Starting phenix.real_space_refine on Sun Feb 8 02:28:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8swk_40820/02_2026/8swk_40820_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8swk_40820/02_2026/8swk_40820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8swk_40820/02_2026/8swk_40820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8swk_40820/02_2026/8swk_40820.map" model { file = "/net/cci-nas-00/data/ceres_data/8swk_40820/02_2026/8swk_40820_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8swk_40820/02_2026/8swk_40820_neut.cif" } resolution = 4.32 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= 0.005 sd= 0.039 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 P 18 5.49 5 S 342 5.16 5 C 25152 2.51 5 N 6672 2.21 5 O 7326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39510 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6526 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 23, 'TRANS': 794} Chain breaks: 4 Chain: "B" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6526 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 23, 'TRANS': 794} Chain breaks: 4 Chain: "C" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6526 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 23, 'TRANS': 794} Chain breaks: 4 Chain: "D" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6526 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 23, 'TRANS': 794} Chain breaks: 4 Chain: "E" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6526 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 23, 'TRANS': 794} Chain breaks: 4 Chain: "F" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6526 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 23, 'TRANS': 794} Chain breaks: 4 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.04, per 1000 atoms: 0.23 Number of scatterers: 39510 At special positions: 0 Unit cell: (163.904, 157.248, 133.952, 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 342 16.00 P 18 15.00 O 7326 8.00 N 6672 7.00 C 25152 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: 3.54 Conformation dependent library (CDL) restraints added in 1.7 seconds 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9312 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 24 sheets defined 51.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 351 through 357 removed outlier: 4.163A pdb=" N GLU A 356 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 411 through 428 Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 465 through 479 Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 497 through 505 Processing helix chain 'A' and resid 522 through 534 removed outlier: 3.609A pdb=" N TYR A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 564 Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 592 through 596 removed outlier: 3.774A pdb=" N LEU A 596 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 617 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 639 through 647 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 659 through 672 removed outlier: 3.608A pdb=" N ASN A 672 " --> pdb=" O PHE A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'A' and resid 730 through 738 removed outlier: 4.194A pdb=" N VAL A 736 " --> pdb=" O GLY A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 765 Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.835A pdb=" N VAL A 820 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 843 through 854 Processing helix chain 'A' and resid 868 through 880 removed outlier: 4.283A pdb=" N ILE A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 878 " --> pdb=" O ILE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 900 through 909 Processing helix chain 'A' and resid 924 through 937 Processing helix chain 'A' and resid 954 through 956 No H-bonds generated for 'chain 'A' and resid 954 through 956' Processing helix chain 'A' and resid 957 through 968 Processing helix chain 'A' and resid 981 through 993 removed outlier: 3.599A pdb=" N VAL A 986 " --> pdb=" O GLY A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 351 through 357 removed outlier: 4.158A pdb=" N GLU B 356 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 388 through 401 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 438 through 452 Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 465 through 479 Processing helix chain 'B' and resid 485 through 491 Processing helix chain 'B' and resid 497 through 505 Processing helix chain 'B' and resid 522 through 534 removed outlier: 3.554A pdb=" N TYR B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 564 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 592 through 596 removed outlier: 3.757A pdb=" N LEU B 596 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 617 Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 639 through 647 Processing helix chain 'B' and resid 648 through 650 No H-bonds generated for 'chain 'B' and resid 648 through 650' Processing helix chain 'B' and resid 659 through 672 Processing helix chain 'B' and resid 727 through 729 No H-bonds generated for 'chain 'B' and resid 727 through 729' Processing helix chain 'B' and resid 730 through 738 removed outlier: 4.329A pdb=" N VAL B 736 " --> pdb=" O GLY B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 765 Processing helix chain 'B' and resid 783 through 785 No H-bonds generated for 'chain 'B' and resid 783 through 785' Processing helix chain 'B' and resid 786 through 795 Processing helix chain 'B' and resid 811 through 823 removed outlier: 3.873A pdb=" N VAL B 820 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 842 No H-bonds generated for 'chain 'B' and resid 840 through 842' Processing helix chain 'B' and resid 843 through 854 Processing helix chain 'B' and resid 868 through 880 removed outlier: 4.278A pdb=" N ILE B 874 " --> pdb=" O SER B 870 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 878 " --> pdb=" O ILE B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 899 No H-bonds generated for 'chain 'B' and resid 897 through 899' Processing helix chain 'B' and resid 900 through 909 Processing helix chain 'B' and resid 924 through 937 Processing helix chain 'B' and resid 954 through 956 No H-bonds generated for 'chain 'B' and resid 954 through 956' Processing helix chain 'B' and resid 957 through 968 Processing helix chain 'B' and resid 981 through 993 removed outlier: 3.619A pdb=" N VAL B 986 " --> pdb=" O GLY B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1025 Processing helix chain 'C' and resid 135 through 148 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 231 through 245 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 328 through 337 Processing helix chain 'C' and resid 351 through 357 removed outlier: 4.139A pdb=" N GLU C 356 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 388 through 401 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 411 through 428 Processing helix chain 'C' and resid 438 through 452 Processing helix chain 'C' and resid 462 through 464 No H-bonds generated for 'chain 'C' and resid 462 through 464' Processing