 (tt) REVERT: D 366 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8243 (mm-30) REVERT: D 469 LEU cc_start: 0.9430 (mp) cc_final: 0.8901 (mp) REVERT: D 521 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7213 (p0) REVERT: D 569 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9196 (mmtp) REVERT: D 613 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7023 (mt-10) REVERT: D 625 SER cc_start: 0.8792 (m) cc_final: 0.8510 (p) REVERT: D 655 ARG cc_start: 0.8706 (mtp85) cc_final: 0.8468 (ttm110) REVERT: D 656 ASP cc_start: 0.8215 (m-30) cc_final: 0.7754 (m-30) REVERT: D 731 TRP cc_start: 0.8183 (t-100) cc_final: 0.7763 (t-100) REVERT: D 736 TYR cc_start: 0.8333 (t80) cc_final: 0.7615 (t80) REVERT: D 762 LEU cc_start: 0.8525 (mm) cc_final: 0.7882 (tt) REVERT: D 829 PHE cc_start: 0.8921 (m-10) cc_final: 0.8629 (m-10) REVERT: D 980 ASN cc_start: 0.7916 (t0) cc_final: 0.7376 (m-40) outliers start: 70 outliers final: 38 residues processed: 987 average time/residue: 0.1584 time to fit residues: 255.0200 Evaluate side-chains 879 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 840 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 858 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 38 optimal weight: 0.0770 chunk 110 optimal weight: 7.9990 chunk 197 optimal weight: 0.5980 chunk 136 optimal weight: 0.5980 chunk 323 optimal weight: 6.9990 chunk 318 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS B 474 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 GLN ** C1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 ASN D 491 ASN D 835 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.172705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140288 restraints weight = 42170.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144832 restraints weight = 23091.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.147787 restraints weight = 16074.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149543 restraints weight = 12802.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150783 restraints weight = 11123.239| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27856 Z= 0.126 Angle : 0.629 12.356 37708 Z= 0.318 Chirality : 0.042 0.211 4248 Planarity : 0.004 0.051 4632 Dihedral : 6.257 53.414 3836 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.28 % Allowed : 19.45 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.13), residues: 3232 helix: -1.48 (0.10), residues: 2176 sheet: -2.93 (0.36), residues: 144 loop : -3.05 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 153 TYR 0.018 0.001 TYR D 763 PHE 0.031 0.001 PHE B 969 TRP 0.020 0.001 TRP B 984 HIS 0.003 0.001 HIS D1070 Details of bonding type rmsd covalent geometry : bond 0.00288 (27856) covalent geometry : angle 0.62857 (37708) hydrogen bonds : bond 0.03563 ( 1238) hydrogen bonds : angle 4.56309 ( 3678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 920 time to evaluate : 0.967 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.6115 (p0) cc_final: 0.5289 (t70) REVERT: A 132 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8161 (m) REVERT: A 135 LEU cc_start: 0.9255 (tt) cc_final: 0.9045 (tt) REVERT: A 250 HIS cc_start: 0.8792 (m-70) cc_final: 0.8452 (m-70) REVERT: A 351 ARG cc_start: 0.6730 (ttp-110) cc_final: 0.6520 (ptp90) REVERT: A 421 LEU cc_start: 0.9267 (tp) cc_final: 0.9054 (tp) REVERT: A 425 LEU cc_start: 0.9102 (tp) cc_final: 0.8876 (tp) REVERT: A 469 LEU cc_start: 0.9547 (mp) cc_final: 0.8970 (mp) REVERT: A 611 GLU cc_start: 0.8230 (pt0) cc_final: 0.7752 (pt0) REVERT: A 682 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8797 (mmmm) REVERT: A 731 TRP cc_start: 0.8408 (t-100) cc_final: 0.8090 (t-100) REVERT: A 736 TYR cc_start: 0.8702 (t80) cc_final: 0.8102 (t80) REVERT: A 745 TYR cc_start: 0.7653 (t80) cc_final: 0.7291 (t80) REVERT: A 771 CYS cc_start: 0.7108 (p) cc_final: 0.6889 (p) REVERT: A 829 PHE cc_start: 0.9167 (m-10) cc_final: 0.8744 (m-10) REVERT: A 856 ASP cc_start: 0.8685 (m-30) cc_final: 0.8427 (m-30) REVERT: A 953 TYR cc_start: 0.7442 (t80) cc_final: 0.7081 (t80) REVERT: A 980 ASN cc_start: 0.8339 (t0) cc_final: 0.8129 (t0) REVERT: A 1081 ASP cc_start: 0.8713 (t70) cc_final: 0.8405 (t0) REVERT: B 153 ARG cc_start: 0.9023 (mtm180) cc_final: 0.8632 (mtm110) REVERT: B 250 HIS cc_start: 0.8808 (m-70) cc_final: 0.8523 (m-70) REVERT: B 425 LEU cc_start: 0.9182 (tp) cc_final: 0.8975 (tp) REVERT: B 460 ASP cc_start: 0.7857 (t0) cc_final: 0.7429 (t70) REVERT: B 611 GLU cc_start: 0.8369 (pt0) cc_final: 0.7765 (pt0) REVERT: B 627 ASP cc_start: 0.7148 (t70) cc_final: 0.6602 (t70) REVERT: B 682 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8607 (mmmm) REVERT: B 745 TYR cc_start: 0.7501 (t80) cc_final: 0.7153 (t80) REVERT: B 953 TYR cc_start: 0.7372 (t80) cc_final: 0.6980 (t80) REVERT: B 980 ASN cc_start: 0.8286 (t0) cc_final: 0.8054 (t0) REVERT: B 1074 GLN cc_start: 0.8145 (mt0) cc_final: 0.7797 (mp10) REVERT: B 1081 ASP cc_start: 0.8702 (t70) cc_final: 0.8452 (t0) REVERT: C 122 ASP cc_start: 0.5847 (p0) cc_final: 0.5210 (t70) REVERT: C 250 HIS cc_start: 0.8726 (m-70) cc_final: 0.8428 (m-70) REVERT: C 271 GLN cc_start: 0.6420 (tm-30) cc_final: 0.6215 (tm-30) REVERT: C 460 ASP cc_start: 0.8117 (t0) cc_final: 0.7776 (t70) REVERT: C 469 LEU cc_start: 0.9618 (mp) cc_final: 0.9245 (mp) REVERT: C 565 LYS cc_start: 0.8503 (tttp) cc_final: 0.8268 (tptm) REVERT: C 587 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8577 (ttmm) REVERT: C 613 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7489 (mt-10) REVERT: C 672 GLN cc_start: 0.8406 (tp40) cc_final: 0.8124 (tp40) REVERT: C 682 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8575 (mmmm) REVERT: C 745 TYR cc_start: 0.7519 (t80) cc_final: 0.7122 (t80) REVERT: C 825 ASP cc_start: 0.8513 (t0) cc_final: 0.8244 (t0) REVERT: C 953 TYR cc_start: 0.7483 (t80) cc_final: 0.7082 (t80) REVERT: C 1051 GLU cc_start: 0.8955 (tp30) cc_final: 0.8560 (tp30) REVERT: D 122 ASP cc_start: 0.5537 (p0) cc_final: 0.4962 (t70) REVERT: D 164 GLN cc_start: 0.8488 (tp40) cc_final: 0.7820 (tp40) REVERT: D 371 TRP cc_start: 0.7938 (m100) cc_final: 0.7524 (m100) REVERT: D 469 LEU cc_start: 0.9465 (mp) cc_final: 0.8920 (mp) REVERT: D 613 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7479 (mt-10) REVERT: D 625 SER cc_start: 0.8717 (m) cc_final: 0.8493 (p) REVERT: D 633 GLN cc_start: 0.8292 (mt0) cc_final: 0.7540 (mp10) REVERT: D 655 ARG cc_start: 0.8718 (mtp85) cc_final: 0.8392 (ttm110) REVERT: D 656 ASP cc_start: 0.8204 (m-30) cc_final: 0.7891 (t70) REVERT: D 731 TRP