Starting phenix.real_space_refine on Mon Sep 14 02:10:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o6a_0631/09_2026/6o6a_0631.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o6a_0631/09_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_0631/09_2026/6o6a_0631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o6a_0631/09_2026/6o6a_0631.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6o6a_0631/09_2026/6o6a_0631.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o6a_0631/09_2026/6o6a_0631.cif" model { file = "/net/cci-nas-00/data/ceres_data/6o6a_0631/09_2026/6o6a_0631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o6a_0631/09_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 8.01, per 1000 atoms: 0.29 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: 2.00 Conformation dependent library (CDL) restraints added in 1.1 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: 0.78 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: 4.88 Time building geometry restraints manager: 2.77 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: 14432 17.85 - 35.70: 1533 35.70 - 53.56: 295 53.56 - 71.41: 52 71.41 - 89.26: 32 Dihedral angle restraints: 16344 sinusoidal: 6628 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 16341 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: 0.09 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.180 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 : 15.673 89.262 10024 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/Z covalent geometry : bond 0.00818 / 0.40 (27856) covalent geometry : angle 0.98822 / 0.52 (37708) hydrogen bonds : bond 0.30405 / 20.02 ( 1238) hydrogen bonds : angle 10.11159 / 6.93 ( 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 : 1.024 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: 0.1819 time to fit residues: 299.1668 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 : 0.921 ------------------------------------------------------------------------------- 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... 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 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN A1052 ASN A1074 GLN B 127 HIS B 176 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: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140240 restraints weight = 42173.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144771 restraints weight = 23032.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147716 restraints weight = 15991.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149589 restraints weight = 12740.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150746 restraints weight = 11000.827| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27856 Z= 0.142 Angle : 0.664 11.750 37708 Z= 0.344 Chirality : 0.043 0.228 4248 Planarity : 0.005 0.050 4632 Dihedral : 6.581 57.164 3604 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.47 % Allowed : 15.97 % Favored : 81.56 % 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: -4.31 (0.11), residues: 3232 helix: -2.53 (0.08), residues: 2188 sheet: -2.93 (0.34), residues: 144 loop : -3.14 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 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 0.013 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (27856) covalent geometry : angle 0.66352 / 0.34 (37708) hydrogen bonds : bond 0.03980 / 2.62 ( 1238) hydrogen bonds : angle 5.04700 / 3.51 ( 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 1057 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 984 time to evaluate : 1.102 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: symmetry clash REVERT: A 135 LEU cc_start: 0.9247 (tt) cc_final: 0.8998 (tt) REVERT: A 250 HIS cc_start: 0.8806 (m-70) cc_final: 0.8469 (m-70) REVERT: A 271 GLN cc_start: 0.6107 (tm-30) cc_final: 0.5852 (tm-30) REVERT: A 425 LEU cc_start: 0.9174 (tp) cc_final: 0.8934 (tp) REVERT: A 469 LEU cc_start: 0.9569 (mp) cc_final: 0.9030 (mp) REVERT: A 626 ASN cc_start: 0.8393 (m-40) cc_final: 0.7099 (m-40) REVERT: A 731 TRP cc_start: 0.8348 (t-100) cc_final: 0.8061 (t-100) REVERT: A 736 TYR cc_start: 0.8755 (t80) cc_final: 0.8267 (t80) REVERT: A 769 LEU cc_start: 0.8395 (tt) cc_final: 0.8148 (tt) REVERT: A 825 ASP cc_start: 0.8593 (t0) cc_final: 0.8295 (t0) REVERT: A 829 PHE cc_start: 0.9205 (m-10) cc_final: 0.8821 (m-10) REVERT: A 835 HIS cc_start: 0.8585 (t70) cc_final: 0.8231 (t-90) REVERT: A 856 ASP cc_start: 0.8681 (m-30) cc_final: 0.8419 (m-30) REVERT: A 896 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7865 (mt-10) REVERT: A 953 TYR cc_start: 0.7388 (t80) cc_final: 0.6978 (t80) REVERT: A 980 ASN cc_start: 0.8232 (t0) cc_final: 0.7995 (t0) REVERT: A 1074 GLN cc_start: 0.8308 (mt0) cc_final: 0.7981 (mp10) REVERT: A 1081 ASP cc_start: 0.8702 (t70) cc_final: 0.8400 (t0) REVERT: B 250 HIS cc_start: 0.8793 (m-70) cc_final: 0.8503 (m-70) REVERT: B 655 ARG cc_start: 0.8683 (mtp85) cc_final: 0.8369 (ttm110) REVERT: B 745 TYR cc_start: 0.7479 (t80) cc_final: 0.7111 (t80) REVERT: B 953 TYR cc_start: 0.7334 (t80) cc_final: 0.6896 (t80) REVERT: B 980 ASN cc_start: 0.8234 (t0) cc_final: 0.8003 (t0) REVERT: B 1074 GLN cc_start: 0.8188 (mt0) cc_final: 0.7815 (mp10) REVERT: B 1081 ASP cc_start: 0.8709 (t70) cc_final: 0.8444 (t0) REVERT: C 122 ASP cc_start: 0.5652 (p0) cc_final: 0.5243 (t70) REVERT: C 271 GLN cc_start: 0.6482 (tm-30) cc_final: 0.5966 (tm-30) REVERT: C 286 TYR cc_start: 0.8149 (t80) cc_final: 0.7933 (t80) REVERT: C 460 ASP cc_start: 0.8172 (t0) cc_final: 0.7837 (t70) REVERT: C 587 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8686 (ttmm) REVERT: C 626 ASN cc_start: 0.8317 (m-40) cc_final: 0.7110 (m-40) REVERT: C 682 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8646 (mmmm) REVERT: C 736 TYR cc_start: 0.8862 (t80) cc_final: 0.8095 (t80) REVERT: C 775 ARG cc_start: 0.6801 (mmm160) cc_final: 0.6537 (ptp90) REVERT: C 953 TYR cc_start: 0.7312 (t80) cc_final: 0.6883 (t80) REVERT: C 980 ASN cc_start: 0.8243 (t0) cc_final: 0.8030 (t0) REVERT: C 1074 GLN cc_start: 0.8166 (mt0) cc_final: 0.7938 (mp10) REVERT: C 1081 ASP cc_start: 0.8654 (t0) cc_final: 0.8424 (t0) REVERT: D 164 GLN cc_start: 0.8455 (tp40) cc_final: 0.7836 (tp40) REVERT: D 290 ILE cc_start: 0.8911 (mm) cc_final: 0.8522 (tt) REVERT: D 366 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8245 (mm-30) REVERT: D 469 LEU cc_start: 0.9427 (mp) cc_final: 0.8902 (mp) REVERT: D 521 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7218 (p0) REVERT: D 569 LYS cc_start: 0.9403 (mmtt) cc_final: 0.9195 (mmtp) REVERT: D 613 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7057 (mt-10) REVERT: D 622 GLU cc_start: 0.7513 (tp30) cc_final: 0.7243 (tp30) REVERT: D 625 SER cc_start: 0.8802 (m) cc_final: 0.8501 (p) REVERT: D 655 ARG cc_start: 0.8703 (mtp85) cc_final: 0.8469 (ttm110) REVERT: D 656 ASP cc_start: 0.8196 (m-30) cc_final: 0.7758 (m-30) REVERT: D 731 TRP cc_start: 0.8187 (t-100) cc_final: 0.7775 (t-100) REVERT: D 736 TYR cc_start: 0.8340 (t80) cc_final: 0.7630 (t80) REVERT: D 762 LEU cc_start: 0.8482 (mm) cc_final: 0.7847 (tt) REVERT: D 896 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7756 (mt-10) REVERT: D 980 ASN cc_start: 0.7917 (t0) cc_final: 0.7417 (m-40) outliers start: 73 outliers final: 40 residues processed: 1002 average time/residue: 0.1692 time to fit residues: 277.3611 Evaluate side-chains 886 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 845 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 272 LEU 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 B residue 1069 VAL 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 742 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 1069 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 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: 2.9990 chunk 114 optimal weight: 0.6980 chunk 198 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 197 optimal weight: 0.2980 chunk 136 optimal weight: 0.6980 chunk 323 optimal weight: 2.9990 chunk 318 optimal weight: 0.8980 chunk 107 optimal weight: 0.0020 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 ASN D 491 ASN ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 835 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.173747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141325 restraints weight = 42207.