helix chain 'C' and resid 465 through 479 Processing helix chain 'C' and resid 485 through 491 Processing helix chain 'C' and resid 497 through 505 Processing helix chain 'C' and resid 522 through 534 removed outlier: 3.555A pdb=" N TYR C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 564 Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 592 through 596 removed outlier: 3.760A pdb=" N LEU C 596 " --> pdb=" O GLU C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 617 Processing helix chain 'C' and resid 628 through 637 Processing helix chain 'C' and resid 639 through 647 Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 659 through 672 removed outlier: 3.614A pdb=" N ASN C 672 " --> pdb=" O PHE C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 729 No H-bonds generated for 'chain 'C' and resid 727 through 729' Processing helix chain 'C' and resid 730 through 738 removed outlier: 4.446A pdb=" N VAL C 736 " --> pdb=" O GLY C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 765 Processing helix chain 'C' and resid 783 through 785 No H-bonds generated for 'chain 'C' and resid 783 through 785' Processing helix chain 'C' and resid 786 through 795 Processing helix chain 'C' and resid 811 through 823 removed outlier: 3.992A pdb=" N VAL C 820 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 842 No H-bonds generated for 'chain 'C' and resid 840 through 842' Processing helix chain 'C' and resid 843 through 854 Processing helix chain 'C' and resid 868 through 880 removed outlier: 4.237A pdb=" N ILE C 874 " --> pdb=" O SER C 870 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 878 " --> pdb=" O ILE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 899 No H-bonds generated for 'chain 'C' and resid 897 through 899' Processing helix chain 'C' and resid 900 through 909 Processing helix chain 'C' and resid 924 through 937 Processing helix chain 'C' and resid 954 through 956 No H-bonds generated for 'chain 'C' and resid 954 through 956' Processing helix chain 'C' and resid 957 through 968 Processing helix chain 'C' and resid 981 through 993 removed outlier: 3.603A pdb=" N VAL C 986 " --> pdb=" O GLY C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1025 Processing helix chain 'D' and resid 135 through 148 Processing helix chain 'D' and resid 164 through 168 Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 328 through 337 Processing helix chain 'D' and resid 351 through 357 removed outlier: 4.163A pdb=" N GLU D 356 " --> pdb=" O VAL D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 363 Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 388 through 401 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 411 through 428 Processing helix chain 'D' and resid 438 through 452 Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 465 through 479 Processing helix chain 'D' and resid 485 through 491 Processing helix chain 'D' and resid 497 through 505 Processing helix chain 'D' and resid 522 through 534 removed outlier: 3.567A pdb=" N TYR D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 564 Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 592 through 596 removed outlier: 3.778A pdb=" N LEU D 596 " --> pdb=" O GLU D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 617 Processing helix chain 'D' and resid 628 through 637 Processing helix chain 'D' and resid 639 through 647 Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 659 through 672 removed outlier: 3.615A pdb=" N ASN D 672 " --> pdb=" O PHE D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 729 No H-bonds generated for 'chain 'D' and resid 727 through 729' Processing helix chain 'D' and resid 730 through 738 removed outlier: 4.172A pdb=" N VAL D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 765 Processing helix chain 'D' and resid 783 through 785 No H-bonds generated for 'chain 'D' and resid 783 through 785' Processing helix chain 'D' and resid 786 through 795 Processing helix chain 'D' and resid 811 through 823 removed outlier: 3.889A pdb=" N VAL D 820 " --> pdb=" O ARG D 816 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY D 821 " --> pdb=" O LEU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 842 No H-bonds generated for 'chain 'D' and resid 840 through 842' Processing helix chain 'D' and resid 843 through 854 Processing helix chain 'D' and resid 868 through 880 removed outlier: 4.286A pdb=" N ILE D 874 " --> pdb=" O SER D 870 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 878 " --> pdb=" O ILE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 899 No H-bonds generated for 'chain 'D' and resid 897 through 899' Processing helix chain 'D' and resid 900 through 909 Processing helix chain 'D' and resid 924 through 937 Processing helix chain 'D' and resid 954 through 956 No H-bonds generated for 'chain 'D' and resid 954 through 956' Processing helix chain 'D' and resid 957 through 968 Processing helix chain 'D' and resid 981 through 993 removed outlier: 3.615A pdb=" N VAL D 986 " --> pdb=" O GLY D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1011 through 1025 Processing helix chain 'E' and resid 135 through 148 Processing helix chain 'E' and resid 164 through 168 Processing helix chain 'E' and resid 231 through 245 Processing helix chain 'E' and resid 262 through 264 No H-bonds generated for 'chain 'E' and resid 262 through 264' Processing helix chain 'E' and resid 273 through 278 Processing helix chain 'E' and resid 289 through 293 Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 328 through 337 Processing helix chain 'E' and resid 351 through 357 removed outlier: 4.143A pdb=" N GLU E 356 " --> pdb=" O VAL E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 363 Processing helix chain 'E' and resid 374 through 386 Processing helix chain 'E' and resid 388 through 401 Processing helix chain 'E' and resid 402 through 409 Processing helix chain 'E' and resid 411 through 428 Processing helix chain 'E' and resid 438 through 452 Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 465 through 479 Processing helix chain 'E' and resid 485 through 491 Processing helix chain 'E' and resid 497 through 505 Processing helix chain 'E' and resid 522 through 534 removed outlier: 3.545A pdb=" N TYR E 534 " --> pdb=" O ALA E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 564 Processing helix chain 'E' and resid 573 through 584 Processing helix chain 'E' and resid 592 through 596 removed outlier: 3.730A pdb=" N LEU E 596 " --> pdb=" O GLU E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 617 Processing helix chain 'E' and resid 628 through 637 Processing helix chain 'E' and resid 639 through 647 Processing helix chain 'E' and resid 648 through 650 No H-bonds generated for 'chain 'E' and resid 648 through 650' Processing helix chain 'E' and resid 659 through 672 removed outlier: 3.613A pdb=" N ASN E 672 " --> pdb=" O PHE E 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 727 through 729 No H-bonds generated for 'chain 'E' and resid 727 through 729' Processing helix chain 'E' and resid 730 through 738 removed outlier: 4.406A pdb=" N VAL E 736 " --> pdb=" O GLY E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 754 through 765 Processing helix chain 'E' and resid 783 through 785 No H-bonds generated for 'chain 'E' and resid 783 through 785' Processing helix chain 'E' and resid 786 through 795 Processing helix chain 'E' and resid 811 through 823 removed outlier: 3.838A pdb=" N VAL E 820 " --> pdb=" O ARG E 816 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY E 821 " --> pdb=" O LEU E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 840 through 842 No H-bonds generated for 'chain 'E' and resid 840 through 842' Processing helix chain 'E' and resid 843 through 854 Processing helix chain 'E' and resid 868 through 880 removed outlier: 4.208A pdb=" N ILE E 874 " --> pdb=" O SER E 870 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS E 878 " --> pdb=" O ILE E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 899 No H-bonds generated for 'chain 'E' and resid 897 through 899' Processing helix chain 'E' and resid 900 through 909 Processing helix chain 'E' and resid 924 through 937 Processing helix chain 'E' and resid 954 through 956 No H-bonds generated for 'chain 'E' and resid 954 through 956' Processing helix chain 'E' and resid 957 through 968 Processing helix chain 'E' and resid 981 through 993 removed outlier: 3.613A pdb=" N VAL E 986 " --> pdb=" O GLY E 982 " (cutoff:3.500A) Processing helix chain 'E' and resid 1011 through 1025 Processing helix chain 'F' and resid 135 through 148 Processing helix chain 'F' and resid 164 through 168 Processing helix chain 'F' and resid 231 through 245 Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'F' and resid 289 through 293 Processing helix chain 'F' and resid 304 through 307 Processing helix chain 'F' and resid 328 through 337 Processing helix chain 'F' and resid 351 through 357 removed outlier: 4.145A pdb=" N GLU F 356 " --> pdb=" O VAL F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 363 Processing helix chain 'F' and resid 374 through 386 Processing helix chain 'F' and resid 388 through 401 Processing helix chain 'F' and resid 402 through 409 Processing helix chain 'F' and resid 411 through 428 Processing helix chain 'F' and resid 438 through 452 Processing helix chain 'F' and resid 462 through 464 No H-bonds generated for 'chain 'F' and resid 462 through 464' Processing helix chain 'F' and resid 465 through 479 Processing helix chain 'F' and resid 485 through 491 Processing helix chain 'F' and resid 497 through 505 Processing helix chain 'F' and resid 522 through 534 removed outlier: 3.586A pdb=" N TYR F 534 " --> pdb=" O ALA F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 564 Processing helix chain 'F' and resid 573 through 584 Processing helix chain 'F' and resid 592 through 596 removed outlier: 3.759A pdb=" N LEU F 596 " --> pdb=" O GLU F 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 597 through 617 Processing helix chain 'F' and resid 628 through 637 Processing helix chain 'F' and resid 639 through 647 Processing helix chain 'F' and resid 648 through 650 No H-bonds generated for 'chain 'F' and resid 648 through 650' Processing helix chain 'F' and resid 659 through 672 removed outlier: 3.614A pdb=" N ASN F 672 " --> pdb=" O PHE F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 727 through 729 No H-bonds generated for 'chain 'F' and resid 727 through 729' Processing helix chain 'F' and resid 730 through 738 removed outlier: 4.338A pdb=" N VAL F 736 " --> pdb=" O GLY F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 754 through 765 Processing helix chain 'F' and resid 783 through 785 No H-bonds generated for 'chain 'F' and resid 783 through 785' Processing helix chain 'F' and resid 786 through 795 Processing helix chain 'F' and resid 811 through 823 removed outlier: 3.833A pdb=" N VAL F 820 " --> pdb=" O ARG F 816 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY F 821 " --> pdb=" O LEU F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 840 through 842 No H-bonds generated for 'chain 'F' and resid 840 through 842' Processing helix chain 'F' and resid 843 through 854 Processing helix chain 'F' and resid 868 through 880 removed outlier: 4.236A pdb=" N ILE F 874 " --> pdb=" O SER F 870 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS F 878 " --> pdb=" O ILE F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 899 No H-bonds generated for 'chain 'F' and resid 897 through 899' Processing helix chain 'F' and resid 900 through 909 Processing helix chain 'F' and resid 924 through 937 Processing helix chain 'F' and resid 954 through 956 No H-bonds generated for 'chain 'F' and resid 954 through 956' Processing helix chain 'F' and resid 957 through 968 Processing helix chain 'F' and resid 981 through 993 removed outlier: 3.622A pdb=" N VAL F 986 " --> pdb=" O GLY F 982 " (cutoff:3.500A) Processing helix chain 'F' and resid 1011 through 1025 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.752A pdb=" N ARG A 172 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 509 Processing sheet with id=AA4, first strand: chain 'A' and resid 652 through 657 removed outlier: 6.528A pdb=" N ILE A 653 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLY A 682 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 655 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 679 " --> pdb=" O ASP A 747 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU A 860 " --> pdb=" O GLY A 890 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 175 removed outlier: 3.784A pdb=" N ARG B 172 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR B 221 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL B 368 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 223 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE B 370 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN B 225 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA7, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AA8, first strand: chain 'B' and resid 652 through 657 removed outlier: 6.512A pdb=" N ILE B 653 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N GLY B 682 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 655 " --> pdb=" O GLY B 682 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 679 " --> pdb=" O ASP B 747 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU B 860 " --> pdb=" O GLY B 890 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 172 through 175 removed outlier: 3.791A pdb=" N ARG C 172 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR C 255 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N LEU C 300 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE C 257 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASP C 302 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE C 259 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AB2, first strand: chain 'C' and resid 508 through 509 Processing sheet with id=AB3, first strand: chain 'C' and resid 652 through 657 removed outlier: 6.523A pdb=" N ILE C 653 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLY C 682 " --> pdb=" O ILE C 653 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 