cc_start: 0.8302 (t-100) cc_final: 0.7738 (t-100) REVERT: D 736 TYR cc_start: 0.8545 (t80) cc_final: 0.7649 (t80) REVERT: D 762 LEU cc_start: 0.8541 (mm) cc_final: 0.7947 (tt) REVERT: D 829 PHE cc_start: 0.8893 (m-10) cc_final: 0.8512 (m-10) REVERT: D 980 ASN cc_start: 0.7961 (t0) cc_final: 0.7434 (m-40) outliers start: 97 outliers final: 49 residues processed: 955 average time/residue: 0.1542 time to fit residues: 241.2249 Evaluate side-chains 897 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 845 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 754 GLU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 858 PHE Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 157 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 302 optimal weight: 0.0980 chunk 1 optimal weight: 8.9990 chunk 321 optimal weight: 2.9990 chunk 148 optimal weight: 0.0670 chunk 118 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN B 667 ASN B1052 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 ASN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS D 248 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 ASN ** D1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.173821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141942 restraints weight = 42129.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.146512 restraints weight = 22919.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149434 restraints weight = 15847.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151335 restraints weight = 12593.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152447 restraints weight = 10852.394| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27856 Z= 0.112 Angle : 0.610 12.809 37708 Z= 0.304 Chirality : 0.042 0.170 4248 Planarity : 0.004 0.051 4632 Dihedral : 5.999 56.166 3836 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.15 % Allowed : 20.84 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.14), residues: 3232 helix: -0.91 (0.11), residues: 2180 sheet: -2.80 (0.37), residues: 144 loop : -2.92 (0.17), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 655 TYR 0.017 0.001 TYR D 763 PHE 0.025 0.001 PHE A 969 TRP 0.024 0.001 TRP B 984 HIS 0.003 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00254 (27856) covalent geometry : angle 0.60960 (37708) hydrogen bonds : bond 0.03143 ( 1238) hydrogen bonds : angle 4.24950 ( 3678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 920 time to evaluate : 0.814 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8133 (m) REVERT: A 135 LEU cc_start: 0.9239 (tt) cc_final: 0.9013 (tt) REVERT: A 351 ARG cc_start: 0.6712 (ttp-110) cc_final: 0.6355 (ptp90) REVERT: A 430 LEU cc_start: 0.8950 (tp) cc_final: 0.8679 (mp) REVERT: A 469 LEU cc_start: 0.9496 (mp) cc_final: 0.8883 (mp) REVERT: A 498 LYS cc_start: 0.8322 (mmtp) cc_final: 0.8058 (mmtp) REVERT: A 611 GLU cc_start: 0.8071 (pt0) cc_final: 0.7317 (pt0) REVERT: A 612 TYR cc_start: 0.9046 (m-80) cc_final: 0.8653 (m-80) REVERT: A 682 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8795 (mmmm) REVERT: A 736 TYR cc_start: 0.8727 (t80) cc_final: 0.7991 (t80) REVERT: A 745 TYR cc_start: 0.7746 (t80) cc_final: 0.7496 (t80) REVERT: A 775 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6403 (tmt170) REVERT: A 829 PHE cc_start: 0.9070 (m-10) cc_final: 0.8621 (m-10) REVERT: A 856 ASP cc_start: 0.8608 (m-30) cc_final: 0.8369 (m-30) REVERT: A 980 ASN cc_start: 0.8335 (t0) cc_final: 0.8134 (t0) REVERT: A 1081 ASP cc_start: 0.8693 (t70) cc_final: 0.8408 (t0) REVERT: B 312 LYS cc_start: 0.7837 (pttp) cc_final: 0.7458 (mmmt) REVERT: B 469 LEU cc_start: 0.9471 (mp) cc_final: 0.8930 (mp) REVERT: B 613 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7047 (mt-10) REVERT: B 627 ASP cc_start: 0.7170 (t70) cc_final: 0.6777 (t70) REVERT: B 655 ARG cc_start: 0.8600 (mtp-110) cc_final: 0.8328 (ttm110) REVERT: B 672 GLN cc_start: 0.8399 (tp40) cc_final: 0.8094 (tp40) REVERT: B 682 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8580 (mmmm) REVERT: B 745 TYR cc_start: 0.7525 (t80) cc_final: 0.7228 (t80) REVERT: B 825 ASP cc_start: 0.8413 (t0) cc_final: 0.8141 (t0) REVERT: B 980 ASN cc_start: 0.8274 (t0) cc_final: 0.8066 (t0) REVERT: B 1074 GLN cc_start: 0.8132 (mt0) cc_final: 0.7809 (mp10) REVERT: B 1081 ASP cc_start: 0.8767 (t70) cc_final: 0.8509 (t0) REVERT: C 250 HIS cc_start: 0.8709 (m-70) cc_final: 0.8428 (m-70) REVERT: C 271 GLN cc_start: 0.6370 (tm-30) cc_final: 0.6075 (tm-30) REVERT: C 275 TYR cc_start: 0.6429 (t80) cc_final: 0.6087 (t80) REVERT: C 297 GLN cc_start: 0.9268 (pm20) cc_final: 0.9010 (pm20) REVERT: C 460 ASP cc_start: 0.7865 (t0) cc_final: 0.7506 (t70) REVERT: C 469 LEU cc_start: 0.9550 (mp) cc_final: 0.9003 (mp) REVERT: C 627 ASP cc_start: 0.7034 (t70) cc_final: 0.6642 (t70) REVERT: C 672 GLN cc_start: 0.8326 (tp40) cc_final: 0.8057 (tp40) REVERT: C 682 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8457 (mmmm) REVERT: C 745 TYR cc_start: 0.7522 (t80) cc_final: 0.7183 (t80) REVERT: C 825 ASP cc_start: 0.8422 (t0) cc_final: 0.8207 (t0) REVERT: D 122 ASP cc_start: 0.5464 (p0) cc_final: 0.4888 (t70) REVERT: D 164 GLN cc_start: 0.8487 (tp40) cc_final: 0.7804 (tp40) REVERT: D 290 ILE cc_start: 0.8894 (mm) cc_final: 0.8551 (tt) REVERT: D 371 TRP cc_start: 0.7798 (m100) cc_final: 0.7344 (m100) REVERT: D 430 LEU cc_start: 0.8924 (tp) cc_final: 0.8657 (mp) REVERT: D 448 ASP cc_start: 0.7034 (p0) cc_final: 0.6827 (p0) REVERT: D 469 LEU cc_start: 0.9406 (mp) cc_final: 0.8837 (mp) REVERT: D 498 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7775 (mmtt) REVERT: D 613 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7019 (mt-10) REVERT: D 633 GLN cc_start: 0.8277 (mt0) cc_final: 0.7510 (mp10) REVERT: D 655 ARG cc_start: 0.8677 (mtp85) cc_final: 0.8380 (ttm110) REVERT: D 656 ASP cc_start: 0.8183 (m-30) cc_final: 0.7620 (m-30) REVERT: D 731 TRP cc_start: 0.8272 (t-100) cc_final: 0.7942 (t-100) REVERT: D 736 TYR cc_start: 0.8687 (t80) cc_final: 0.7757 (t80) REVERT: D 829 PHE cc_start: 0.8885 (m-10) cc_final: 0.8422 (m-10) REVERT: D 980 ASN cc_start: 0.7955 (t0) cc_final: 0.7468 (m-40) REVERT: D 1070 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.7497 (t70) REVERT: D 1076 ASP cc_start: 0.8241 (t0) cc_final: 0.8028 (t0) REVERT: D 1081 ASP cc_start: 0.8762 (t70) cc_final: 0.8437 (t0) outliers start: 93 outliers final: 53 residues processed: 955 average time/residue: 0.1571 time to fit residues: 247.9405 Evaluate side-chains 915 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 857 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 968 MET Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 749 MET Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 207 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 286 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 315 optimal weight: 0.0770 chunk 240 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 ASN C 667 ASN C 963 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 ASN D 563 ASN D 835 HIS ** D1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.172428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.139979 restraints weight = 42135.