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145913 restraints weight = 23093.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148873 restraints weight = 16055.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150747 restraints weight = 12791.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151861 restraints weight = 11065.575| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27856 Z= 0.119 Angle : 0.618 12.509 37708 Z= 0.312 Chirality : 0.041 0.187 4248 Planarity : 0.004 0.051 4632 Dihedral : 6.116 59.374 3604 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.18 % Allowed : 19.89 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.09 (0.13), residues: 3232 helix: -1.45 (0.10), residues: 2176 sheet: -2.89 (0.36), residues: 144 loop : -3.02 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 655 TYR 0.017 0.001 TYR D 763 PHE 0.032 0.001 PHE B 969 TRP 0.021 0.001 TRP B 984 HIS 0.003 0.001 HIS D1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (27856) covalent geometry : angle 0.61838 / 0.31 (37708) hydrogen bonds : bond 0.03487 / 2.29 ( 1238) hydrogen bonds : angle 4.50512 / 3.15 ( 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 1021 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 927 time to evaluate : 1.057 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: 0.6133 (p0) cc_final: 0.5239 (t70) REVERT: A 132 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8085 (m) REVERT: A 250 HIS cc_start: 0.8812 (m-70) cc_final: 0.8472 (m-70) REVERT: A 351 ARG cc_start: 0.6949 (ttp-110) cc_final: 0.6727 (ptp90) REVERT: A 469 LEU cc_start: 0.9518 (mp) cc_final: 0.8927 (mp) REVERT: A 507 TYR cc_start: 0.7539 (m-80) cc_final: 0.7198 (m-80) REVERT: A 611 GLU cc_start: 0.8452 (pt0) cc_final: 0.7874 (pt0) REVERT: A 615 ARG cc_start: 0.8932 (tpp80) cc_final: 0.8543 (tpp80) REVERT: A 627 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6712 (t70) REVERT: A 682 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8769 (mmmm) REVERT: A 731 TRP cc_start: 0.8393 (t-100) cc_final: 0.8079 (t-100) REVERT: A 736 TYR cc_start: 0.8659 (t80) cc_final: 0.8042 (t80) REVERT: A 745 TYR cc_start: 0.7682 (t80) cc_final: 0.7329 (t80) REVERT: A 829 PHE cc_start: 0.9136 (m-10) cc_final: 0.8735 (m-10) REVERT: A 856 ASP cc_start: 0.8663 (m-30) cc_final: 0.8389 (m-30) REVERT: A 953 TYR cc_start: 0.7385 (t80) cc_final: 0.7050 (t80) REVERT: A 1081 ASP cc_start: 0.8664 (t70) cc_final: 0.8371 (t0) REVERT: B 250 HIS cc_start: 0.8804 (m-70) cc_final: 0.8513 (m-70) REVERT: B 469 LEU cc_start: 0.9496 (mp) cc_final: 0.9002 (mp) REVERT: B 611 GLU cc_start: 0.8350 (pt0) cc_final: 0.7765 (pt0) REVERT: B 682 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8593 (mmmm) REVERT: B 745 TYR cc_start: 0.7467 (t80) cc_final: 0.7137 (t80) REVERT: B 825 ASP cc_start: 0.8466 (t0) cc_final: 0.8162 (t0) REVERT: B 980 ASN cc_start: 0.8283 (t0) cc_final: 0.8030 (t0) REVERT: B 1074 GLN cc_start: 0.8099 (mt0) cc_final: 0.7763 (mp10) REVERT: B 1081 ASP cc_start: 0.8714 (t70) cc_final: 0.8450 (t0) REVERT: C 122 ASP cc_start: 0.5783 (p0) cc_final: 0.5185 (t70) REVERT: C 250 HIS cc_start: 0.8716 (m-70) cc_final: 0.8452 (m-70) REVERT: C 271 GLN cc_start: 0.6391 (tm-30) cc_final: 0.6179 (tm-30) REVERT: C 460 ASP cc_start: 0.8060 (t0) cc_final: 0.7711 (t70) REVERT: C 469 LEU cc_start: 0.9584 (mp) cc_final: 0.9230 (mp) REVERT: C 587 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8552 (ttmm) REVERT: C 613 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7555 (mt-10) REVERT: C 672 GLN cc_start: 0.8339 (tp40) cc_final: 0.8051 (tp40) REVERT: C 682 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8538 (mmmm) REVERT: C 745 TYR cc_start: 0.7498 (t80) cc_final: 0.7103 (t80) REVERT: C 825 ASP cc_start: 0.8490 (t0) cc_final: 0.8223 (t0) REVERT: C 980 ASN cc_start: 0.8333 (t0) cc_final: 0.8127 (t0) REVERT: C 1051 GLU cc_start: 0.8949 (tp30) cc_final: 0.8718 (tp30) REVERT: C 1074 GLN cc_start: 0.8054 (mt0) cc_final: 0.7818 (mp10) REVERT: D 122 ASP cc_start: 0.5509 (p0) cc_final: 0.4927 (t70) REVERT: D 164 GLN cc_start: 0.8489 (tp40) cc_final: 0.7826 (tp40) REVERT: D 290 ILE cc_start: 0.8923 (mm) cc_final: 0.8449 (tt) REVERT: D 371 TRP cc_start: 0.7951 (m100) cc_final: 0.7552 (m100) REVERT: D 413 ASP cc_start: 0.4219 (p0) cc_final: 0.3890 (p0) REVERT: D 448 ASP cc_start: 0.7241 (p0) cc_final: 0.6981 (p0) REVERT: D 469 LEU cc_start: 0.9441 (mp) cc_final: 0.8922 (mp) REVERT: D 613 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7127 (mt-10) REVERT: D 625 SER cc_start: 0.8694 (m) cc_final: 0.8475 (p) REVERT: D 633 GLN cc_start: 0.8286 (mt0) cc_final: 0.7501 (mp10) REVERT: D 655 ARG cc_start: 0.8715 (mtp85) cc_final: 0.8416 (ttm110) REVERT: D 656 ASP cc_start: 0.8124 (m-30) cc_final: 0.7661 (m-30) REVERT: D 731 TRP cc_start: 0.8287 (t-100) cc_final: 0.7737 (t-100) REVERT: D 736 TYR cc_start: 0.8590 (t80) cc_final: 0.7775 (t80) REVERT: D 762 LEU cc_start: 0.8541 (mm) cc_final: 0.7936 (tt) REVERT: D 980 ASN cc_start: 0.7958 (t0) cc_final: 0.7414 (m-40) REVERT: D 1076 ASP cc_start: 0.8298 (t0) cc_final: 0.8086 (t0) outliers start: 94 outliers final: 42 residues processed: 966 average time/residue: 0.1650 time to fit residues: 263.1518 Evaluate side-chains 901 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 855 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 356 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 858 PHE 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 771 CYS Chi-restraints excluded: chain B residue 836 ILE 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 356 THR Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 805 VAL 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 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 1070 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 321 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN A 662 GLN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN B 563 ASN B 667 ASN B1052 ASN C 491 ASN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.169577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137153 restraints weight = 42098.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.141604 restraints weight = 23018.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144486 restraints weight = 16041.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146154 restraints weight = 12801.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.147466 restraints weight = 11183.017| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27856 Z= 0.157 Angle : 0.651 12.242 37708 Z= 0.326 Chirality : 0.043 0.184 4248 Planarity : 0.004 0.050 4632 Dihedral : 6.065 58.299 3604 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.99 % Allowed : 20.26 % Favored : 75.74 % 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: -2.53 (0.14), residues: 3232 helix: -0.97 (0.11), residues: 2176 sheet: -2.82 (0.37), residues: 144 loop : -2.93 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 655 TYR 0.015 0.001 TYR D 763 PHE 0.028 0.001 PHE B 969 TRP 0.023 0.001 TRP B 984 HIS 0.004 0.001 HIS B 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (27856) covalent geometry : angle 0.65128 / 0.33 (37708) hydrogen bonds : bond 0.03370 / 2.20 ( 1238) hydrogen bonds : angle 4.32194 / 3.02 ( 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 1006 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 888 time to evaluate : 1.030 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: symmetry clash REVERT: A 132 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8269 (m) REVERT: A 469 LEU cc_start: 0.9555 (mp) cc_final: 0.8951 (mp) REVERT: A 501 GLN cc_start: 0.7446 (mt0) cc_final: 0.7117 (mp10) REVERT: A 507 TYR cc_start: 0.7580 (m-80) cc_final: 0.7314 (m-80) REVERT: A 611 GLU cc_start: 0.8326 (pt0) cc_final: 0.8022 (pt0) REVERT: A 682 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8733 (mmmm) REVERT: A 731 TRP cc_start: 0.8394 (t-100) cc_final: 0.8115 (t-100) REVERT: A 736 TYR cc_start: 0.8843 (t80) cc_final: 0.8104 (t80) REVERT: A 745 