655 " --> pdb=" O GLY C 682 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 679 " --> pdb=" O ASP C 747 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU C 860 " --> pdb=" O GLY C 890 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 172 through 175 removed outlier: 3.906A pdb=" N ARG D 172 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE D 297 " --> pdb=" O SER D 345 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU D 347 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE D 299 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR D 349 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET D 301 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AB6, first strand: chain 'D' and resid 508 through 509 Processing sheet with id=AB7, first strand: chain 'D' and resid 652 through 657 removed outlier: 6.586A pdb=" N ILE D 653 " --> pdb=" O SER D 680 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLY D 682 " --> pdb=" O ILE D 653 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE D 655 " --> pdb=" O GLY D 682 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU D 679 " --> pdb=" O ASP D 747 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU D 860 " --> pdb=" O GLY D 890 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 172 through 175 removed outlier: 3.894A pdb=" N ARG E 172 " --> pdb=" O LEU E 371 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 269 through 270 Processing sheet with id=AC1, first strand: chain 'E' and resid 508 through 509 Processing sheet with id=AC2, first strand: chain 'E' and resid 652 through 657 removed outlier: 6.544A pdb=" N ILE E 653 " --> pdb=" O SER E 680 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLY E 682 " --> pdb=" O ILE E 653 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 655 " --> pdb=" O GLY E 682 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU E 679 " --> pdb=" O ASP E 747 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU E 860 " --> pdb=" O GLY E 890 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 172 through 175 removed outlier: 3.915A pdb=" N ARG F 172 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR F 255 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU F 300 " --> pdb=" O TYR F 255 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE F 257 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP F 302 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE F 259 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 269 through 270 Processing sheet with id=AC5, first strand: chain 'F' and resid 508 through 509 Processing sheet with id=AC6, first strand: chain 'F' and resid 652 through 657 removed outlier: 6.532A pdb=" N ILE F 653 " --> pdb=" O SER F 680 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY F 682 " --> pdb=" O ILE F 653 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE F 655 " --> pdb=" O GLY F 682 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU F 679 " --> pdb=" O ASP F 747 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU F 860 " --> pdb=" O GLY F 890 " (cutoff:3.500A) 1721 hydrogen bonds defined for protein. 4935 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: 9.83 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6451 1.30 - 1.43: 10263 1.43 - 1.57: 23015 1.57 - 1.70: 84 1.70 - 1.84: 453 Bond restraints: 40266 Sorted by residual: bond pdb=" C08 7YN B1101 " pdb=" C09 7YN B1101 " ideal model delta sigma weight residual 1.340 1.519 -0.179 2.00e-02 2.50e+03 8.00e+01 bond pdb=" C08 7YN D1101 " pdb=" C09 7YN D1101 " ideal model delta sigma weight residual 1.340 1.518 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" C08 7YN C1101 " pdb=" C09 7YN C1101 " ideal model delta sigma weight residual 1.340 1.518 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" C08 7YN A1101 " pdb=" C09 7YN A1101 " ideal model delta sigma weight residual 1.340 1.516 -0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" C08 7YN E1101 " pdb=" C09 7YN E1101 " ideal model delta sigma weight residual 1.340 1.515 -0.175 2.00e-02 2.50e+03 7.69e+01 ... (remaining 40261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.79: 54098 5.79 - 11.57: 256 11.57 - 17.36: 0 17.36 - 23.14: 6 23.14 - 28.93: 12 Bond angle restraints: 54372 Sorted by residual: angle pdb=" PB ATP F1102 " pdb=" O3B ATP F1102 " pdb=" PG ATP F1102 " ideal model delta sigma weight residual 139.87 110.94 28.93 1.00e+00 1.00e+00 8.37e+02 angle pdb=" PB ATP D1102 " pdb=" O3B ATP D1102 " pdb=" PG ATP D1102 " ideal model delta sigma weight residual 139.87 110.95 28.92 1.00e+00 1.00e+00 8.36e+02 angle pdb=" PB ATP A1102 " pdb=" O3B ATP A1102 " pdb=" PG ATP A1102 " ideal model delta sigma weight residual 139.87 111.00 28.87 1.00e+00 1.00e+00 8.34e+02 angle pdb=" PB ATP B1102 " pdb=" O3B ATP B1102 " pdb=" PG ATP B1102 " ideal model delta sigma weight residual 139.87 111.01 28.86 1.00e+00 1.00e+00 8.33e+02 angle pdb=" PB ATP C1102 " pdb=" O3B ATP C1102 " pdb=" PG ATP C1102 " ideal model delta sigma weight residual 139.87 111.02 28.85 1.00e+00 1.00e+00 8.32e+02 ... (remaining 54367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.92: 24127 33.92 - 67.84: 293 67.84 - 101.76: 85 101.76 - 135.68: 8 135.68 - 169.60: 3 Dihedral angle restraints: 24516 sinusoidal: 10188 harmonic: 14328 Sorted by residual: dihedral pdb=" C14 7YN F1101 " pdb=" N15 7YN F1101 " pdb=" S17 7YN F1101 " pdb=" O18 7YN F1101 " ideal model delta sinusoidal sigma weight residual 196.22 26.62 169.60 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C14 7YN D1101 " pdb=" N15 7YN D1101 " pdb=" S17 7YN D1101 " pdb=" O18 7YN D1101 " ideal model delta sinusoidal sigma weight residual 196.22 59.03 137.19 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C14 7YN A1101 " pdb=" N15 7YN A1101 " pdb=" S17 7YN A1101 " pdb=" O18 7YN A1101 " ideal model delta sinusoidal sigma weight residual 196.22 60.36 135.86 1 3.00e+01 1.11e-03 1.83e+01 ... (remaining 24513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3592 0.049 - 0.098: 1560 0.098 - 0.147: 655 0.147 - 0.195: 305 0.195 - 0.244: 44 Chirality restraints: 6156 Sorted by residual: chirality pdb=" CG LEU B 971 " pdb=" CB LEU B 971 " pdb=" CD1 LEU B 971 " pdb=" CD2 LEU B 971 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CG LEU A 971 " pdb=" CB LEU A 971 " pdb=" CD1 LEU A 971 " pdb=" CD2 LEU A 971 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU E 971 " pdb=" CB LEU E 971 " pdb=" CD1 LEU E 971 " pdb=" CD2 LEU E 971 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 6153 not shown) Planarity restraints: 6810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 7YN B1101 " -0.072 2.00e-02 2.50e+03 2.00e-01 1.30e+03 pdb=" C02 7YN B1101 " -0.082 2.00e-02 2.50e+03 pdb=" C03 7YN B1101 " -0.097 2.00e-02 2.50e+03 pdb=" C04 7YN B1101 " -0.071 2.00e-02 2.50e+03 pdb=" C05 7YN B1101 " -0.115 2.00e-02 2.50e+03 pdb=" C06 7YN B1101 " -0.097 2.00e-02 2.50e+03 pdb=" C07 7YN B1101 " -0.075 2.00e-02 2.50e+03 pdb=" C08 7YN B1101 " 0.462 2.00e-02 2.50e+03 pdb=" C09 7YN B1101 " -0.100 2.00e-02 2.50e+03 pdb=" C10 7YN B1101 " -0.076 2.00e-02 2.50e+03 