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.144586 restraints weight = 23058.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.147531 restraints weight = 16013.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149356 restraints weight = 12790.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150590 restraints weight = 11111.221| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27856 Z= 0.125 Angle : 0.628 12.737 37708 Z= 0.311 Chirality : 0.042 0.232 4248 Planarity : 0.004 0.054 4632 Dihedral : 5.910 58.490 3836 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.52 % Allowed : 22.46 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.14), residues: 3232 helix: -0.64 (0.11), residues: 2192 sheet: -2.72 (0.37), residues: 144 loop : -2.80 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 655 TYR 0.021 0.001 TYR A 895 PHE 0.030 0.001 PHE A 969 TRP 0.024 0.001 TRP B 984 HIS 0.005 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00291 (27856) covalent geometry : angle 0.62836 (37708) hydrogen bonds : bond 0.03125 ( 1238) hydrogen bonds : angle 4.16825 ( 3678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 886 time to evaluate : 1.012 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 LYS cc_start: 0.7907 (ptmm) cc_final: 0.7502 (mmmt) REVERT: A 435 ASP cc_start: 0.7986 (m-30) cc_final: 0.7756 (m-30) REVERT: A 469 LEU cc_start: 0.9510 (mp) cc_final: 0.8919 (mp) REVERT: A 612 TYR cc_start: 0.9121 (m-80) cc_final: 0.8800 (m-80) REVERT: A 613 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7268 (mt-10) REVERT: A 656 ASP cc_start: 0.8361 (m-30) cc_final: 0.7862 (m-30) REVERT: A 682 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8681 (mmmm) REVERT: A 736 TYR cc_start: 0.8740 (t80) cc_final: 0.7961 (t80) REVERT: A 745 TYR cc_start: 0.7798 (t80) cc_final: 0.7537 (t80) REVERT: A 775 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6444 (tmt170) REVERT: A 829 PHE cc_start: 0.9114 (m-10) cc_final: 0.8642 (m-10) REVERT: A 850 LEU cc_start: 0.8947 (tp) cc_final: 0.8719 (mp) REVERT: A 856 ASP cc_start: 0.8628 (m-30) cc_final: 0.8387 (m-30) REVERT: A 1081 ASP cc_start: 0.8689 (t70) cc_final: 0.8443 (t0) REVERT: B 432 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8591 (tt) REVERT: B 435 ASP cc_start: 0.8069 (m-30) cc_final: 0.7867 (m-30) REVERT: B 469 LEU cc_start: 0.9502 (mp) cc_final: 0.8963 (mp) REVERT: B 611 GLU cc_start: 0.8429 (pt0) cc_final: 0.7702 (pt0) REVERT: B 622 GLU cc_start: 0.7326 (tp30) cc_final: 0.7003 (tp30) REVERT: B 627 ASP cc_start: 0.7177 (t70) cc_final: 0.6810 (t70) REVERT: B 672 GLN cc_start: 0.8508 (tp40) cc_final: 0.8229 (tp40) REVERT: B 682 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8611 (mmmm) REVERT: B 745 TYR cc_start: 0.7658 (t80) cc_final: 0.7382 (t80) REVERT: B 825 ASP cc_start: 0.8397 (t0) cc_final: 0.8144 (t0) REVERT: B 899 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6209 (pp) REVERT: B 1070 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6344 (t70) REVERT: B 1074 GLN cc_start: 0.8147 (mt0) cc_final: 0.7842 (mp10) REVERT: B 1081 ASP cc_start: 0.8778 (t70) cc_final: 0.8511 (t0) REVERT: C 250 HIS cc_start: 0.8710 (m-70) cc_final: 0.8407 (m-70) REVERT: C 297 GLN cc_start: 0.9272 (pm20) cc_final: 0.9046 (pm20) REVERT: C 460 ASP cc_start: 0.7925 (t0) cc_final: 0.7563 (t70) REVERT: C 469 LEU cc_start: 0.9560 (mp) cc_final: 0.9025 (mp) REVERT: C 498 LYS cc_start: 0.8139 (mmtp) cc_final: 0.7493 (mmtp) REVERT: C 613 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7043 (mt-10) REVERT: C 622 GLU cc_start: 0.7292 (tp30) cc_final: 0.6979 (tp30) REVERT: C 627 ASP cc_start: 0.7079 (t70) cc_final: 0.6724 (t70) REVERT: C 656 ASP cc_start: 0.8393 (m-30) cc_final: 0.7757 (m-30) REVERT: C 672 GLN cc_start: 0.8424 (tp40) cc_final: 0.8150 (tp40) REVERT: C 731 TRP cc_start: 0.8348 (t-100) cc_final: 0.7669 (t-100) REVERT: C 745 TYR cc_start: 0.7595 (t80) cc_final: 0.7230 (t80) REVERT: C 850 LEU cc_start: 0.8788 (tp) cc_final: 0.8482 (mp) REVERT: C 1074 GLN cc_start: 0.7719 (mp10) cc_final: 0.7164 (mp10) REVERT: D 122 ASP cc_start: 0.5505 (p0) cc_final: 0.4771 (t70) REVERT: D 164 GLN cc_start: 0.8473 (tp40) cc_final: 0.7782 (tp40) REVERT: D 297 GLN cc_start: 0.9275 (pm20) cc_final: 0.8620 (pm20) REVERT: D 371 TRP cc_start: 0.7850 (m100) cc_final: 0.7370 (m100) REVERT: D 413 ASP cc_start: 0.4319 (p0) cc_final: 0.4051 (p0) REVERT: D 448 ASP cc_start: 0.7058 (p0) cc_final: 0.6815 (p0) REVERT: D 454 PHE cc_start: 0.8596 (t80) cc_final: 0.8328 (t80) REVERT: D 469 LEU cc_start: 0.9471 (mp) cc_final: 0.8935 (mp) REVERT: D 498 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7890 (mmtt) REVERT: D 613 GLU cc_start: 0.7673 (mt-10) cc_final: 0.6821 (mt-10) REVERT: D 622 GLU cc_start: 0.7521 (tp30) cc_final: 0.7209 (tp30) REVERT: D 633 GLN cc_start: 0.8331 (mt0) cc_final: 0.7557 (mp10) REVERT: D 655 ARG cc_start: 0.8687 (mtp85) cc_final: 0.8475 (ttm110) REVERT: D 656 ASP cc_start: 0.8199 (m-30) cc_final: 0.7440 (m-30) REVERT: D 736 TYR cc_start: 0.8801 (t80) cc_final: 0.7907 (t80) REVERT: D 861 LEU cc_start: 0.9326 (mt) cc_final: 0.8983 (mt) REVERT: D 980 ASN cc_start: 0.8016 (t0) cc_final: 0.7559 (m-40) REVERT: D 1070 HIS cc_start: 0.8252 (OUTLIER) cc_final: 0.7609 (t70) REVERT: D 1076 ASP cc_start: 0.8245 (t0) cc_final: 0.8037 (t0) outliers start: 104 outliers final: 69 residues processed: 927 average time/residue: 0.1557 time to fit residues: 237.2130 Evaluate side-chains 919 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 843 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 667 ASN Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 749 MET Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 267 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 256 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 126 optimal weight: 0.3980 chunk 225 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 chunk 279 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 ASN A1052 ASN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 963 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 ASN C 667 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 ASN D 958 ASN ** D1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.170912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.138384 restraints weight = 42247.