TYR cc_start: 0.7743 (t80) cc_final: 0.7476 (t80) REVERT: A 829 PHE cc_start: 0.9180 (m-10) cc_final: 0.8719 (m-10) REVERT: A 856 ASP cc_start: 0.8688 (m-30) cc_final: 0.8479 (m-30) REVERT: A 1081 ASP cc_start: 0.8674 (t70) cc_final: 0.8405 (t0) REVERT: B 312 LYS cc_start: 0.8011 (pttp) cc_final: 0.7554 (mmmt) REVERT: B 469 LEU cc_start: 0.9537 (mp) cc_final: 0.9028 (mp) REVERT: B 611 GLU cc_start: 0.8207 (pt0) cc_final: 0.7854 (pt0) REVERT: B 613 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6914 (mt-10) REVERT: B 656 ASP cc_start: 0.8147 (m-30) cc_final: 0.7762 (m-30) REVERT: B 672 GLN cc_start: 0.8519 (tp40) cc_final: 0.8225 (tp40) REVERT: B 682 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8621 (mmmm) REVERT: B 745 TYR cc_start: 0.7692 (t80) cc_final: 0.7301 (t80) REVERT: B 825 ASP cc_start: 0.8487 (t0) cc_final: 0.8212 (t0) REVERT: B 899 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6493 (pp) REVERT: B 980 ASN cc_start: 0.8343 (t0) cc_final: 0.8121 (t0) REVERT: B 1074 GLN cc_start: 0.8240 (mt0) cc_final: 0.7831 (mp10) REVERT: B 1081 ASP cc_start: 0.8768 (t70) cc_final: 0.8504 (t0) REVERT: C 250 HIS cc_start: 0.8760 (m-70) cc_final: 0.8484 (m-70) REVERT: C 297 GLN cc_start: 0.9319 (pm20) cc_final: 0.9008 (pm20) REVERT: C 460 ASP cc_start: 0.8057 (t0) cc_final: 0.7712 (t70) REVERT: C 469 LEU cc_start: 0.9599 (mp) cc_final: 0.9167 (mp) REVERT: C 672 GLN cc_start: 0.8479 (tp40) cc_final: 0.8194 (tp40) REVERT: C 745 TYR cc_start: 0.7677 (t80) cc_final: 0.7320 (t80) REVERT: C 825 ASP cc_start: 0.8491 (t0) cc_final: 0.8237 (t0) REVERT: C 980 ASN cc_start: 0.8503 (t0) cc_final: 0.8266 (t0) REVERT: C 1051 GLU cc_start: 0.8985 (tp30) cc_final: 0.8783 (tp30) REVERT: C 1074 GLN cc_start: 0.8179 (mt0) cc_final: 0.7898 (mp10) REVERT: D 164 GLN cc_start: 0.8584 (tp40) cc_final: 0.7869 (tp40) REVERT: D 371 TRP cc_start: 0.7896 (m100) cc_final: 0.7370 (m100) REVERT: D 425 LEU cc_start: 0.9246 (tp) cc_final: 0.8973 (tp) REVERT: D 448 ASP cc_start: 0.7113 (p0) cc_final: 0.6886 (p0) REVERT: D 469 LEU cc_start: 0.9479 (mp) cc_final: 0.8962 (mp) REVERT: D 498 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7914 (mmtt) REVERT: D 613 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7129 (mt-10) REVERT: D 633 GLN cc_start: 0.8314 (mt0) cc_final: 0.7507 (mp10) REVERT: D 655 ARG cc_start: 0.8723 (mtp85) cc_final: 0.8488 (ttm110) REVERT: D 656 ASP cc_start: 0.8236 (m-30) cc_final: 0.7653 (m-30) REVERT: D 736 TYR cc_start: 0.8806 (t80) cc_final: 0.7933 (t80) REVERT: D 980 ASN cc_start: 0.8028 (t0) cc_final: 0.7484 (m-40) REVERT: D 1070 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.7052 (t70) outliers start: 118 outliers final: 79 residues processed: 929 average time/residue: 0.1661 time to fit residues: 255.5578 Evaluate side-chains 920 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 836 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 728 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1075 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 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 728 VAL Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 754 GLU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 805 VAL 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 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 413 ASP Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 749 MET Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 761 ILE Chi-restraints excluded: chain C residue 771 CYS 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 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 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 575 THR 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 749 MET 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 794 THR Chi-restraints excluded: chain D residue 797 ILE Chi-restraints excluded: chain D residue 805 VAL 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 873 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 207 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 315 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 216 optimal weight: 0.2980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 ASN A 963 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** B1052 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 ** 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 = 0.3961 r_free = 0.3961 target = 0.168877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136936 restraints weight = 42052.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.141408 restraints weight = 22876.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.144266 restraints weight = 15818.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.146102 restraints weight = 12586.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.147212 restraints weight = 10892.538| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27856 Z= 0.149 Angle : 0.643 12.376 37708 Z= 0.319 Chirality : 0.043 0.280 4248 Planarity : 0.004 0.052 4632 Dihedral : 5.946 59.447 3604 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.76 % Allowed : 22.26 % Favored : 73.99 % 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: -2.15 (0.14), residues: 3232 helix: -0.66 (0.11), residues: 2176 sheet: -2.78 (0.38), residues: 144 loop : -2.83 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 655 TYR 0.017 0.001 TYR D 763 PHE 0.026 0.001 PHE A 969 TRP 0.020 0.001 TRP B 984 HIS 0.004 0.001 HIS B 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (27856) covalent geometry : angle 0.64284 / 0.32 (37708) hydrogen bonds : bond 0.03237 / 2.13 ( 1238) hydrogen bonds : angle 4.25781 / 2.99 ( 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 981 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 870 time to evaluate : 1.035 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: symmetry clash REVERT: A 132 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8185 (m) REVERT: A 312 LYS cc_start: 0.8087 (pttp) cc_final: 0.7627 (mmmt) REVERT: A 469 LEU cc_start: 0.9557 (mp) cc_final: 0.8967 (mp) REVERT: A 498 LYS cc_start: 0.8287 (mmtp) cc_final: 0.7734 (mmtp) REVERT: A 501 GLN cc_start: 0.7473 (mt0) cc_final: 0.7228 (mt0) REVERT: A 507 TYR cc_start: 0.7537 (m-80) cc_final: 0.7265 (m-80) REVERT: A 613 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7610 (mt-10) REVERT: A 627 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6767 (t70) REVERT: A 682 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8732 (mmmm) REVERT: A 736 TYR cc_start: 0.8808 (t80) cc_final: 0.8045 (t80) REVERT: A 745 TYR cc_start: 0.7705 (t80) cc_final: 0.7486 (t80) REVERT: A 775 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6412 (tmt170) REVERT: A 829 PHE cc_start: 0.9121 (m-10) cc_final: 0.8697 (m-10) REVERT: A 856 ASP cc_start: 0.8645 (m-30) cc_final: 0.8433 (m-30) REVERT: A 953 TYR cc_start: 0.7363 (t80) cc_final: 0.7005 (t80) REVERT: A 1081 ASP cc_start: 0.8693 (t70) cc_final: 0.8447 (t0) REVERT: B 132 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8417 (m) REVERT: B 469 LEU cc_start: 0.9522 (mp) cc_final: 0.8981 (mp) REVERT: B 611 GLU cc_start: 0.8064 (pt0) cc_final: 0.7619 (pt0) REVERT: B 613 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6976 (mt-10) REVERT: B 622 GLU cc_start: 0.7444 (tp30) cc_final: 0.7054 (tp30) REVERT: B 655 ARG cc_start: 0.8645 (mtp-110) cc_final: 0.8356 (ttm110) REVERT: B 656 ASP cc_start: 0.8158 (m-30) cc_final: 0.7917 (m-30) REVERT: B 672 GLN cc_start: 0.8546 (tp40) cc_final: 0.8266 (tp40) REVERT: B 682 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8606 (mmmm) REVERT: B 736 TYR cc_start: 0.8995 (t80) cc_final: 0.8137 (t80) REVERT: B 745 TYR cc_start: 0.7777 (t80) cc_final: 0.7438 (t80) REVERT: B 825 ASP cc_start: 0.8463 (t0) cc_final: 0.8171 (t0) REVERT: B 980 ASN cc_start: 0.8310 (t0) cc_final: 0.8099 (t0) REVERT: B 1070 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.6356 (t70) REVERT: B 1074 GLN cc_start: 0.8232 (mt0) cc_final: 0.7643 (mp10) REVERT: B 1081 ASP cc_start: 0.8781 (t70) cc_final: 0.8506 (t0) REVERT: C 290 ILE cc_start: 0.8933 (mm) cc_final: 0.8552 (tt) REVERT: C 297 GLN cc_start: 0.9322 (pm20) cc_final: 0.8930 (pm20) REVERT: C 460 ASP cc_start: 0.8042 (t0) cc_final: 0.7713 (t70) REVERT: C 469 LEU cc_start: 0.9572 (mp) cc_final: 0.9112 (mp) REVERT: C 498 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7842 (mmtp) REVERT: C 587 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8644 (ttmm) REVERT: C 613 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7495 (mt-10) REVERT: C 622 GLU cc_start: 0.7393 (tp30) cc_final: 0.7034 (tp30) REVERT: C 627 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6735 (t70) REVERT: C 669 LEU cc_start: 0.9102 (tp) cc_final: 0.8864 (tp) REVERT: C 672 GLN cc_start: 0.8509 (tp40) cc_final: 0.8249 (tp40) REVERT: C 736 TYR cc_start: 0.8989 (t80) cc_final: 0.8119 (t80) REVERT: C 745 TYR cc_start: 0.7729 (t80) cc_final: 0.7399 (t80) REVERT: C 980 ASN cc_start: 0.8481 (t0) cc_final: 0.8257 (t0) REVERT: C 1074 GLN cc_start: 0.8290 (mt0) cc_final: 0.7985 (mp10) REVERT: D 290 ILE cc_start: 0.8998 (mm) cc_final: 0.8618 (tt) REVERT: D 297 GLN cc_start: 0.9346 (pm20) cc_final: 0.8733 (pm20) REVERT: D 371 TRP cc_start: 0.7897 (m100) cc_final: 0.7464 (m100) REVERT: D 425 LEU cc_start: 0.9218 (tp) cc_final: 0.8914 (tp) REVERT: D 430 LEU cc_start: 0.8955 (tp) cc_final: 0.8694 (mp) REVERT: D 448 ASP cc_start: 0.7094 (p0) cc_final: 0.6854 (p0) REVERT: D 469 LEU cc_start: 0.9496 (mp) cc_final: 0.8957 (mp) REVERT: D 498 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7970 (mmtt) REVERT: D 613 GLU cc_start: 0.7724 (mt-10) cc_final: 0.6825 (mt-10) REVERT: D 633 GLN cc_start: 0.8331 (mt0) cc_final: 0.7554 (mp10) REVERT: D 655 ARG cc_start: 0.8717 (mtp85) cc_final: 0.8469 (ttm110) REVERT: D 656 ASP cc_start: 0.8170 (m-30) cc_final: 0.7468 (m-30) REVERT: D 731 TRP cc_start: 0.8430 (t-100) cc_final: 0.8103 (t-100) REVERT: D 736 TYR cc_start: 0.8891 (t80) cc_final: 0.8005 (t80) REVERT: D 804 ILE cc_start: 0.7631 (mm) cc_final: 0.7104 (mm) REVERT: D 980 ASN cc_start: 0.8027 (t0) cc_final: 0.7577 (m-40) REVERT: D 1068 MET cc_start: 0.5012 (pmm) cc_final: 0.4811 (pmm) REVERT: D 1070 HIS cc_start: 0.8415 (OUTLIER) cc_final: 0.7813 (t70) REVERT: D 1076 ASP cc_start: 0.8266 (t0) cc_final: 0.8058 (t0) outliers start: 111 outliers final: 75 residues processed: 905 average time/residue: 0.1645 time to fit residues: 245.8515 Evaluate side-chains 919 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 835 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 384 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1070 HIS 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 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 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 749 MET Chi-restraints excluded: chain B residue 754 GLU 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 836 ILE Chi-restraints excluded: chain B residue 956 SER 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 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 627 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 749 MET Chi-restraints excluded: chain C residue 761 ILE 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 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 384 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 586 SER 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 805 VAL 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: 1.9990 chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 193 optimal weight: 0.0980 chunk 145 optimal weight: 0.8980 chunk 279 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 GLN A 963 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 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 882 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS ** 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 882 ASN D 958 ASN ** D1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.171832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141192 restraints weight = 42793.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145452 restraints weight = 24699.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148167 restraints weight = 17690.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.149890 restraints weight = 14313.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.150920 restraints weight = 12496.678| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4004 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= 0.143 Angle : 0.643 12.518 37708 Z= 0.318 Chirality : 0.043 0.241 4248 Planarity : 0.004 0.054 4632 Dihedral : 5.832 57.691 3604 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.72 % Allowed : 23.65 % Favored : 72.63 % 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: -1.87 (0.14), residues: 3232 helix: -0.46 (0.11), residues: 2184 sheet: -2.68 (0.39), residues: 144 loop : -2.71 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 655 TYR 0.017 0.001 TYR D 763 PHE 0.025 0.001 PHE B 969 TRP 0.022 0.001 TRP B 984 HIS 0.005 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (27856) covalent geometry : angle 0.64327 / 0.32 (37708) hydrogen bonds : bond 0.03164 / 2.08 ( 1238) hydrogen bonds : angle 4.22098 / 2.96 ( 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 990 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 880 time to evaluate : 0.953 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: symmetry clash REVERT: A 413 ASP cc_start: 0.4737 (OUTLIER) cc_final: 0.4398 (p0) REVERT: A 469 LEU cc_start: 0.9541 (mp) cc_final: 0.8952 (mp) REVERT: A 498 LYS cc_start: 0.8275 (mmtp) cc_final: 0.7836 (mmtp) REVERT: A 507 TYR cc_start: 0.7535 (m-80) cc_final: 0.7307 (m-80) REVERT: A 682 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8855 (mmmm) REVERT: A 731 TRP cc_start: 0.8252 (t-100) cc_final: 0.7947 (t-100) REVERT: A 736 TYR cc_start: 0.8847 (t80) cc_final: 0.8054 (t80) REVERT: A 775 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6360 (tmt170) REVERT: A 829 PHE cc_start: 0.9040 (m-10) cc_final: 0.8583 (m-10) REVERT: A 1081 ASP cc_start: 0.8716 (t70) cc_final: 0.8438 (t0) REVERT: B 132 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8402 (m) REVERT: B 469 LEU cc_start: 0.9544 (mp) cc_final: 0.9019 (mp) REVERT: B 613 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7149 (mt-10) REVERT: B 622 GLU cc_start: 0.7437 (tp30) cc_final: 0.7022 (tp30) REVERT: B 655 ARG cc_start: 0.8558 (mtp-110) cc_final: 0.8275 (ttm110) REVERT: B 672 GLN cc_start: 0.8448 (tp40) cc_final: 0.8205 (tp40) REVERT: B 682 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8709 (mmmm) REVERT: B 736 TYR cc_start: 0.8944 (t80) cc_final: 0.8134 (t80) REVERT: B 745 TYR cc_start: 0.7817 (t80) cc_final: 0.7514 (t80) REVERT: B 825 ASP cc_start: 0.8362 (t0) cc_final: 0.8147 (t0) REVERT: B 899 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6347 (pp) REVERT: B 980 ASN cc_start: 0.8244 (t0) cc_final: 0.8041 (t0) REVERT: B 1070 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6260 (t70) REVERT: B 1074 GLN cc_start: 0.8151 (mt0) cc_final: 0.7796 (mp10) REVERT: B 1081 ASP cc_start: 0.8828 (t70) cc_final: 0.8598 (t0) REVERT: C 290 ILE cc_start: 0.8897 (mm) cc_final: 0.8588 (tt) REVERT: C 312 LYS cc_start: 0.7976 (ptmm) cc_final: 0.7510 (mmmt) REVERT: C 460 ASP cc_start: 0.7935 (t0) cc_final: 0.7661 (t70) REVERT: C 469 LEU cc_start: 0.9551 (mp) cc_final: 0.9069 (mp) REVERT: C 498 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7788 (mmtp) REVERT: C 622 GLU cc_start: 0.7326 (tp30) cc_final: 0.6943 (tp30) REVERT: C 669 LEU cc_start: 0.9016 (tp) cc_final: 0.8760 (tp) REVERT: C 672 GLN cc_start: 0.8407 (tp40) cc_final: 0.8185 (tp40) REVERT: C 736 TYR cc_start: 0.8938 (t80) cc_final: 0.8122 (t80) REVERT: C 745 TYR cc_start: 0.7738 (t80) cc_final: 0.7460 (t80) REVERT: C 775 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6570 (tmt170) REVERT: C 858 PHE cc_start: 0.8042 (t80) cc_final: 0.7700 (t80) REVERT: C 899 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.6160 (pp) REVERT: C 980 ASN cc_start: 0.8482 (t0) cc_final: 0.8150 (t0) REVERT: C 1074 GLN cc_start: 0.8270 (mt0) cc_final: 0.7988 (mp10) REVERT: D 290 ILE cc_start: 0.9015 (mm) cc_final: 0.8671 (tt) REVERT: D 297 GLN cc_start: 0.9280 (pm20) cc_final: 0.8655 (pm20) REVERT: D 371 TRP cc_start: 0.7925 (m100) cc_final: 