pdb=" C11 7YN B1101 " 0.473 2.00e-02 2.50e+03 pdb=" C12 7YN B1101 " -0.108 2.00e-02 2.50e+03 pdb=" N13 7YN B1101 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN D1101 " -0.073 2.00e-02 2.50e+03 1.97e-01 1.26e+03 pdb=" C02 7YN D1101 " -0.060 2.00e-02 2.50e+03 pdb=" C03 7YN D1101 " -0.103 2.00e-02 2.50e+03 pdb=" C04 7YN D1101 " -0.102 2.00e-02 2.50e+03 pdb=" C05 7YN D1101 " -0.114 2.00e-02 2.50e+03 pdb=" C06 7YN D1101 " -0.076 2.00e-02 2.50e+03 pdb=" C07 7YN D1101 " -0.061 2.00e-02 2.50e+03 pdb=" C08 7YN D1101 " 0.452 2.00e-02 2.50e+03 pdb=" C09 7YN D1101 " -0.100 2.00e-02 2.50e+03 pdb=" C10 7YN D1101 " -0.069 2.00e-02 2.50e+03 pdb=" C11 7YN D1101 " 0.468 2.00e-02 2.50e+03 pdb=" C12 7YN D1101 " -0.112 2.00e-02 2.50e+03 pdb=" N13 7YN D1101 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN C1101 " 0.062 2.00e-02 2.50e+03 1.95e-01 1.23e+03 pdb=" C02 7YN C1101 " 0.074 2.00e-02 2.50e+03 pdb=" C03 7YN C1101 " 0.109 2.00e-02 2.50e+03 pdb=" C04 7YN C1101 " 0.089 2.00e-02 2.50e+03 pdb=" C05 7YN C1101 " 0.106 2.00e-02 2.50e+03 pdb=" C06 7YN C1101 " 0.085 2.00e-02 2.50e+03 pdb=" C07 7YN C1101 " 0.061 2.00e-02 2.50e+03 pdb=" C08 7YN C1101 " -0.454 2.00e-02 2.50e+03 pdb=" C09 7YN C1101 " 0.107 2.00e-02 2.50e+03 pdb=" C10 7YN C1101 " 0.069 2.00e-02 2.50e+03 pdb=" C11 7YN C1101 " -0.455 2.00e-02 2.50e+03 pdb=" C12 7YN C1101 " 0.100 2.00e-02 2.50e+03 pdb=" N13 7YN C1101 " 0.046 2.00e-02 2.50e+03 ... (remaining 6807 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 14634 2.89 - 3.39: 38451 3.39 - 3.89: 67041 3.89 - 4.40: 79054 4.40 - 4.90: 127167 Nonbonded interactions: 326347 Sorted by model distance: nonbonded pdb=" OG1 THR B 221 " pdb=" NZ LYS B 338 " model vdw 2.383 3.120 nonbonded pdb=" OG1 THR A 221 " pdb=" NZ LYS A 338 " model vdw 2.385 3.120 nonbonded pdb=" OG1 THR C 221 " pdb=" NZ LYS C 338 " model vdw 2.388 3.120 nonbonded pdb=" OG1 THR D 221 " pdb=" NZ LYS D 338 " model vdw 2.395 3.120 nonbonded pdb=" OG1 THR D 233 " pdb=" O2G ATP D1102 " model vdw 2.404 3.040 ... (remaining 326342 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 38.270 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.012 0.179 40266 Z= 0.637 Angle : 1.277 28.927 54372 Z= 0.913 Chirality : 0.069 0.244 6156 Planarity : 0.007 0.200 6810 Dihedral : 12.464 169.596 15204 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.63 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.66 (0.12), residues: 4848 helix: -0.31 (0.10), residues: 2298 sheet: 0.07 (0.22), residues: 588 loop : -0.54 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 605 TYR 0.024 0.003 TYR D 249 PHE 0.019 0.003 PHE C 406 TRP 0.021 0.004 TRP E 611 HIS 0.005 0.001 HIS E 916 Details of bonding type rmsd covalent geometry : bond 0.01170 (40266) covalent geometry : angle 1.27676 (54372) hydrogen bonds : bond 0.18454 ( 1721) hydrogen bonds : angle 6.92107 ( 4935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1604 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1604 time to evaluate : 1.524 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: 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 142 LYS cc_start: 0.9369 (mttt) cc_final: 0.9054 (pttm) REVERT: A 220 HIS cc_start: 0.8264 (m90) cc_final: 0.7676 (p-80) REVERT: A 238 LYS cc_start: 0.8744 (tptp) cc_final: 0.8470 (tttt) REVERT: A 240 MET cc_start: 0.8608 (mtm) cc_final: 0.7870 (mmt) REVERT: A 253 PHE cc_start: 0.7651 (m-80) cc_final: 0.4650 (m-10) REVERT: A 304 PHE cc_start: 0.8913 (t80) cc_final: 0.8507 (t80) REVERT: A 368 VAL cc_start: 0.9514 (t) cc_final: 0.9172 (t) REVERT: A 381 TYR cc_start: 0.8340 (t80) cc_final: 0.7870 (t80) REVERT: A 403 GLU cc_start: 0.8735 (tt0) cc_final: 0.7991 (tp30) REVERT: A 408 MET cc_start: 0.8679 (mtm) cc_final: 0.8085 (mtm) REVERT: A 415 CYS cc_start: 0.8306 (p) cc_final: 0.7772 (p) REVERT: A 419 CYS cc_start: 0.7713 (m) cc_final: 0.7316 (p) REVERT: A 517 PHE cc_start: 0.7322 (p90) cc_final: 0.6721 (p90) REVERT: A 521 ILE cc_start: 0.8705 (tt) cc_final: 0.8287 (tt) REVERT: A 527 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8608 (tt0) REVERT: A 535 LEU cc_start: 0.9495 (mt) cc_final: 0.9210 (mm) REVERT: A 669 CYS cc_start: 0.8666 (m) cc_final: 0.7779 (m) REVERT: A 737 LEU cc_start: 0.9256 (mt) cc_final: 0.8956 (tp) REVERT: A 738 SER cc_start: 0.9313 (p) cc_final: 0.8883 (m) REVERT: A 743 LEU cc_start: 0.8974 (tp) cc_final: 0.7778 (tt) REVERT: A 751 ASN cc_start: 0.8725 (m-40) cc_final: 0.8248 (m110) REVERT: A 755 ASP cc_start: 0.8396 (m-30) cc_final: 0.7890 (t0) REVERT: A 762 CYS cc_start: 0.9104 (m) cc_final: 0.8551 (p) REVERT: A 790 ILE cc_start: 0.8845 (mt) cc_final: 0.8645 (tp) REVERT: A 802 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8349 (mt-10) REVERT: A 831 LYS cc_start: 0.8550 (mttt) cc_final: 0.8186 (mmtp) REVERT: A 989 PHE cc_start: 0.9211 (m-10) cc_final: 0.8461 (m-80) REVERT: A 1006 SER cc_start: 0.8466 (t) cc_final: 0.8108 (p) REVERT: A 1008 MET cc_start: 0.8258 (mmm) cc_final: 0.8013 (mmp) REVERT: B 220 HIS cc_start: 0.8278 (m90) cc_final: 0.7690 (p-80) REVERT: B 240 MET cc_start: 0.8143 (mtm) cc_final: 0.7699 (mmt) REVERT: B 288 HIS cc_start: 0.8941 (p-80) cc_final: 0.8721 (m90) REVERT: B 304 PHE cc_start: 0.8881 (t80) cc_final: 0.8536 (t80) REVERT: B 381 TYR cc_start: 0.8488 (t80) cc_final: 0.8048 (t80) REVERT: B 403 GLU cc_start: 0.8665 (tt0) cc_final: 0.7827 (tp30) REVERT: B 415 CYS cc_start: 0.8374 (p) cc_final: 0.8159 (p) REVERT: B 419 CYS cc_start: 0.7600 (m) cc_final: 0.7379 (p) REVERT: B 517 PHE cc_start: 0.7290 (p90) cc_final: 0.6683 (p90) REVERT: B 521 ILE cc_start: 0.8773 (tt) cc_final: 0.8299 (tt) REVERT: B 526 GLN cc_start: 0.9632 (tt0) cc_final: 0.9204 (tt0) REVERT: B 535 LEU cc_start: 0.9445 (mt) cc_final: 0.9212 (mm) REVERT: B 671 GLU cc_start: 0.8798 (tt0) cc_final: 0.8559 (tm-30) REVERT: B 743 LEU cc_start: 0.8976 (tp) cc_final: 0.7842 (tp) REVERT: B 751 ASN cc_start: 0.8823 (m-40) cc_final: 0.8161 (m110) REVERT: B 755 ASP cc_start: 0.8320 (m-30) cc_final: 0.7970 (t0) REVERT: B 761 LEU cc_start: 0.9553 (tp) cc_final: 0.9352 (tp) REVERT: B 790 ILE cc_start: 0.8923 (mt) cc_final: 0.8679 (tp) REVERT: B 802 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 831 LYS cc_start: 0.8572 (mttt) cc_final: 0.8023 (mmtp) REVERT: B 953 LEU cc_start: 0.9123 (mt) cc_final: 0.8777 (mp) REVERT: B 989 PHE cc_start: 0.9154 (m-10) cc_final: 0.8370 (m-80) REVERT: B 1008 MET cc_start: 0.8331 (mmm) cc_final: 0.8041 (mmp) REVERT: C 220 HIS cc_start: 0.8537 (m-70) cc_final: 0.7439 (p-80) REVERT: C 240 MET cc_start: 0.8406 (mtm) cc_final: 0.7999 (mmt) REVERT: C 249 TYR cc_start: 0.8077 (m-80) cc_final: 0.7658 (m-80) REVERT: C 253 PHE cc_start: 0.7802 (m-80) cc_final: 0.5459 (m-80) REVERT: C 301 MET cc_start: 0.8641 (ttt) cc_final: 0.8399 (ptm) REVERT: C 403 GLU cc_start: 0.8759 (tt0) cc_final: 0.7872 (tp30) REVERT: C 419 CYS cc_start: 0.8256 (m) cc_final: 0.8015 (p) REVERT: C 517 PHE cc_start: 0.7460 (p90) cc_final: 0.7062 (p90) REVERT: C 526 GLN cc_start: 0.9537 (tt0) cc_final: 0.9001 (tt0) REVERT: C 535 LEU cc_start: 0.9479 (mt) cc_final: 0.9169 (mm) REVERT: C 669 CYS cc_start: 0.8627 (m) cc_final: 0.7394 (m) REVERT: C 737 LEU cc_start: 0.9313 (mt) cc_final: 0.8856 (tp) REVERT: C 738 SER cc_start: 0.9292 (p) cc_final: 0.8851 (m) REVERT: C 743 LEU cc_start: 0.8936 (tp) cc_final: 0.7536 (tp) REVERT: C 748 LEU cc_start: 0.8950 (mt) cc_final: 0.8054 (tp) REVERT: C 751 ASN cc_start: 0.8724 (m-40) cc_final: 0.7970 (m-40) REVERT: C 755 ASP cc_start: 0.8397 (m-30) cc_final: 0.7868 (t0) REVERT: C 802 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7939 (mt-10) REVERT: C 831 LYS cc_start: 0.8541 (mttt) cc_final: 0.8196 (mmtp) REVERT: C 911 ASN cc_start: 0.8467 (t0) cc_final: 0.8243 (t0) REVERT: C 940 ASP cc_start: 0.8553 (m-30) cc_final: 0.7972 (t70) REVERT: C 953 LEU cc_start: 0.8970 (mt) cc_final: 0.8651 (mp) REVERT: C 989 PHE cc_start: 0.9144 (m-10) cc_final: 0.8834 (m-80) REVERT: C 1006 SER cc_start: 0.8607 (t) cc_final: 0.7493 (p) REVERT: C 1008 MET cc_start: 0.8184 (mmm) cc_final: 0.7607 (mmm) REVERT: D 220 HIS cc_start: 0.8380 (m90) cc_final: 0.7704 (p-80) REVERT: D 304 PHE cc_start: 0.8719 (t80) cc_final: 0.8362 (t80) REVERT: D 381 TYR cc_start: 0.8681 (t80) cc_final: 0.8126 (t80) REVERT: D 408 MET cc_start: 0.8402 (mtm) cc_final: 0.7881 (mtm) REVERT: D 415 CYS cc_start: 0.9181 (t) cc_final: 0.8688 (t) REVERT: D 492 HIS cc_start: 0.7837 (m90) cc_final: 0.7610 (m170) REVERT: D 517 PHE cc_start: 0.7390 (p90) cc_final: 0.6781 (p90) REVERT: D 526 GLN cc_start: 0.9477 (tt0) cc_final: 0.8939 (tt0) REVERT: D 535 LEU cc_start: 0.9440 (mt) cc_final: 0.9149 (mm) REVERT: D 669 CYS cc_start: 0.8646 (m) cc_final: 0.7513 (m) REVERT: D 671 GLU cc_start: 0.8785 (tt0) cc_final: 0.8567 (tm-30) REVERT: D 737 LEU cc_start: 0.9262 (mt) cc_final: 0.8901 (tp) REVERT: D 738 SER cc_start: 0.9371 (p) cc_final: 0.8906 (m) REVERT: D 743 LEU cc_start: 0.8978 (tp) cc_final: 0.7765 (tt) REVERT: D 751 ASN cc_start: 0.8781 (m-40) cc_final: 0.8364 (m110) REVERT: D 755 ASP cc_start: 0.8371 (m-30) cc_final: 0.7888 (t0) REVERT: D 802 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7989 (mt-10) REVERT: D 831 LYS cc_start: 0.8543 (mttt) cc_final: 0.8199 (mmtp) REVERT: D 911 ASN cc_start: 0.8472 (t0) cc_final: 0.8246 (t0) REVERT: D 989 PHE cc_start: 0.9226 (m-10) cc_final: 0.8514 (m-80) REVERT: D 1006 SER cc_start: 0.8688 (t) cc_final: 0.7512 (p) REVERT: D 1008 MET cc_start: 0.8191 (mmm) cc_final: 0.7677 (mmm) REVERT: E 220 HIS cc_start: 0.8406 (m90) cc_final: 0.8191 (m-70) REVERT: E 235 LEU cc_start: 0.9394 (tp) cc_final: 0.9133 (tp) REVERT: E 240 MET cc_start: 0.8436 (mtm) cc_final: 0.7704 (mmt) REVERT: E 253 PHE cc_start: 0.6471 (m-80) cc_final: 0.6177 (m-80) REVERT: E 291 VAL cc_start: 0.8448 (t) cc_final: 0.8098 (t) REVERT: E 381 TYR cc_start: 0.8458 (t80) cc_final: 0.7957 (t80) REVERT: E 407 THR cc_start: 0.9162 (m) cc_final: 0.8748 (p) REVERT: E 408 MET cc_start: 0.8421 (mtm) cc_final: 0.7943 (mtm) REVERT: E 415 CYS cc_start: 0.9066 (t) cc_final: 0.8594 (t) REVERT: E 505 MET cc_start: 0.7829 (mtm) cc_final: 0.7303 (mtm) REVERT: E 526 GLN cc_start: 0.9599 (tt0) cc_final: 0.9080 (tt0) REVERT: E 527 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8625 (tt0) REVERT: E 535 LEU cc_start: 0.9463 (mt) cc_final: 0.9140 (mm) REVERT: E 669 CYS cc_start: 0.8762 (m) cc_final: 0.7733 (m) REVERT: E 730 CYS cc_start: 0.8808 (p) cc_final: 0.8579 (t) REVERT: E 737 LEU cc_start: 0.9236 (mt) cc_final: 0.8979 (tp) REVERT: E 738 SER cc_start: 0.9278 (p) cc_final: 0.8681 (m) REVERT: E 743 LEU cc_start: 0.8891 (tp) cc_final: 0.8082 (tp) REVERT: E 751 ASN cc_start: 0.8845 (m-40) cc_final: 0.8298 (m110) REVERT: E 755 ASP cc_start: 0.8438 (m-30) cc_final: 0.7951 (t0) REVERT: E 802 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8317 (mt-10) REVERT: E 831 LYS cc_start: 0.8538 (mttt) cc_final: 0.8151 (mmtm) REVERT: E 940 ASP cc_start: 0.8610 (m-30) cc_final: 0.8029 (t70) REVERT: E 953 LEU cc_start: 0.9074 (mt) cc_final: 0.8853 (mt) REVERT: E 989 PHE cc_start: 0.9215 (m-10) cc_final: 0.8507 (m-80) REVERT: E 1008 MET cc_start: 0.8210 (mmm) cc_final: 0.7972 (mmp) REVERT: F 220 HIS cc_start: 0.8308 (m90) cc_final: 0.7823 (p-80) REVERT: F 235 LEU cc_start: 0.9428 (tp) cc_final: 0.9181 (tp) REVERT: F 240 MET cc_start: 0.8232 (mtm) cc_final: 0.7745 (mmt) REVERT: F 253 PHE cc_start: 0.7973 (m-80) cc_final: 0.5782 (m-80) REVERT: F 300 LEU cc_start: 0.7692 (tt) cc_final: 0.7125 (tt) REVERT: F 304 PHE cc_start: 0.8839 (t80) cc_final: 0.8610 (t80) REVERT: F 381 TYR cc_start: 0.8672 (t80) cc_final: 0.7982 (t80) REVERT: F 407 THR cc_start: 0.9082 (m) cc_final: 0.8839 (p) REVERT: F 415 CYS cc_start: 0.9196 (t) cc_final: 0.8587 (t) REVERT: F 517 PHE cc_start: 0.7247 (p90) cc_final: 0.6965 (p90) REVERT: F 535 LEU cc_start: 0.9440 (mt) cc_final: 0.9126 (mm) REVERT: F 671 GLU cc_start: 0.8821 (tt0) cc_final: 0.8538 (tm-30) REVERT: F 737 LEU cc_start: 0.9313 (mt) cc_final: 0.8947 (tp) REVERT: F 738 SER cc_start: 0.9257 (p) cc_final: 0.8859 (m) REVERT: F 743 LEU cc_start: 0.8909 (tp) cc_final: 0.7785 (tp) REVERT: F 751 ASN cc_start: 0.8786 (m-40) cc_final: 0.8174 (m110) REVERT: F 755 ASP cc_start: 0.8084 (m-30) cc_final: 0.7812 (t0) REVERT: F 802 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8266 (mt-10) REVERT: F 831 LYS cc_start: 0.8489 (mttt) cc_final: 0.8064 (mmtp) REVERT: F 940 ASP cc_start: 0.8632 (m-30) cc_final: 0.8048 (t70) REVERT: F 989 PHE cc_start: 0.9154 (m-10) cc_final: 0.8341 (m-80) REVERT: F 1006 SER cc_start: 0.8531 (t) cc_final: 0.8132 (m) outliers start: 0 outliers final: 0 residues processed: 1604 average time/residue: 0.2498 time to fit residues: 644.7903 Evaluate side-chains 933 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 933 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 400 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN A 465 HIS ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 GLN B 215 HIS B 400 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN B 465 HIS B1001 GLN C 260 HIS C 465 HIS C 480 GLN C 506 ASN C1001 GLN D 215 HIS ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 HIS D 522 HIS D1001 GLN E 364 HIS E 465 HIS E 480 GLN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1001 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 HIS F 480 GLN F1001 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.134997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.100837 restraints weight = 94278.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.103978 restraints weight = 58572.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.106335 restraints weight = 41342.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.107909 restraints weight = 31916.