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142951 restraints weight = 23162.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145754 restraints weight = 16158.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.147690 restraints weight = 12951.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148707 restraints weight = 11240.144| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27856 Z= 0.138 Angle : 0.636 12.706 37708 Z= 0.315 Chirality : 0.043 0.384 4248 Planarity : 0.004 0.058 4632 Dihedral : 5.843 59.373 3836 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.48 % Allowed : 24.02 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.14), residues: 3232 helix: -0.41 (0.11), residues: 2188 sheet: -2.62 (0.38), residues: 144 loop : -2.72 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 655 TYR 0.020 0.001 TYR D 763 PHE 0.015 0.001 PHE A 743 TRP 0.023 0.001 TRP B 984 HIS 0.004 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00323 (27856) covalent geometry : angle 0.63631 (37708) hydrogen bonds : bond 0.03130 ( 1238) hydrogen bonds : angle 4.16975 ( 3678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 876 time to evaluate : 0.979 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.5993 (p0) cc_final: 0.5326 (p0) REVERT: A 132 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8272 (m) REVERT: A 435 ASP cc_start: 0.8002 (m-30) cc_final: 0.7783 (m-30) REVERT: A 469 LEU cc_start: 0.9523 (mp) cc_final: 0.8940 (mp) REVERT: A 622 GLU cc_start: 0.7502 (tp30) cc_final: 0.7175 (tp30) REVERT: A 682 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8711 (mmmm) REVERT: A 736 TYR cc_start: 0.8825 (t80) cc_final: 0.7996 (t80) REVERT: A 742 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7509 (tp) REVERT: A 775 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6526 (tmt170) REVERT: A 829 PHE cc_start: 0.9116 (m-10) cc_final: 0.8660 (m-10) REVERT: A 856 ASP cc_start: 0.8635 (m-30) cc_final: 0.8400 (m-30) REVERT: A 885 ARG cc_start: 0.5898 (mpp-170) cc_final: 0.5492 (ptp-170) REVERT: A 953 TYR cc_start: 0.7323 (t80) cc_final: 0.7060 (t80) REVERT: A 1081 ASP cc_start: 0.8713 (t70) cc_final: 0.8440 (t0) REVERT: B 432 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8532 (tt) REVERT: B 469 LEU cc_start: 0.9507 (mp) cc_final: 0.8980 (mp) REVERT: B 587 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8597 (ttmm) REVERT: B 622 GLU cc_start: 0.7379 (tp30) cc_final: 0.6979 (tp30) REVERT: B 672 GLN cc_start: 0.8502 (tp40) cc_final: 0.8187 (tp40) REVERT: B 682 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8628 (mmmm) REVERT: B 736 TYR cc_start: 0.8965 (t80) cc_final: 0.8129 (t80) REVERT: B 745 TYR cc_start: 0.7706 (t80) cc_final: 0.7452 (t80) REVERT: B 825 ASP cc_start: 0.8433 (t0) cc_final: 0.8205 (t0) REVERT: B 861 LEU cc_start: 0.9384 (mt) cc_final: 0.9175 (mt) REVERT: B 899 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6242 (pp) REVERT: B 953 TYR cc_start: 0.7417 (t80) cc_final: 0.7074 (t80) REVERT: B 1070 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6271 (t70) REVERT: B 1074 GLN cc_start: 0.8217 (mt0) cc_final: 0.7876 (mp10) REVERT: B 1081 ASP cc_start: 0.8798 (t70) cc_final: 0.8572 (t0) REVERT: C 250 HIS cc_start: 0.8731 (m-70) cc_final: 0.8449 (m-70) REVERT: C 290 ILE cc_start: 0.8960 (mm) cc_final: 0.8605 (tt) REVERT: C 312 LYS cc_start: 0.8088 (ptmt) cc_final: 0.7662 (mmmt) REVERT: C 460 ASP cc_start: 0.8002 (t0) cc_final: 0.7636 (t70) REVERT: C 469 LEU cc_start: 0.9559 (mp) cc_final: 0.9002 (mp) REVERT: C 498 LYS cc_start: 0.8147 (mmtp) cc_final: 0.7496 (mmtp) REVERT: C 587 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8560 (ttmm) REVERT: C 612 TYR cc_start: 0.9179 (m-80) cc_final: 0.8802 (m-80) REVERT: C 622 GLU cc_start: 0.7363 (tp30) cc_final: 0.6985 (tp30) REVERT: C 627 ASP cc_start: 0.7153 (t70) cc_final: 0.6777 (t70) REVERT: C 669 LEU cc_start: 0.9049 (tp) cc_final: 0.8792 (tp) REVERT: C 672 GLN cc_start: 0.8452 (tp40) cc_final: 0.8207 (tp40) REVERT: C 682 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8562 (mmmm) REVERT: C 731 TRP cc_start: 0.8310 (t-100) cc_final: 0.7918 (t-100) REVERT: C 736 TYR cc_start: 0.8968 (t80) cc_final: 0.8116 (t80) REVERT: C 745 TYR cc_start: 0.7701 (t80) cc_final: 0.7378 (t80) REVERT: C 804 ILE cc_start: 0.7773 (mm) cc_final: 0.6863 (mm) REVERT: C 829 PHE cc_start: 0.9076 (m-10) cc_final: 0.8418 (m-10) REVERT: C 858 PHE cc_start: 0.8093 (t80) cc_final: 0.7806 (t80) REVERT: C 1074 GLN cc_start: 0.7677 (mp10) cc_final: 0.7130 (mp10) REVERT: D 122 ASP cc_start: 0.5644 (p0) cc_final: 0.4759 (t70) REVERT: D 164 GLN cc_start: 0.8465 (tp40) cc_final: 0.7718 (tp40) REVERT: D 250 HIS cc_start: 0.8572 (m-70) cc_final: 0.8245 (m-70) REVERT: D 297 GLN cc_start: 0.9262 (pm20) cc_final: 0.8462 (pm20) REVERT: D 371 TRP cc_start: 0.7877 (m100) cc_final: 0.7272 (m100) REVERT: D 430 LEU cc_start: 0.8940 (tp) cc_final: 0.8692 (mp) REVERT: D 441 ASP cc_start: 0.8007 (p0) cc_final: 0.7683 (p0) REVERT: D 448 ASP cc_start: 0.7054 (p0) cc_final: 0.6826 (p0) REVERT: D 469 LEU cc_start: 0.9472 (mp) cc_final: 0.8907 (mp) REVERT: D 498 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7916 (mmtt) REVERT: D 633 GLN cc_start: 0.8378 (mt0) cc_final: 0.7605 (mp10) REVERT: D 655 ARG cc_start: 0.8703 (mtp85) cc_final: 0.8497 (ttm110) REVERT: D 669 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9150 (mp) REVERT: D 731 TRP cc_start: 0.8352 (t-100) cc_final: 0.8050 (t-100) REVERT: D 736 TYR cc_start: 0.8888 (t80) cc_final: 0.8061 (t80) REVERT: D 980 ASN cc_start: 0.8096 (t0) cc_final: 0.7543 (m-40) REVERT: D 1070 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7939 (t70) REVERT: D 1076 ASP cc_start: 0.8275 (t0) cc_final: 0.8063 (t0) outliers start: 103 outliers final: 71 residues processed: 915 average time/residue: 0.1553 time to fit residues: 234.0229 Evaluate side-chains 926 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 844 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 667 ASN Chi-restraints excluded: chain C residue 682 LYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 749 MET Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 182 optimal weight: 0.0970 chunk 247 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 324 optimal weight: 0.9990 chunk 176 optimal weight: 0.3980 chunk 249 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN A 501 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN A 963 ASN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN ** B 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 882 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 ASN C 667 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 835 HIS D 882 ASN ** D1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.176875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145770 restraints weight = 42765.