0.7478 (m100) REVERT: D 425 LEU cc_start: 0.9270 (tp) cc_final: 0.8976 (tp) REVERT: D 448 ASP cc_start: 0.6910 (p0) cc_final: 0.6692 (p0) REVERT: D 469 LEU cc_start: 0.9501 (mp) cc_final: 0.8961 (mp) REVERT: D 498 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7949 (mmtt) REVERT: D 633 GLN cc_start: 0.8253 (mt0) cc_final: 0.7553 (mp10) REVERT: D 655 ARG cc_start: 0.8639 (mtp85) cc_final: 0.8428 (ttm110) REVERT: D 731 TRP cc_start: 0.8297 (t-100) cc_final: 0.8003 (t-100) REVERT: D 736 TYR cc_start: 0.8902 (t80) cc_final: 0.8100 (t80) REVERT: D 980 ASN cc_start: 0.7963 (t0) cc_final: 0.7456 (m110) REVERT: D 1070 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.7848 (t70) REVERT: D 1076 ASP cc_start: 0.8223 (t0) cc_final: 0.8021 (t0) outliers start: 110 outliers final: 78 residues processed: 919 average time/residue: 0.1639 time to fit residues: 248.3883 Evaluate side-chains 931 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 843 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 413 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 728 VAL 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 794 THR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 132 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 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 805 VAL Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 873 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 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 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 749 MET Chi-restraints excluded: chain C residue 761 ILE Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 775 ARG 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 834 ILE 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 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 413 ASP Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 586 SER 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 840 SER Chi-restraints excluded: chain D residue 849 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 182 optimal weight: 10.0000 chunk 247 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 324 optimal weight: 0.8980 chunk 176 optimal weight: 0.0040 chunk 249 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 ASN B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN ** 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 ** 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 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 GLN D 776 GLN ** D1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.170538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139956 restraints weight = 42534.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144178 restraints weight = 24767.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146889 restraints weight = 17715.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148626 restraints weight = 14317.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149659 restraints weight = 12471.250| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27856 Z= 0.162 Angle : 0.671 12.421 37708 Z= 0.334 Chirality : 0.044 0.371 4248 Planarity : 0.004 0.056 4632 Dihedral : 5.831 57.473 3604 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.43 % Allowed : 24.15 % Favored : 71.41 % 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: -1.73 (0.14), residues: 3232 helix: -0.37 (0.11), residues: 2188 sheet: -2.63 (0.39), residues: 144 loop : -2.62 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 655 TYR 0.018 0.001 TYR D 763 PHE 0.027 0.001 PHE B 969 TRP 0.021 0.001 TRP D 684 HIS 0.003 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (27856) covalent geometry : angle 0.67126 / 0.33 (37708) hydrogen bonds : bond 0.03263 / 2.15 ( 1238) hydrogen bonds : angle 4.25581 / 2.99 ( 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 1010 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 879 time to evaluate : 1.081 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: symmetry clash REVERT: A 469 LEU cc_start: 0.9526 (mp) cc_final: 0.8964 (mp) REVERT: A 507 TYR cc_start: 0.7557 (m-80) cc_final: 0.7311 (m-80) REVERT: A 565 LYS cc_start: 0.8526 (tppp) cc_final: 0.8236 (tptt) REVERT: A 622 GLU cc_start: 0.7592 (tp30) cc_final: 0.7185 (tp30) REVERT: A 682 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8762 (mmmm) REVERT: A 858 PHE cc_start: 0.8187 (t80) cc_final: 0.7800 (t80) REVERT: A 1074 GLN cc_start: 0.7524 (mp10) cc_final: 0.7176 (mp10) REVERT: A 1081 ASP cc_start: 0.8736 (t70) cc_final: 0.8460 (t0) REVERT: B 132 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8420 (m) REVERT: B 469 LEU cc_start: 0.9558 (mp) cc_final: 0.9042 (mp) REVERT: B 622 GLU cc_start: 0.7540 (tp30) cc_final: 0.7099 (tp30) REVERT: B 672 GLN cc_start: 0.8454 (tp40) cc_final: 0.8218 (tp40) REVERT: B 682 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8705 (mmmm) REVERT: B 736 TYR cc_start: 0.9006 (t80) cc_final: 0.8243 (t80) REVERT: B 745 TYR cc_start: 0.7785 (t80) cc_final: 0.7521 (t80) REVERT: B 858 PHE cc_start: 0.8126 (t80) cc_final: 0.7777 (t80) REVERT: B 899 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6543 (pp) REVERT: B 980 ASN cc_start: 0.8359 (t0) cc_final: 0.8090 (t0) REVERT: B 1070 HIS cc_start: 0.7256 (OUTLIER) cc_final: 0.6237 (t70) REVERT: B 1074 GLN cc_start: 0.8166 (mt0) cc_final: 0.7787 (mp10) REVERT: B 1081 ASP cc_start: 0.8831 (t70) cc_final: 0.8571 (t0) REVERT: C 153 ARG cc_start: 0.8954 (ptp-170) cc_final: 0.8598 (mtm180) REVERT: C 297 GLN cc_start: 0.9350 (pm20) cc_final: 0.9004 (pm20) REVERT: C 312 LYS cc_start: 0.8107 (ptmm) cc_final: 0.7642 (mmmt) REVERT: C 460 ASP cc_start: 0.7917 (t0) cc_final: 0.7671 (t70) REVERT: C 469 LEU cc_start: 0.9581 (mp) cc_final: 0.9073 (mp) REVERT: C 498 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7798 (mmtp) REVERT: C 622 GLU cc_start: 0.7301 (tp30) cc_final: 0.6948 (tp30) REVERT: C 627 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6707 (t70) REVERT: C 669 LEU cc_start: 0.9077 (tp) cc_final: 0.8868 (tp) REVERT: C 672 GLN cc_start: 0.8443 (tp40) cc_final: 0.8237 (tp40) REVERT: C 682 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8618 (mmmm) REVERT: C 736 TYR cc_start: 0.8981 (t80) cc_final: 0.8141 (t80) REVERT: C 775 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6424 (tmt170) REVERT: C 858 PHE cc_start: 0.8199 (t80) cc_final: 0.7878 (t80) REVERT: C 899 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6154 (pp) REVERT: C 953 TYR cc_start: 0.7396 (t80) cc_final: 0.7129 (t80) REVERT: C 980 ASN cc_start: 0.8485 (t0) cc_final: 0.8165 (t0) REVERT: C 1074 GLN cc_start: 0.8312 (mt0) cc_final: 0.8022 (mp10) REVERT: D 297 GLN cc_start: 0.9261 (pm20) cc_final: 0.8569 (pm20) REVERT: D 371 TRP cc_start: 0.7916 (m100) cc_final: 0.7423 (m100) REVERT: D 425 LEU cc_start: 0.9282 (tp) cc_final: 0.8985 (tp) REVERT: D 430 LEU cc_start: 0.8950 (tp) cc_final: 0.8728 (mp) REVERT: D 448 ASP cc_start: 0.6833 (p0) cc_final: 0.6614 (p0) REVERT: D 469 LEU cc_start: 0.9537 (mp) cc_final: 0.9038 (mp) REVERT: D 498 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7981 (mmtt) REVERT: D 633 GLN cc_start: 0.8285 (mt0) cc_final: 0.7563 (mp10) REVERT: D 669 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9106 (mp) REVERT: D 731 TRP cc_start: 0.8291 (t-100) cc_final: 0.8044 (t-100) REVERT: D 736 TYR cc_start: 0.8973 (t80) cc_final: 0.8206 (t80) REVERT: D 980 ASN cc_start: 0.8060 (t0) cc_final: 0.7546 (m-40) REVERT: D 1049 MET cc_start: 0.8443 (ptm) cc_final: 0.8152 (ttp) REVERT: D 1068 MET cc_start: 0.5268 (pmm) cc_final: 0.5050 (pmm) REVERT: D 1070 HIS cc_start: 0.8211 (OUTLIER) cc_final: 0.7996 (t70) outliers start: 131 outliers final: 96 residues processed: 928 average time/residue: 0.1630 time to fit residues: 249.4524 Evaluate side-chains 956 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 849 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 413 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 VAL 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 794 THR Chi-restraints excluded: chain A residue 805 VAL 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 132 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 251 