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150070 restraints weight = 24704.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.152757 restraints weight = 17685.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154426 restraints weight = 14350.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.155592 restraints weight = 12611.135| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27856 Z= 0.141 Angle : 0.647 12.682 37708 Z= 0.320 Chirality : 0.043 0.300 4248 Planarity : 0.004 0.059 4632 Dihedral : 5.834 57.653 3836 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.86 % Allowed : 24.22 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.14), residues: 3232 helix: -0.24 (0.11), residues: 2196 sheet: -2.53 (0.39), residues: 144 loop : -2.63 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 655 TYR 0.021 0.001 TYR D 763 PHE 0.019 0.001 PHE D 969 TRP 0.022 0.001 TRP B 984 HIS 0.003 0.001 HIS C 884 Details of bonding type rmsd covalent geometry : bond 0.00331 (27856) covalent geometry : angle 0.64688 (37708) hydrogen bonds : bond 0.03123 ( 1238) hydrogen bonds : angle 4.15998 ( 3678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 863 time to evaluate : 0.997 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 LEU cc_start: 0.9508 (mp) cc_final: 0.8922 (mp) REVERT: A 622 GLU cc_start: 0.7457 (tp30) cc_final: 0.7067 (tp30) REVERT: A 682 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8742 (mmmm) REVERT: A 736 TYR cc_start: 0.8851 (t80) cc_final: 0.8060 (t80) REVERT: A 742 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7529 (tp) REVERT: A 775 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6422 (tmt170) REVERT: A 829 PHE cc_start: 0.9052 (m-10) cc_final: 0.8543 (m-10) REVERT: A 856 ASP cc_start: 0.8479 (m-30) cc_final: 0.8273 (m-30) REVERT: A 858 PHE cc_start: 0.8076 (t80) cc_final: 0.7729 (t80) REVERT: A 953 TYR cc_start: 0.7276 (t80) cc_final: 0.7070 (t80) REVERT: A 1081 ASP cc_start: 0.8700 (t70) cc_final: 0.8432 (t0) REVERT: B 432 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8581 (tp) REVERT: B 469 LEU cc_start: 0.9508 (mp) cc_final: 0.8979 (mp) REVERT: B 622 GLU cc_start: 0.7309 (tp30) cc_final: 0.6931 (tp30) REVERT: B 672 GLN cc_start: 0.8377 (tp40) cc_final: 0.8105 (tp40) REVERT: B 682 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8625 (mmmm) REVERT: B 736 TYR cc_start: 0.8976 (t80) cc_final: 0.8156 (t80) REVERT: B 745 TYR cc_start: 0.7657 (t80) cc_final: 0.7446 (t80) REVERT: B 858 PHE cc_start: 0.8050 (t80) cc_final: 0.7743 (t80) REVERT: B 899 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6201 (pp) REVERT: B 1070 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6421 (t70) REVERT: B 1074 GLN cc_start: 0.8190 (mt0) cc_final: 0.7869 (mp10) REVERT: B 1081 ASP cc_start: 0.8789 (t70) cc_final: 0.8521 (t0) REVERT: C 290 ILE cc_start: 0.9002 (mm) cc_final: 0.8630 (tt) REVERT: C 297 GLN cc_start: 0.9271 (pm20) cc_final: 0.9061 (pm20) REVERT: C 469 LEU cc_start: 0.9530 (mp) cc_final: 0.8953 (mp) REVERT: C 498 LYS cc_start: 0.8083 (mmtp) cc_final: 0.7403 (mmtp) REVERT: C 612 TYR cc_start: 0.9148 (m-80) cc_final: 0.8755 (m-80) REVERT: C 622 GLU cc_start: 0.7293 (tp30) cc_final: 0.6947 (tp30) REVERT: C 627 ASP cc_start: 0.7146 (t70) cc_final: 0.6797 (t70) REVERT: C 669 LEU cc_start: 0.9046 (tp) cc_final: 0.8835 (tp) REVERT: C 682 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8601 (mmmm) REVERT: C 736 TYR cc_start: 0.8976 (t80) cc_final: 0.8155 (t80) REVERT: C 858 PHE cc_start: 0.8100 (t80) cc_final: 0.7758 (t80) REVERT: C 899 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6173 (pp) REVERT: C 1074 GLN cc_start: 0.7727 (mp10) cc_final: 0.7163 (mp10) REVERT: D 122 ASP cc_start: 0.5381 (p0) cc_final: 0.4447 (t0) REVERT: D 297 GLN cc_start: 0.9218 (pm20) cc_final: 0.8465 (pm20) REVERT: D 371 TRP cc_start: 0.7959 (m100) cc_final: 0.7521 (m100) REVERT: D 441 ASP cc_start: 0.7963 (p0) cc_final: 0.7687 (p0) REVERT: D 469 LEU cc_start: 0.9498 (mp) cc_final: 0.8970 (mp) REVERT: D 498 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7944 (mmtt) REVERT: D 613 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7150 (mt-10) REVERT: D 622 GLU cc_start: 0.7405 (tp30) cc_final: 0.6907 (tp30) REVERT: D 633 GLN cc_start: 0.8351 (mt0) cc_final: 0.7630 (mp10) REVERT: D 656 ASP cc_start: 0.8316 (m-30) cc_final: 0.8037 (m-30) REVERT: D 669 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9149 (mp) REVERT: D 731 TRP cc_start: 0.8254 (t-100) cc_final: 0.7989 (t-100) REVERT: D 736 TYR cc_start: 0.8916 (t80) cc_final: 0.8161 (t80) REVERT: D 980 ASN cc_start: 0.7999 (t0) cc_final: 0.7491 (m-40) REVERT: D 1049 MET cc_start: 0.8621 (ptm) cc_final: 0.8380 (ptm) REVERT: D 1070 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7237 (t70) REVERT: D 1081 ASP cc_start: 0.8915 (t70) cc_final: 0.8605 (t0) outliers start: 114 outliers final: 82 residues processed: 907 average time/residue: 0.1528 time to fit residues: 228.9539 Evaluate side-chains 918 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 825 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 667 ASN Chi-restraints excluded: chain C residue 682 LYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 749 MET Chi-restraints excluded: chain C residue 761 ILE Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1070 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 12 optimal weight: 0.0000 chunk 124 optimal weight: 0.8980 chunk 313 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 287 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 285 optimal weight: 0.0170 chunk 327 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 182 optimal weight: 8.9990 overall best weight: 0.3420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 ASN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN B 474 ASN ** B 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 HIS ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 776 GLN D1070 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.176936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146626 restraints weight = 42812.