LEU 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 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 627 ASP 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 794 THR Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 965 LEU 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 413 ASP Chi-restraints excluded: chain C residue 521 ASP Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 682 LYS Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 746 VAL 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 775 ARG 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 834 ILE 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 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 413 ASP Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 586 SER Chi-restraints excluded: chain D residue 665 VAL 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 746 VAL 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 805 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 849 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 12 optimal weight: 0.0770 chunk 124 optimal weight: 0.9980 chunk 313 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 327 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN ** B 474 ASN ** 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 563 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 ASN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1070 HIS ** 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 = 0.4019 r_free = 0.4019 target = 0.172741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.142346 restraints weight = 42705.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146653 restraints weight = 24799.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149395 restraints weight = 17676.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151161 restraints weight = 14258.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152189 restraints weight = 12404.093| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27856 Z= 0.132 Angle : 0.663 12.803 37708 Z= 0.326 Chirality : 0.044 0.362 4248 Planarity : 0.004 0.057 4632 Dihedral : 5.712 55.683 3604 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.82 % Allowed : 25.07 % Favored : 71.11 % 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: -1.54 (0.14), residues: 3232 helix: -0.20 (0.11), residues: 2172 sheet: -2.55 (0.39), residues: 144 loop : -2.58 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 655 TYR 0.018 0.001 TYR D 763 PHE 0.026 0.001 PHE B 969 TRP 0.022 0.001 TRP D 684 HIS 0.003 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (27856) covalent geometry : angle 0.66267 / 0.33 (37708) hydrogen bonds : bond 0.03102 / 2.05 ( 1238) hydrogen bonds : angle 4.20825 / 2.96 ( 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 987 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 874 time to evaluate : 0.958 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: symmetry clash REVERT: A 351 ARG cc_start: 0.6933 (ptp90) cc_final: 0.6610 (ptp90) REVERT: A 469 LEU cc_start: 0.9509 (mp) cc_final: 0.8937 (mp) REVERT: A 507 TYR cc_start: 0.7526 (m-80) cc_final: 0.7289 (m-80) REVERT: A 565 LYS cc_start: 0.8532 (tppp) cc_final: 0.8322 (tptt) REVERT: A 613 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7019 (tp30) REVERT: A 622 GLU cc_start: 0.7607 (tp30) cc_final: 0.7203 (tp30) REVERT: A 656 ASP cc_start: 0.8148 (m-30) cc_final: 0.7501 (m-30) REVERT: A 682 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8830 (mmmm) REVERT: A 858 PHE cc_start: 0.8186 (t80) cc_final: 0.7849 (t80) REVERT: A 899 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6334 (pp) REVERT: A 1081 ASP cc_start: 0.8749 (t70) cc_final: 0.8497 (t0) REVERT: B 132 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8354 (m) REVERT: B 469 LEU cc_start: 0.9531 (mp) cc_final: 0.9004 (mp) REVERT: B 498 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7465 (mmtt) REVERT: B 507 TYR cc_start: 0.7446 (m-80) cc_final: 0.7147 (m-80) REVERT: B 622 GLU cc_start: 0.7521 (tp30) cc_final: 0.7082 (tp30) REVERT: B 672 GLN cc_start: 0.8404 (tp40) cc_final: 0.8173 (tp40) REVERT: B 682 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8614 (mmmm) REVERT: B 736 TYR cc_start: 0.8975 (t80) cc_final: 0.8179 (t80) REVERT: B 858 PHE cc_start: 0.8140 (t80) cc_final: 0.7836 (t80) REVERT: B 885 ARG cc_start: 0.5765 (mpp-170) cc_final: 0.5259 (ptp-170) REVERT: B 899 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6475 (pp) REVERT: B 953 TYR cc_start: 0.7225 (t80) cc_final: 0.7023 (t80) REVERT: B 980 ASN cc_start: 0.8362 (t0) cc_final: 0.8092 (t0) REVERT: B 1070 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6537 (t70) REVERT: B 1074 GLN cc_start: 0.8107 (mt0) cc_final: 0.7773 (mp10) REVERT: B 1081 ASP cc_start: 0.8818 (t70) cc_final: 0.8547 (t0) REVERT: C 297 GLN cc_start: 0.9296 (pm20) cc_final: 0.8693 (pm20) REVERT: C 460 ASP cc_start: 0.7918 (t0) cc_final: 0.7688 (t70) REVERT: C 469 LEU cc_start: 0.9532 (mp) cc_final: 0.8986 (mp) REVERT: C 498 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7359 (mmtp) REVERT: C 622 GLU cc_start: 0.7320 (tp30) cc_final: 0.6952 (tp30) REVERT: C 656 ASP cc_start: 0.8113 (m-30) cc_final: 0.7490 (m-30) REVERT: C 669 LEU cc_start: 0.8997 (tp) cc_final: 0.8754 (tp) REVERT: C 682 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8556 (mmmm) REVERT: C 736 TYR cc_start: 0.8958 (t80) cc_final: 0.8206 (t80) REVERT: C 858 PHE cc_start: 0.8182 (t80) cc_final: 0.7885 (t80) REVERT: C 899 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6188 (pp) REVERT: C 953 TYR cc_start: 0.7329 (t80) cc_final: 0.7100 (t80) REVERT: C 980 ASN cc_start: 0.8468 (t0) cc_final: 0.8171 (t0) REVERT: D 297 GLN cc_start: 0.9243 (pm20) cc_final: 0.8725 (pm20) REVERT: D 371 TRP cc_start: 0.7883 (m100) cc_final: 0.7413 (m100) REVERT: D 469 LEU cc_start: 0.9447 (mp) cc_final: 0.9002 (mp) REVERT: D 498 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7931 (mmtt) REVERT: D 613 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6827 (mt-10) REVERT: D 622 GLU cc_start: 0.7417 (tp30) cc_final: 0.6776 (tp30) REVERT: D 633 GLN cc_start: 0.8290 (mt0) cc_final: 0.7547 (mp10) REVERT: D 656 ASP cc_start: 0.8375 (m-30) cc_final: 0.7769 (m-30) REVERT: D 731 TRP cc_start: 0.8240 (t-100) cc_final: 0.7973 (t-100) REVERT: D 736 TYR cc_start: 0.8942 (t80) cc_final: 0.8170 (t80) REVERT: D 980 ASN cc_start: 0.8048 (t0) cc_final: 0.7542 (m-40) REVERT: D 1049 MET cc_start: 0.8328 (ptm) cc_final: 0.7955 (ttp) REVERT: D 1068 MET cc_start: 0.5417 (pmm) cc_final: 0.5108 (pmm) REVERT: D 1070 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7353 (t70) REVERT: D 1073 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7535 (mtm-85) outliers start: 113 outliers final: 83 residues processed: 923 average time/residue: 0.1692 time to fit residues: 256.6652 Evaluate side-chains 942 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 850 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 413 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 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 794 THR Chi-restraints excluded: chain A residue 805 VAL 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 132 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 VAL 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 413 ASP Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 682 LYS 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 836 ILE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 965 LEU 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 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 474 ASN 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 688 MET Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 761 ILE Chi-restraints excluded: chain C residue 771 CYS Chi-restraints excluded: chain C residue 775 ARG 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 834 ILE 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 1070 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 586 SER 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 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 805 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 40 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 109 optimal weight: 0.3980 chunk 67 optimal weight: 0.6980 chunk 217 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 214 optimal weight: 0.0970 chunk 75 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 308 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** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN C 563 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 ASN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1070 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.169345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.137007 restraints weight = 42580.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.141442 restraints weight = 23464.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144348 restraints weight = 16377.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.146184 restraints weight = 13054.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147349 restraints weight = 11292.764| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27856 Z= 0.122 Angle : 0.668 13.079 37708 Z= 0.328 Chirality : 0.044 0.470 4248 Planarity : 0.004 0.057 4632 Dihedral : 5.644 55.312 3604 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.04 % Allowed : 26.35 % Favored : 70.60 % 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: -1.39 (0.14), residues: 3232 helix: -0.10 (0.11), residues: 2180 sheet: -2.42 (0.40), residues: 144 loop : -2.52 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 655 TYR 0.017 0.001 TYR D 763 PHE 0.024 0.001 PHE B 969 TRP 0.024 0.001 TRP D 684 HIS 0.003 0.001 HIS D 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (27856) covalent geometry : angle 0.66776 / 0.33 (37708) hydrogen bonds : bond 0.03055 / 2.02 ( 1238) hydrogen bonds : angle 4.18905 / 2.94 ( 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 960 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 870 time to evaluate : 1.089 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: symmetry clash REVERT: A 351 ARG cc_start: 0.7040 (ptp90) cc_final: 0.6778 (ptp90) REVERT: A 469 LEU cc_start: 0.9515 (mp) cc_final: 0.8931 (mp) REVERT: A 507 TYR cc_start: 0.7601 (m-80) cc_final: 0.7397 (m-80) REVERT: A 565 LYS cc_start: 0.8509 (tppp) cc_final: 0.8303 (tptt) REVERT: A 612 TYR cc_start: 0.9174 (m-80) cc_final: 0.8754 (m-80) REVERT: A 613 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7143 (tp30) REVERT: A 622 GLU cc_start: 0.7624 (tp30) cc_final: 0.7078 (tp30) REVERT: A 656 ASP cc_start: 0.8225 (m-30) cc_final: 0.7565 (m-30) REVERT: A 682 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8669 (mmmm) REVERT: A 731 TRP cc_start: 0.8300 (t-100) cc_final: 0.7945 (t-100) REVERT: A 858 PHE cc_start: 0.8273 (t80) cc_final: 0.7910 (t80) REVERT: A 899 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6565 (pp) REVERT: A 1081 ASP cc_start: 0.8743 (t70) cc_final: 0.8469 (t0) REVERT: B 132 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8395 (m) REVERT: B 271 GLN cc_start: 0.6802 (tm-30) cc_final: 0.6399 (tm-30) REVERT: B 469 LEU cc_start: 0.9489 (mp) cc_final: 0.8937 (mp) REVERT: B 498 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7384 (mmtt) REVERT: B 507 TYR cc_start: 0.7441 (m-80) cc_final: 0.7128 (m-80) REVERT: B 612 TYR cc_start: 0.9171 (m-80) cc_final: 0.8754 (m-80) REVERT: B 622 GLU cc_start: 0.7578 (tp30) cc_final: 0.7131 (tp30) REVERT: B 672 GLN cc_start: 0.8484 (tp40) cc_final: 0.8213 (tp40) REVERT: B 682 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8566 (mmmm) REVERT: B 736 TYR cc_start: 0.8991 (t80) cc_final: 0.8252 (t80) REVERT: B 775 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6999 (mmt180) REVERT: B 858 PHE cc_start: 0.8166 (t80) cc_final: 0.7864 (t80) REVERT: B 899 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6421 (pp) REVERT: B 953 TYR cc_start: 0.7249 (t80) cc_final: 0.7007 (t80) REVERT: B 980 ASN cc_start: 0.8437 (t0) cc_final: 0.8144 (t0) REVERT: B 1049 MET cc_start: 0.8819 (ptp) cc_final: 0.8298 (ptm) REVERT: B 1070 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6652 (t70) REVERT: B 1074 GLN cc_start: 0.8036 (mt0) cc_final: 0.7683 (mp10) REVERT: B 1081 ASP cc_start: 0.8829 (t70) cc_final: 0.8553 (t0) REVERT: C 297 GLN cc_start: 0.9311 (pm20) cc_final: 0.8644 (pm20) REVERT: C 469 LEU cc_start: 0.9518 (mp) cc_final: 0.8944 (mp) REVERT: C 498 LYS cc_start: 0.8143 (mmtp) cc_final: 0.7354 (mmtp) REVERT: C 613 GLU cc_start: 0.7829 (tp30) cc_final: 0.6175 (tp30) REVERT: C 622 GLU cc_start: 0.7404 (tp30) cc_final: 0.6985 (tp30) REVERT: C 656 ASP cc_start: 0.8253 (m-30) cc_final: 0.7168 (m-30) REVERT: C 669 LEU cc_start: 0.9013 (tp) cc_final: 0.8743 (tp) REVERT: C 682 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8439 (mmmm) REVERT: C 736 TYR cc_start: 0.9000 (t80) cc_final: 0.8215 (t80) REVERT: C 858 PHE cc_start: 0.8237 (t80) cc_final: 0.7914 (t80) REVERT: C 899 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6268 (pp) REVERT: C 953 TYR cc_start: 0.7340 (t80) cc_final: 0.7083 (t80) REVERT: C 960 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9075 (mm) REVERT: C 980 ASN cc_start: 0.8502 (t0) cc_final: 0.8213 (t0) REVERT: C 1076 ASP cc_start: 0.8279 (t0) cc_final: 0.8071 (t0) REVERT: D 297 GLN cc_start: 0.9249 (pm20) cc_final: 0.8741 (pm20) REVERT: D 371 TRP cc_start: 0.7883 (m100) cc_final: 0.7407 (m100) REVERT: D 469 LEU cc_start: 0.9457 (mp) cc_final: 0.8891 (mp) REVERT: D 498 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7888 (mmtt) REVERT: D 613 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6940 (mt-10) REVERT: D 622 GLU cc_start: 0.7453 (tp30) cc_final: 0.6747 (tp30) REVERT: D 633 GLN cc_start: 0.8382 (mt0) cc_final: 0.7567 (mp10) REVERT: D 656 ASP cc_start: 0.8437 (m-30) cc_final: 0.7728 (m-30) REVERT: D 731 TRP cc_start: 0.8272 (t-100) cc_final: 0.7962 (t-100) REVERT: D 736 TYR cc_start: 0.8963 (t80) cc_final: 0.8164 (t80) REVERT: D 769 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8230 (tt) REVERT: D 980 ASN cc_start: 0.8117 (t0) cc_final: 0.7571 (m-40) REVERT: D 1049 MET cc_start: 0.8381 (ptm) cc_final: 0.7984 (ttp) REVERT: D 1068 MET cc_start: 0.5339 (pmm) cc_final: 0.4988 (pmm) REVERT: D 1081 ASP cc_start: 0.8936 (t70) cc_final: 0.8644 (t0) outliers start: 90 outliers final: 65 residues processed: 912 average time/residue: 0.1664 time to fit residues: 250.2078 Evaluate side-chains 916 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 840 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 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 575 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 794 THR 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 132 THR 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 430 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 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 251 LEU 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 474 ASN 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 688 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 775 ARG Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 563 ASN 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 749 MET 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 Chi-restraints excluded: chain D residue 966 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 170 optimal weight: 0.9990 chunk 18 optimal weight: 0.0060 chunk 198 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 317 optimal weight: 0.7980 chunk 294 optimal weight: 0.5980 chunk 177 optimal weight: 0.8980 chunk 324 optimal weight: 0.7980 chunk 285 optimal weight: 0.0870 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 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 563 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 ASN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 835 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.170182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138232 restraints weight = 42427.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142576 restraints weight = 23715.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145382 restraints weight = 16679.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147021 restraints weight = 13379.