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150972 restraints weight = 24571.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153765 restraints weight = 17540.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155548 restraints weight = 14159.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.156428 restraints weight = 12324.831| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27856 Z= 0.114 Angle : 0.646 13.087 37708 Z= 0.318 Chirality : 0.043 0.288 4248 Planarity : 0.004 0.072 4632 Dihedral : 5.718 59.032 3836 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.01 % Allowed : 25.74 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3232 helix: 0.00 (0.11), residues: 2156 sheet: -2.43 (0.39), residues: 144 loop : -2.53 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D1073 TYR 0.019 0.001 TYR B 895 PHE 0.014 0.001 PHE A 989 TRP 0.024 0.001 TRP B 984 HIS 0.003 0.000 HIS D 835 Details of bonding type rmsd covalent geometry : bond 0.00262 (27856) covalent geometry : angle 0.64598 (37708) hydrogen bonds : bond 0.02979 ( 1238) hydrogen bonds : angle 4.14454 ( 3678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 883 time to evaluate : 0.967 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 ASP cc_start: 0.7894 (m-30) cc_final: 0.7623 (m-30) REVERT: A 454 PHE cc_start: 0.8536 (t80) cc_final: 0.8308 (t80) REVERT: A 469 LEU cc_start: 0.9458 (mp) cc_final: 0.8891 (mp) REVERT: A 498 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7517 (mmtt) REVERT: A 622 GLU cc_start: 0.7439 (tp30) cc_final: 0.7026 (tp30) REVERT: A 656 ASP cc_start: 0.8202 (m-30) cc_final: 0.7274 (m-30) REVERT: A 682 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8669 (mmmm) REVERT: A 736 TYR cc_start: 0.8813 (t80) cc_final: 0.8011 (t80) REVERT: A 742 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7545 (tp) REVERT: A 829 PHE cc_start: 0.8988 (m-10) cc_final: 0.8515 (m-10) REVERT: A 856 ASP cc_start: 0.8475 (m-30) cc_final: 0.8234 (m-30) REVERT: A 858 PHE cc_start: 0.8061 (t80) cc_final: 0.7718 (t80) REVERT: A 1081 ASP cc_start: 0.8691 (t70) cc_final: 0.8424 (t0) REVERT: B 351 ARG cc_start: 0.6712 (ptp90) cc_final: 0.6318 (ptp90) REVERT: B 469 LEU cc_start: 0.9445 (mp) cc_final: 0.8890 (mp) REVERT: B 622 GLU cc_start: 0.7250 (tp30) cc_final: 0.6917 (tp30) REVERT: B 672 GLN cc_start: 0.8363 (tp40) cc_final: 0.8071 (tp40) REVERT: B 682 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8596 (mmmm) REVERT: B 736 TYR cc_start: 0.8935 (t80) cc_final: 0.8213 (t80) REVERT: B 745 TYR cc_start: 0.7527 (t80) cc_final: 0.7322 (t80) REVERT: B 858 PHE cc_start: 0.8044 (t80) cc_final: 0.7689 (t80) REVERT: B 885 ARG cc_start: 0.5778 (mpp-170) cc_final: 0.5308 (ptp-170) REVERT: B 899 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6142 (pp) REVERT: B 953 TYR cc_start: 0.7213 (t80) cc_final: 0.6978 (t80) REVERT: B 1070 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6461 (t70) REVERT: B 1074 GLN cc_start: 0.8069 (mt0) cc_final: 0.7803 (mp10) REVERT: B 1081 ASP cc_start: 0.8794 (t70) cc_final: 0.8538 (t0) REVERT: C 250 HIS cc_start: 0.8699 (m-70) cc_final: 0.8411 (m-70) REVERT: C 297 GLN cc_start: 0.9265 (pm20) cc_final: 0.9018 (pm20) REVERT: C 469 LEU cc_start: 0.9470 (mp) cc_final: 0.8880 (mp) REVERT: C 498 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7312 (mmtp) REVERT: C 521 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7319 (p0) REVERT: C 622 GLU cc_start: 0.7296 (tp30) cc_final: 0.6969 (tp30) REVERT: C 627 ASP cc_start: 0.7066 (t70) cc_final: 0.6719 (t70) REVERT: C 637 TYR cc_start: 0.5383 (t80) cc_final: 0.5059 (t80) REVERT: C 656 ASP cc_start: 0.8155 (m-30) cc_final: 0.7111 (m-30) REVERT: C 669 LEU cc_start: 0.9017 (tp) cc_final: 0.8800 (tp) REVERT: C 682 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8481 (mmmm) REVERT: C 731 TRP cc_start: 0.8171 (t-100) cc_final: 0.7889 (t-100) REVERT: C 736 TYR cc_start: 0.8957 (t80) cc_final: 0.8239 (t80) REVERT: C 829 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8358 (m-10) REVERT: C 858 PHE cc_start: 0.8029 (t80) cc_final: 0.7695 (t80) REVERT: C 899 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6139 (pp) REVERT: C 1074 GLN cc_start: 0.7704 (mp10) cc_final: 0.7163 (mp10) REVERT: D 122 ASP cc_start: 0.5336 (p0) cc_final: 0.4426 (t0) REVERT: D 297 GLN cc_start: 0.9144 (pm20) cc_final: 0.8599 (pm20) REVERT: D 371 TRP cc_start: 0.7965 (m100) cc_final: 0.7550 (m100) REVERT: D 441 ASP cc_start: 0.7778 (p0) cc_final: 0.7537 (p0) REVERT: D 469 LEU cc_start: 0.9480 (mp) cc_final: 0.8972 (mp) REVERT: D 498 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7805 (mmtt) REVERT: D 613 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7108 (mt-10) REVERT: D 622 GLU cc_start: 0.7456 (tp30) cc_final: 0.6899 (tp30) REVERT: D 633 GLN cc_start: 0.8310 (mt0) cc_final: 0.7584 (mp10) REVERT: D 656 ASP cc_start: 0.8111 (m-30) cc_final: 0.7878 (m-30) REVERT: D 731 TRP cc_start: 0.8136 (t-100) cc_final: 0.7858 (t-100) REVERT: D 736 TYR cc_start: 0.8874 (t80) cc_final: 0.8104 (t80) REVERT: D 769 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8318 (tt) REVERT: D 829 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8252 (m-10) REVERT: D 980 ASN cc_start: 0.8042 (t0) cc_final: 0.7471 (m110) REVERT: D 1049 MET cc_start: 0.8577 (ptm) cc_final: 0.8332 (ptm) REVERT: D 1068 MET cc_start: 0.5000 (pmm) cc_final: 0.4672 (pmm) outliers start: 89 outliers final: 66 residues processed: 923 average time/residue: 0.1544 time to fit residues: 236.1876 Evaluate side-chains 907 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 830 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 667 ASN Chi-restraints excluded: chain C residue 682 LYS Chi-restraints excluded: chain C residue 761 ILE Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 829 PHE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 829 PHE Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 40 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 GLN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN B 790 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 ASN D 134 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 776 GLN D 835 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.172191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141411 restraints weight = 43045.