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148311 restraints weight = 11682.900| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4686 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= 0.124 Angle : 0.685 13.355 37708 Z= 0.333 Chirality : 0.043 0.263 4248 Planarity : 0.004 0.057 4632 Dihedral : 5.633 55.207 3604 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.50 % Allowed : 27.50 % Favored : 69.99 % Cbeta Deviations : 0.09 % 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 (0.15), residues: 3232 helix: -0.05 (0.11), residues: 2180 sheet: -2.32 (0.40), residues: 144 loop : -2.46 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 655 TYR 0.017 0.001 TYR B 177 PHE 0.025 0.001 PHE B 969 TRP 0.024 0.001 TRP A 417 HIS 0.003 0.000 HIS D 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (27856) covalent geometry : angle 0.68512 / 0.33 (37708) hydrogen bonds : bond 0.03056 / 2.01 ( 1238) hydrogen bonds : angle 4.18654 / 2.94 ( 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 925 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 851 time to evaluate : 1.164 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: 0.9479 (mp) cc_final: 0.8907 (mp) REVERT: A 498 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7551 (mmtt) REVERT: A 507 TYR cc_start: 0.7573 (m-80) cc_final: 0.7347 (m-80) REVERT: A 565 LYS cc_start: 0.8451 (tppp) cc_final: 0.8228 (tptt) REVERT: A 612 TYR cc_start: 0.9169 (m-80) cc_final: 0.8774 (m-80) REVERT: A 613 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7172 (tp30) REVERT: A 622 GLU cc_start: 0.7658 (tp30) cc_final: 0.7143 (tp30) REVERT: A 656 ASP cc_start: 0.8166 (m-30) cc_final: 0.7576 (m-30) REVERT: A 682 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8589 (mmmm) REVERT: A 858 PHE cc_start: 0.8223 (t80) cc_final: 0.7866 (t80) REVERT: A 1081 ASP cc_start: 0.8741 (t70) cc_final: 0.8466 (t0) REVERT: B 132 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8193 (m) REVERT: B 271 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6453 (tm-30) REVERT: B 469 LEU cc_start: 0.9492 (mp) cc_final: 0.8937 (mp) REVERT: B 498 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7357 (mmtt) REVERT: B 507 TYR cc_start: 0.7437 (m-80) cc_final: 0.7127 (m-80) REVERT: B 622 GLU cc_start: 0.7582 (tp30) cc_final: 0.7103 (tp30) REVERT: B 672 GLN cc_start: 0.8460 (tp40) cc_final: 0.8206 (tp40) REVERT: B 682 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8518 (mmmm) REVERT: B 736 TYR cc_start: 0.8996 (t80) cc_final: 0.8278 (t80) REVERT: B 775 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6890 (mmt180) REVERT: B 858 PHE cc_start: 0.8140 (t80) cc_final: 0.7843 (t80) REVERT: B 899 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6331 (pp) REVERT: B 980 ASN cc_start: 0.8423 (t0) cc_final: 0.8134 (t0) REVERT: B 1049 MET cc_start: 0.8787 (ptp) cc_final: 0.8301 (ptm) REVERT: B 1070 HIS cc_start: 0.7405 (OUTLIER) cc_final: 0.6673 (t70) REVERT: B 1074 GLN cc_start: 0.8018 (mt0) cc_final: 0.7729 (mp10) REVERT: B 1081 ASP cc_start: 0.8820 (t70) cc_final: 0.8550 (t0) REVERT: C 297 GLN cc_start: 0.9307 (pm20) cc_final: 0.8597 (pm20) REVERT: C 469 LEU cc_start: 0.9490 (mp) cc_final: 0.8887 (mp) REVERT: C 498 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7322 (mmtp) REVERT: C 613 GLU cc_start: 0.7734 (tp30) cc_final: 0.6136 (tp30) REVERT: C 622 GLU cc_start: 0.7399 (tp30) cc_final: 0.6951 (tp30) REVERT: C 627 ASP cc_start: 0.7165 (t70) cc_final: 0.6718 (t70) REVERT: C 656 ASP cc_start: 0.8174 (m-30) cc_final: 0.7067 (m-30) REVERT: C 669 LEU cc_start: 0.8979 (tp) cc_final: 0.8714 (tp) REVERT: C 682 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8407 (mmmm) REVERT: C 736 TYR cc_start: 0.9003 (t80) cc_final: 0.8241 (t80) REVERT: C 858 PHE cc_start: 0.8144 (t80) cc_final: 0.7831 (t80) REVERT: C 899 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6257 (pp) REVERT: C 953 TYR cc_start: 0.7287 (t80) cc_final: 0.7071 (t80) REVERT: C 960 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9076 (mm) REVERT: C 980 ASN cc_start: 0.8496 (t0) cc_final: 0.8194 (t0) REVERT: D 297 GLN cc_start: 0.9190 (pm20) cc_final: 0.8710 (pm20) REVERT: D 351 ARG cc_start: 0.6657 (ptp90) cc_final: 0.6203 (ptp90) REVERT: D 371 TRP cc_start: 0.7929 (m100) cc_final: 0.7470 (m100) REVERT: D 469 LEU cc_start: 0.9439 (mp) cc_final: 0.8865 (mp) REVERT: D 498 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7814 (mmtt) REVERT: D 613 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6856 (mt-10) REVERT: D 622 GLU cc_start: 0.7449 (tp30) cc_final: 0.6763 (tp30) REVERT: D 633 GLN cc_start: 0.8371 (mt0) cc_final: 0.7579 (mp10) REVERT: D 637 TYR cc_start: 0.6628 (t80) cc_final: 0.6291 (t80) REVERT: D 656 ASP cc_start: 0.8361 (m-30) cc_final: 0.7724 (m-30) REVERT: D 657 GLN cc_start: 0.8140 (mt0) cc_final: 0.7887 (mt0) REVERT: D 731 TRP cc_start: 0.8217 (t-100) cc_final: 0.7914 (t-100) REVERT: D 736 TYR cc_start: 0.8964 (t80) cc_final: 0.8185 (t80) REVERT: D 769 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8270 (tt) REVERT: D 980 ASN cc_start: 0.8131 (t0) cc_final: 0.7570 (m-40) REVERT: D 1049 MET cc_start: 0.8365 (ptm) cc_final: 0.7993 (ttp) REVERT: D 1068 MET cc_start: 0.5004 (pmm) cc_final: 0.4697 (pmm) REVERT: D 1081 ASP cc_start: 0.8938 (t70) cc_final: 0.8635 (t0) outliers start: 74 outliers final: 58 residues processed: 884 average time/residue: 0.1674 time to fit residues: 244.1424 Evaluate side-chains 900 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 832 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 251 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 575 THR Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 175 THR 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 430 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 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 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 474 ASN 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 688 MET Chi-restraints excluded: chain C residue 746 VAL 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 960 LEU Chi-restraints excluded: chain C residue 1070 HIS 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 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 749 MET 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: 2.9990 chunk 321 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 216 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 235 optimal weight: 0.0970 chunk 270 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN A 835 HIS ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 ASN ** 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 563 ASN C 835 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.170911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138935 restraints weight = 41907.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.143317 restraints weight = 23179.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146080 restraints weight = 16261.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.147940 restraints weight = 13081.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148900 restraints weight = 11315.126| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4757 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= 0.135 Angle : 0.680 12.955 37708 Z= 0.333 Chirality : 0.043 0.256 4248 Planarity : 0.004 0.057 4632 Dihedral : 5.644 59.909 3604 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.71 % Allowed : 27.57 % Favored : 69.72 % 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: -1.25 (0.15), residues: 3232 helix: -0.01 (0.11), residues: 2172 sheet: -2.25 (0.41), residues: 144 loop : -2.41 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 885 TYR 0.020 0.001 TYR A 895 PHE 0.023 0.001 PHE B 969 TRP 0.027 0.001 TRP A 417 HIS 0.003 0.001 HIS D 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (27856) covalent geometry : angle 0.68042 / 0.33 (37708) hydrogen bonds : bond 0.03087 / 2.02 ( 1238) hydrogen bonds : angle 4.19330 / 2.95 ( 3678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6005.76 seconds wall clock time: 104 minutes 9.50 seconds (6249.50 seconds total)