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145678 restraints weight = 25154.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148341 restraints weight = 18063.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150081 restraints weight = 14674.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150863 restraints weight = 12820.519| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27856 Z= 0.160 Angle : 0.690 12.993 37708 Z= 0.340 Chirality : 0.045 0.488 4248 Planarity : 0.004 0.058 4632 Dihedral : 5.845 59.754 3836 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.28 % Allowed : 26.32 % Favored : 70.40 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3232 helix: -0.05 (0.11), residues: 2184 sheet: -2.37 (0.40), residues: 144 loop : -2.51 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1073 TYR 0.029 0.001 TYR C 286 PHE 0.018 0.001 PHE A 986 TRP 0.023 0.001 TRP D 684 HIS 0.003 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00378 (27856) covalent geometry : angle 0.68974 (37708) hydrogen bonds : bond 0.03232 ( 1238) hydrogen bonds : angle 4.18078 ( 3678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 843 time to evaluate : 0.932 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 LEU cc_start: 0.9536 (mp) cc_final: 0.8977 (mp) REVERT: A 498 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7637 (mmtt) REVERT: A 587 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8653 (ttmm) REVERT: A 612 TYR cc_start: 0.9156 (m-80) cc_final: 0.8868 (m-80) REVERT: A 622 GLU cc_start: 0.7541 (tp30) cc_final: 0.7109 (tp30) REVERT: A 656 ASP cc_start: 0.8100 (m-30) cc_final: 0.7492 (m-30) REVERT: A 682 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8750 (mmmm) REVERT: A 742 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7533 (tp) REVERT: A 856 ASP cc_start: 0.8466 (m-30) cc_final: 0.8264 (m-30) REVERT: A 858 PHE cc_start: 0.8191 (t80) cc_final: 0.7843 (t80) REVERT: A 899 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6254 (pp) REVERT: A 1081 ASP cc_start: 0.8716 (t70) cc_final: 0.8443 (t0) REVERT: B 351 ARG cc_start: 0.6866 (ptp90) cc_final: 0.6445 (ptp90) REVERT: B 469 LEU cc_start: 0.9557 (mp) cc_final: 0.9010 (mp) REVERT: B 622 GLU cc_start: 0.7406 (tp30) cc_final: 0.7026 (tp30) REVERT: B 672 GLN cc_start: 0.8414 (tp40) cc_final: 0.8165 (tp40) REVERT: B 682 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8651 (mmmm) REVERT: B 736 TYR cc_start: 0.9030 (t80) cc_final: 0.8276 (t80) REVERT: B 858 PHE cc_start: 0.8148 (t80) cc_final: 0.7839 (t80) REVERT: B 885 ARG cc_start: 0.5832 (mpp-170) cc_final: 0.5353 (ptp-170) REVERT: B 899 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6315 (pp) REVERT: B 953 TYR cc_start: 0.7231 (t80) cc_final: 0.7013 (t80) REVERT: B 1070 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6558 (t70) REVERT: B 1074 GLN cc_start: 0.8012 (mt0) cc_final: 0.7794 (mp10) REVERT: B 1081 ASP cc_start: 0.8817 (t70) cc_final: 0.8551 (t0) REVERT: C 153 ARG cc_start: 0.9008 (ptp-170) cc_final: 0.8675 (mtm180) REVERT: C 297 GLN cc_start: 0.9302 (pm20) cc_final: 0.8686 (pm20) REVERT: C 469 LEU cc_start: 0.9553 (mp) cc_final: 0.8997 (mp) REVERT: C 498 LYS cc_start: 0.8037 (mmtp) cc_final: 0.7338 (mmtp) REVERT: C 521 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7304 (p0) REVERT: C 587 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8646 (ttmm) REVERT: C 612 TYR cc_start: 0.9222 (m-80) cc_final: 0.8618 (m-80) REVERT: C 622 GLU cc_start: 0.7412 (tp30) cc_final: 0.7069 (tp30) REVERT: C 627 ASP cc_start: 0.7196 (t70) cc_final: 0.6855 (t70) REVERT: C 656 ASP cc_start: 0.8142 (m-30) cc_final: 0.7524 (m-30) REVERT: C 682 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8574 (mmmm) REVERT: C 736 TYR cc_start: 0.9027 (t80) cc_final: 0.8288 (t80) REVERT: C 742 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7757 (tp) REVERT: C 858 PHE cc_start: 0.8155 (t80) cc_final: 0.7845 (t80) REVERT: C 899 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6109 (pp) REVERT: C 1074 GLN cc_start: 0.7695 (mp10) cc_final: 0.7117 (mp10) REVERT: D 289 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7726 (mmmt) REVERT: D 290 ILE cc_start: 0.9008 (mm) cc_final: 0.8700 (tt) REVERT: D 297 GLN cc_start: 0.9198 (pm20) cc_final: 0.8523 (pm20) REVERT: D 430 LEU cc_start: 0.8877 (tp) cc_final: 0.8630 (mp) REVERT: D 441 ASP cc_start: 0.7788 (p0) cc_final: 0.7566 (p0) REVERT: D 469 LEU cc_start: 0.9535 (mp) cc_final: 0.9163 (mp) REVERT: D 498 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7901 (mmtt) REVERT: D 587 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8621 (ttmm) REVERT: D 622 GLU cc_start: 0.7506 (tp30) cc_final: 0.7007 (tp30) REVERT: D 633 GLN cc_start: 0.8348 (mt0) cc_final: 0.7660 (mp10) REVERT: D 731 TRP cc_start: 0.8198 (t-100) cc_final: 0.7939 (t-100) REVERT: D 736 TYR cc_start: 0.8982 (t80) cc_final: 0.8276 (t80) REVERT: D 769 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8300 (tt) REVERT: D 980 ASN cc_start: 0.8137 (t0) cc_final: 0.7611 (m110) REVERT: D 989 PHE cc_start: 0.8143 (t80) cc_final: 0.7897 (t80) REVERT: D 1081 ASP cc_start: 0.8908 (t70) cc_final: 0.8617 (t0) outliers start: 97 outliers final: 68 residues processed: 885 average time/residue: 0.1574 time to fit residues: 227.8761 Evaluate side-chains 909 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 830 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain C residue 682 LYS Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 761 ILE Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 170 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 317 optimal weight: 0.9990 chunk 294 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 324 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 835 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.173198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142666 restraints weight = 42844.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.146942 restraints weight = 24831.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149677 restraints weight = 17803.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151425 restraints weight = 14386.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152485 restraints weight = 12553.123| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27856 Z= 0.141 Angle : 0.680 12.836 37708 Z= 0.334 Chirality : 0.044 0.244 4248 Planarity : 0.004 0.059 4632 Dihedral : 5.808 57.745 3836 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.81 % Allowed : 26.73 % Favored : 70.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 3232 helix: 0.07 (0.11), residues: 2160 sheet: -2.34 (0.40), residues: 144 loop : -2.43 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1073 TYR 0.025 0.001 TYR C 286 PHE 0.022 0.001 PHE D 989 TRP 0.028 0.001 TRP A 417 HIS 0.002 0.000 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00334 (27856) covalent geometry : angle 0.67979 (37708) hydrogen bonds : bond 0.03097 ( 1238) hydrogen bonds : angle 4.20250 ( 3678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6464 Ramachandran restraints generated. 3232 Oldfield, 0 Emsley, 3232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 839 time to evaluate : 1.043 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 LEU cc_start: 0.9508 (mp) cc_final: 0.8944 (mp) REVERT: A 498 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7590 (mmtt) REVERT: A 587 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8543 (ttmm) REVERT: A 612 TYR cc_start: 0.9155 (m-80) cc_final: 0.8882 (m-80) REVERT: A 622 GLU cc_start: 0.7564 (tp30) cc_final: 0.7138 (tp30) REVERT: A 656 ASP cc_start: 0.8076 (m-30) cc_final: 0.7586 (m-30) REVERT: A 682 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8841 (mmmm) REVERT: A 742 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7513 (tp) REVERT: A 856 ASP cc_start: 0.8452 (m-30) cc_final: 0.8240 (m-30) REVERT: A 858 PHE cc_start: 0.8174 (t80) cc_final: 0.7851 (t80) REVERT: A 899 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6324 (pp) REVERT: A 980 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7799 (m-40) REVERT: A 1081 ASP cc_start: 0.8721 (t70) cc_final: 0.8452 (t0) REVERT: B 469 LEU cc_start: 0.9534 (mp) cc_final: 0.9011 (mp) REVERT: B 622 GLU cc_start: 0.7398 (tp30) cc_final: 0.7028 (tp30) REVERT: B 672 GLN cc_start: 0.8420 (tp40) cc_final: 0.8196 (tp40) REVERT: B 682 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8594 (mmmm) REVERT: B 736 TYR cc_start: 0.9002 (t80) cc_final: 0.8303 (t80) REVERT: B 742 LEU cc_start: 0.8038 (tp) cc_final: 0.7617 (tp) REVERT: B 858 PHE cc_start: 0.8128 (t80) cc_final: 0.7849 (t80) REVERT: B 899 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6121 (pp) REVERT: B 953 TYR cc_start: 0.7238 (t80) cc_final: 0.7020 (t80) REVERT: B 1070 HIS cc_start: 0.7308 (OUTLIER) cc_final: 0.6588 (t70) REVERT: B 1074 GLN cc_start: 0.7992 (mt0) cc_final: 0.7743 (mp10) REVERT: B 1081 ASP cc_start: 0.8827 (t70) cc_final: 0.8566 (t0) REVERT: C 297 GLN cc_start: 0.9259 (pm20) cc_final: 0.8736 (pm20) REVERT: C 469 LEU cc_start: 0.9543 (mp) cc_final: 0.8987 (mp) REVERT: C 498 LYS cc_start: 0.8052 (mmtp) cc_final: 0.7342 (mmtp) REVERT: C 521 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7296 (p0) REVERT: C 587 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8555 (ttmm) REVERT: C 622 GLU cc_start: 0.7423 (tp30) cc_final: 0.7073 (tp30) REVERT: C 627 ASP cc_start: 0.7183 (t70) cc_final: 0.6821 (t70) REVERT: C 656 ASP cc_start: 0.8114 (m-30) cc_final: 0.7613 (m-30) REVERT: C 682 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8548 (mmmm) REVERT: C 736 TYR cc_start: 0.8989 (t80) cc_final: 0.8293 (t80) REVERT: C 742 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7803 (tp) REVERT: C 858 PHE cc_start: 0.8107 (t80) cc_final: 0.7820 (t80) REVERT: C 899 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6141 (pp) REVERT: C 1074 GLN cc_start: 0.7737 (mp10) cc_final: 0.7176 (mp10) REVERT: D 297 GLN cc_start: 0.9203 (pm20) cc_final: 0.8594 (pm20) REVERT: D 469 LEU cc_start: 0.9527 (mp) cc_final: 0.9128 (mp) REVERT: D 498 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7894 (mmtt) REVERT: D 587 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8614 (ttmm) REVERT: D 613 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7153 (mt-10) REVERT: D 622 GLU cc_start: 0.7471 (tp30) cc_final: 0.6985 (tp30) REVERT: D 633 GLN cc_start: 0.8341 (mt0) cc_final: 0.7644 (mp10) REVERT: D 656 ASP cc_start: 0.8216 (m-30) cc_final: 0.7742 (m-30) REVERT: D 731 TRP cc_start: 0.8172 (t-100) cc_final: 0.7907 (t-100) REVERT: D 736 TYR cc_start: 0.8947 (t80) cc_final: 0.8229 (t80) REVERT: D 769 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8306 (tt) REVERT: D 980 ASN cc_start: 0.7993 (t0) cc_final: 0.7499 (m110) REVERT: D 1081 ASP cc_start: 0.8904 (t70) cc_final: 0.8611 (t0) outliers start: 83 outliers final: 68 residues processed: 874 average time/residue: 0.1529 time to fit residues: 221.5543 Evaluate side-chains 904 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 824 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain C residue 682 LYS Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 761 ILE Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 703 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 956 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 137 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 321 optimal weight: 0.8980 chunk 251 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 235 optimal weight: 0.5980 chunk 270 optimal weight: 0.3980 chunk 195 optimal weight: 0.8980 chunk 287 optimal weight: 0.9980 chunk 263 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN A 980 ASN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.173802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143298 restraints weight = 42441.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147559 restraints weight = 24774.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150280 restraints weight = 17794.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152051 restraints weight = 14390.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.153087 restraints weight = 12547.753| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27856 Z= 0.133 Angle : 0.683 12.929 37708 Z= 0.335 Chirality : 0.044 0.265 4248 Planarity : 0.004 0.058 4632 Dihedral : 5.863 58.369 3836 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.08 % Allowed : 26.69 % Favored : 70.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.15), residues: 3232 helix: 0.11 (0.11), residues: 2160 sheet: -2.31 (0.40), residues: 144 loop : -2.39 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D1073 TYR 0.023 0.001 TYR C 286 PHE 0.028 0.001 PHE C 743 TRP 0.028 0.001 TRP B 984 HIS 0.002 0.000 HIS D 835 Details of bonding type rmsd covalent geometry : bond 0.00315 (27856) covalent geometry : angle 0.68266 (37708) hydrogen bonds : bond 0.03076 ( 1238) hydrogen bonds : angle 4.19160 ( 3678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5582.67 seconds wall clock time: 96 minutes 35.82 seconds (5795.82 seconds total)