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.109052 restraints weight = 26600.972| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40266 Z= 0.161 Angle : 0.692 9.330 54372 Z= 0.353 Chirality : 0.041 0.270 6156 Planarity : 0.005 0.078 6810 Dihedral : 11.276 173.360 5544 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.02 % Favored : 95.81 % Rotamer: Outliers : 0.13 % Allowed : 2.47 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.12 (0.12), residues: 4848 helix: 0.65 (0.11), residues: 2262 sheet: 0.44 (0.23), residues: 558 loop : -0.56 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 270 TYR 0.021 0.002 TYR D 258 PHE 0.026 0.002 PHE E 209 TRP 0.018 0.002 TRP A 959 HIS 0.008 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00353 (40266) covalent geometry : angle 0.69230 (54372) hydrogen bonds : bond 0.05230 ( 1721) hydrogen bonds : angle 5.00705 ( 4935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1102 time to evaluate : 1.452 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: 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: symmetry clash REVERT: A 142 LYS cc_start: 0.9294 (mttt) cc_final: 0.8927 (pttm) REVERT: A 208 LEU cc_start: 0.9442 (mt) cc_final: 0.9056 (mt) REVERT: A 220 HIS cc_start: 0.7882 (m90) cc_final: 0.7560 (p-80) REVERT: A 238 LYS cc_start: 0.8477 (tptp) cc_final: 0.8247 (tttt) REVERT: A 240 MET cc_start: 0.8688 (mtm) cc_final: 0.8149 (mmt) REVERT: A 251 ASP cc_start: 0.8380 (p0) cc_final: 0.8164 (m-30) REVERT: A 253 PHE cc_start: 0.6617 (m-80) cc_final: 0.5681 (m-10) REVERT: A 304 PHE cc_start: 0.8485 (t80) cc_final: 0.8138 (t80) REVERT: A 336 ILE cc_start: 0.9641 (mt) cc_final: 0.9394 (tt) REVERT: A 358 LEU cc_start: 0.8238 (tp) cc_final: 0.7934 (tp) REVERT: A 403 GLU cc_start: 0.8623 (tt0) cc_final: 0.8367 (pm20) REVERT: A 505 MET cc_start: 0.7785 (ptp) cc_final: 0.7423 (ptp) REVERT: A 527 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8382 (tt0) REVERT: A 576 VAL cc_start: 0.9386 (t) cc_final: 0.9050 (t) REVERT: A 664 MET cc_start: 0.8333 (tpp) cc_final: 0.8073 (tpp) REVERT: A 738 SER cc_start: 0.9266 (p) cc_final: 0.8703 (m) REVERT: A 743 LEU cc_start: 0.8887 (tp) cc_final: 0.8620 (tt) REVERT: A 751 ASN cc_start: 0.8496 (m-40) cc_final: 0.8228 (m110) REVERT: A 755 ASP cc_start: 0.8162 (m-30) cc_final: 0.7857 (m-30) REVERT: A 758 MET cc_start: 0.8786 (tpp) cc_final: 0.8520 (tpp) REVERT: A 764 THR cc_start: 0.9077 (p) cc_final: 0.8875 (p) REVERT: A 790 ILE cc_start: 0.8778 (mt) cc_final: 0.8550 (tp) REVERT: A 802 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 831 LYS cc_start: 0.7994 (mttt) cc_final: 0.7466 (mmtp) REVERT: A 917 LEU cc_start: 0.7402 (mt) cc_final: 0.7199 (mp) REVERT: A 919 LEU cc_start: 0.8415 (mt) cc_final: 0.8155 (mp) REVERT: A 922 ASN cc_start: 0.7814 (m-40) cc_final: 0.7583 (m-40) REVERT: A 953 LEU cc_start: 0.8834 (mt) cc_final: 0.8545 (mt) REVERT: A 986 VAL cc_start: 0.9574 (m) cc_final: 0.9352 (p) REVERT: A 1005 LEU cc_start: 0.8792 (mt) cc_final: 0.8323 (tt) REVERT: A 1006 SER cc_start: 0.8649 (t) cc_final: 0.8323 (p) REVERT: A 1008 MET cc_start: 0.8323 (mmm) cc_final: 0.8014 (mmp) REVERT: B 142 LYS cc_start: 0.9238 (mtmm) cc_final: 0.8973 (pttm) REVERT: B 220 HIS cc_start: 0.7891 (m90) cc_final: 0.7609 (p-80) REVERT: B 239 MET cc_start: 0.9156 (mtm) cc_final: 0.8011 (mmp) REVERT: B 240 MET cc_start: 0.8197 (mtm) cc_final: 0.7961 (mmt) REVERT: B 242 ASP cc_start: 0.9211 (m-30) cc_final: 0.8830 (m-30) REVERT: B 304 PHE cc_start: 0.8514 (t80) cc_final: 0.8255 (t80) REVERT: B 326 GLU cc_start: 0.7990 (tp30) cc_final: 0.7476 (tt0) REVERT: B 336 ILE cc_start: 0.9647 (mt) cc_final: 0.9434 (tt) REVERT: B 358 LEU cc_start: 0.8096 (tp) cc_final: 0.7882 (tp) REVERT: B 403 GLU cc_start: 0.8470 (tt0) cc_final: 0.7819 (tp30) REVERT: B 505 MET cc_start: 0.7896 (mtm) cc_final: 0.7156 (mtm) REVERT: B 526 GLN cc_start: 0.9355 (tt0) cc_final: 0.8879 (tt0) REVERT: B 527 GLU cc_start: 0.9012 (tt0) cc_final: 0.8373 (tt0) REVERT: B 575 PHE cc_start: 0.8620 (m-80) cc_final: 0.8388 (m-80) REVERT: B 654 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7800 (tm-30) REVERT: B 738 SER cc_start: 0.9198 (p) cc_final: 0.8863 (m) REVERT: B 751 ASN cc_start: 0.8501 (m-40) cc_final: 0.8038 (m110) REVERT: B 755 ASP cc_start: 0.7890 (m-30) cc_final: 0.7592 (m-30) REVERT: B 802 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7592 (mt-10) REVERT: B 831 LYS cc_start: 0.8207 (mttt) cc_final: 0.7611 (mmtp) REVERT: B 1008 MET cc_start: 0.8548 (mmm) cc_final: 0.8187 (mmp) REVERT: C 220 HIS cc_start: 0.8087 (m-70) cc_final: 0.7374 (p-80) REVERT: C 235 LEU cc_start: 0.9406 (tp) cc_final: 0.9174 (tt) REVERT: C 239 MET cc_start: 0.9236 (mtp) cc_final: 0.9021 (mtp) REVERT: C 240 MET cc_start: 0.8519 (mtm) cc_final: 0.8014 (mmt) REVERT: C 242 ASP cc_start: 0.9157 (m-30) cc_final: 0.8862 (m-30) REVERT: C 253 PHE cc_start: 0.6922 (m-80) cc_final: 0.6183 (m-10) REVERT: C 298 LEU cc_start: 0.8233 (tp) cc_final: 0.7907 (tp) REVERT: C 304 PHE cc_start: 0.8150 (t80) cc_final: 0.7761 (t80) REVERT: C 403 GLU cc_start: 0.8554 (tt0) cc_final: 0.7696 (tp30) REVERT: C 526 GLN cc_start: 0.9333 (tt0) cc_final: 0.8570 (tt0) REVERT: C 527 GLU cc_start: 0.8932 (tt0) cc_final: 0.8689 (tt0) REVERT: C 639 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8140 (tm-30) REVERT: C 662 ASP cc_start: 0.8584 (m-30) cc_final: 0.8363 (m-30) REVERT: C 737 LEU cc_start: 0.9657 (mt) cc_final: 0.9206 (tp) REVERT: C 738 SER cc_start: 0.9188 (p) cc_final: 0.8772 (m) REVERT: C 743 LEU cc_start: 0.8812 (tp) cc_final: 0.7905 (tp) REVERT: C 755 ASP cc_start: 0.8112 (m-30) cc_final: 0.7649 (m-30) REVERT: C 802 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7073 (mt-10) REVERT: C 831 LYS cc_start: 0.8141 (mttt) cc_final: 0.7483 (mmtp) REVERT: C 919 LEU cc_start: 0.8250 (mt) cc_final: 0.8044 (mp) REVERT: C 940 ASP cc_start: 0.8610 (m-30) cc_final: 0.7999 (t70) REVERT: C 1006 SER cc_start: 0.8810 (t) cc_final: 0.7679 (p) REVERT: C 1008 MET cc_start: 0.8186 (mmm) cc_final: 0.7749 (mmm) REVERT: C 1021 LEU cc_start: 0.8928 (mp) cc_final: 0.8619 (mt) REVERT: D 142 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8952 (pttm) REVERT: D 220 HIS cc_start: 0.7779 (m90) cc_final: 0.7538 (p-80) REVERT: D 232 LYS cc_start: 0.8402 (ptpp) cc_final: 0.8138 (ptpp) REVERT: D 239 MET cc_start: 0.9136 (mtm) cc_final: 0.8742 (mtp) REVERT: D 242 ASP cc_start: 0.9194 (m-30) cc_final: 0.8823 (m-30) REVERT: D 304 PHE cc_start: 0.8555 (t80) cc_final: 0.8327 (t80) REVERT: D 379 LYS cc_start: 0.9105 (tttt) cc_final: 0.8826 (tttt) REVERT: D 381 TYR cc_start: 0.8703 (t80) cc_final: 0.8173 (t80) REVERT: D 403 GLU cc_start: 0.8626 (tt0) cc_final: 0.8227 (pm20) REVERT: D 415 CYS cc_start: 0.9164 (t) cc_final: 0.8634 (t) REVERT: D 521 ILE cc_start: 0.8932 (tt) cc_final: 0.8551 (pt) REVERT: D 527 GLU cc_start: 0.8967 (tt0) cc_final: 0.8624 (tt0) REVERT: D 639 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8167 (tm-30) REVERT: D 654 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7927 (tm-30) REVERT: D 665 VAL cc_start: 0.9332 (m) cc_final: 0.8620 (p) REVERT: D 738 SER cc_start: 0.9259 (p) cc_final: 0.8811 (m) REVERT: D 743 LEU cc_start: 0.8892 (tp) cc_final: 0.7900 (tt) REVERT: D 758 MET cc_start: 0.7966 (ttm) cc_final: 0.7679 (ttm) REVERT: D 762 CYS cc_start: 0.8683 (m) cc_final: 0.8318 (p) REVERT: D 789 ASP cc_start: 0.7514 (m-30) cc_final: 0.7187 (m-30) REVERT: D 790 ILE cc_start: 0.8660 (mm) cc_final: 0.7878 (tp) REVERT: D 802 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7253 (mt-10) REVERT: D 831 LYS cc_start: 0.8103 (mttt) cc_final: 0.7473 (mmtp) REVERT: D 917 LEU cc_start: 0.7192 (mt) cc_final: 0.6942 (mp) REVERT: D 989 PHE cc_start: 0.8957 (m-10) cc_final: 0.8713 (m-80) REVERT: D 1006 SER cc_start: 0.8816 (t) cc_final: 0.7711 (p) REVERT: D 1008 MET cc_start: 0.8248 (mmm) cc_final: 0.7876 (mmm) REVERT: E 142 LYS cc_start: 0.8879 (pttm) cc_final: 0.8588 (pttp) REVERT: E 232 LYS cc_start: 0.7603 (ptmt) cc_final: 0.7196 (ptpp) REVERT: E 239 MET cc_start: 0.9092 (mtm) cc_final: 0.8000 (mmp) REVERT: E 240 MET cc_start: 0.8494 (mtm) cc_final: 0.7951 (mmt) REVERT: E 242 ASP cc_start: 0.9175 (m-30) cc_final: 0.8765 (m-30) REVERT: E 248 LEU cc_start: 0.8758 (tp) cc_final: 0.8450 (tp) REVERT: E 253 PHE cc_start: 0.6680 (m-80) cc_final: 0.5029 (m-10) REVERT: E 298 LEU cc_start: 0.8471 (tp) cc_final: 0.8255 (tp) REVERT: E 304 PHE cc_start: 0.8358 (t80) cc_final: 0.7674 (t80) REVERT: E 326 GLU cc_start: 0.8021 (tp30) cc_final: 0.7718 (tp30) REVERT: E 381 TYR cc_start: 0.8512 (t80) cc_final: 0.7833 (t80) REVERT: E 407 THR cc_start: 0.8700 (m) cc_final: 0.8415 (p) REVERT: E 415 CYS cc_start: 0.9210 (t) cc_final: 0.8494 (t) REVERT: E 417 ILE cc_start: 0.9474 (mt) cc_final: 0.9243 (tp) REVERT: E 527 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8352 (tt0) REVERT: E 576 VAL cc_start: 0.9344 (t) cc_final: 0.9044 (t) REVERT: E 669 CYS cc_start: 0.7925 (m) cc_final: 0.6882 (m) REVERT: E 730 CYS cc_start: 0.8882 (p) cc_final: 0.8583 (p) REVERT: E 738 SER cc_start: 0.9188 (p) cc_final: 0.8692 (m) REVERT: E 743 LEU cc_start: 0.8832 (tp) cc_final: 0.7887 (tt) REVERT: E 751 ASN cc_start: 0.8465 (m-40) cc_final: 0.8081 (m110) REVERT: E 802 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7495 (mt-10) REVERT: E 831 LYS cc_start: 0.8086 (mttt) cc_final: 0.7552 (mmtp) REVERT: E 911 ASN cc_start: 0.8199 (t0) cc_final: 0.7948 (t0) REVERT: E 919 LEU cc_start: 0.8239 (mt) cc_final: 0.7929 (mp) REVERT: E 937 LEU cc_start: 0.8231 (mt) cc_final: 0.8026 (pp) REVERT: E 940 ASP cc_start: 0.8620 (m-30) cc_final: 0.8068 (t70) REVERT: E 989 PHE cc_start: 0.8974 (m-10) cc_final: 0.8469 (m-80) REVERT: E 1008 MET cc_start: 0.8333 (mmm) cc_final: 0.8080 (mmp) REVERT: F 142 LYS cc_start: 0.9249 (mtmm) cc_final: 0.8980 (pttm) REVERT: F 208 LEU cc_start: 0.9160 (mp) cc_final: 0.7558 (tp) REVERT: F 232 LYS cc_start: 0.7456 (ptmt) cc_final: 0.7212 (pttm) REVERT: F 235 LEU cc_start: 0.9403 (tp) cc_final: 0.9173 (tp) REVERT: F 239 MET cc_start: 0.9060 (mtm) cc_final: 0.8796 (mtp) REVERT: F 240 MET cc_start: 0.8225 (mtm) cc_final: 0.7943 (mmt) REVERT: F 242 ASP cc_start: 0.9159 (m-30) cc_final: 0.8884 (m-30) REVERT: F 253 PHE cc_start: 0.6607 (m-80) cc_final: 0.6368 (m-10) REVERT: F 255 TYR cc_start: 0.7269 (m-80) cc_final: 0.6815 (m-80) REVERT: F 304 PHE cc_start: 0.8376 (t80) cc_final: 0.7983 (t80) REVERT: F 326 GLU cc_start: 0.8024 (tp30) cc_final: 0.7697 (tt0) REVERT: F 336 ILE cc_start: 0.9686 (mt) cc_final: 0.9444 (tt) REVERT: F 358 LEU cc_start: 0.8147 (tp) cc_final: 0.7920 (tp) REVERT: F 381 TYR cc_start: 0.8641 (t80) cc_final: 0.7748 (t80) REVERT: F 407 THR cc_start: 0.8732 (m) cc_final: 0.8481 (p) REVERT: F 415 CYS cc_start: 0.9165 (t) cc_final: 0.8574 (t) REVERT: F 422 LEU cc_start: 0.9537 (mt) cc_final: 0.9322 (mt) REVERT: F 524 THR cc_start: 0.8737 (p) cc_final: 0.8508 (p) REVERT: F 526 GLN cc_start: 0.9392 (tt0) cc_final: 0.8820 (tt0) REVERT: F 527 GLU cc_start: 0.9090 (tt0) cc_final: 0.8687 (tt0) REVERT: F 630 LEU cc_start: 0.9065 (mt) cc_final: 0.8786 (tt) REVERT: F 671 GLU cc_start: 0.8704 (tt0) cc_final: 0.8424 (tm-30) REVERT: F 738 SER cc_start: 0.9215 (p) cc_final: 0.8753 (m) REVERT: F 751 ASN cc_start: 0.8491 (m-40) cc_final: 0.8145 (m110) REVERT: F 755 ASP cc_start: 0.7912 (m-30) cc_final: 0.7587 (m-30) REVERT: F 762 CYS cc_start: 0.8631 (m) cc_final: 0.8376 (p) REVERT: F 790 ILE cc_start: 0.8823 (mm) cc_final: 0.8069 (tp) REVERT: F 802 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7594 (mt-10) REVERT: F 831 LYS cc_start: 0.8076 (mttt) cc_final: 0.7510 (mmtp) REVERT: F 919 LEU cc_start: 0.8213 (mt) cc_final: 0.7955 (mp) REVERT: F 937 LEU cc_start: 0.8291 (mt) cc_final: 0.8089 (pp) REVERT: F 940 ASP cc_start: 0.8677 (m-30) cc_final: 0.8063 (t70) REVERT: F 989 PHE cc_start: 0.8801 (m-10) cc_final: 0.8399 (m-80) REVERT: F 1006 SER cc_start: 0.8860 (t) cc_final: 0.7839 (p) outliers start: 6 outliers final: 0 residues processed: 1104 average time/residue: 0.2267 time to fit residues: 422.3574 Evaluate side-chains 783 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 783 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 131 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 427 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 338 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 380 optimal weight: 0.0980 chunk 245 optimal weight: 4.9990 chunk 474 optimal weight: 2.9990 chunk 450 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS A 480 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN B 522 HIS C 391 GLN C 522 HIS C 751 ASN D 288 HIS D 391 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 GLN E 260 HIS E 391 GLN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.128943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093889 restraints weight = 96552.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096429 restraints weight = 68858.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097189 restraints weight = 43481.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097778 restraints weight = 41558.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.098062 restraints weight = 37070.244| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 40266 Z= 0.202 Angle : 0.681 13.329 54372 Z= 0.348 Chirality : 0.041 0.191 6156 Planarity : 0.004 0.059 6810 Dihedral : 11.177 174.239 5544 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 0.18 % Allowed : 2.96 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.13 (0.12), residues: 4848 helix: 0.85 (0.11), residues: 2298 sheet: -0.09 (0.22), residues: 582 loop : -0.68 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 675 TYR 0.018 0.002 TYR D 258 PHE 0.023 0.002 PHE E 209 TRP 0.013 0.001 TRP F 833 HIS 0.011 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00429 (40266) covalent geometry : angle 0.68097 (54372) hydrogen bonds : bond 0.04851 ( 1721) hydrogen bonds : angle 4.84113 ( 4935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 924 time to evaluate : 1.570 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: 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 142 LYS cc_start: 0.9294 (mttt) cc_final: 0.8975 (pttm) REVERT: A 220 HIS cc_start: 0.7891 (m90) cc_final: 0.7641 (p-80) REVERT: A 238 LYS cc_start: 0.8547 (tptp) cc_final: 0.8194 (tttt) REVERT: A 239 MET cc_start: 0.9230 (mtp) cc_final: 0.8131 (mmp) REVERT: A 240 MET cc_start: 0.8751 (mtm) cc_final: 0.8431 (mmt) REVERT: A 251 ASP cc_start: 0.8571 (p0) cc_final: 0.8222 (m-30) REVERT: A 253 PHE cc_start: 0.7061 (m-80) cc_final: 0.6566 (m-10) REVERT: A 336 ILE cc_start: 0.9651 (mt) cc_final: 0.9424 (tt) REVERT: A 358 LEU cc_start: 0.8392 (tp) cc_final: 0.8005 (tp) REVERT: A 393 ARG cc_start: 0.9347 (ttm-80) cc_final: 0.8819 (ttm-80) REVERT: A 403 GLU cc_start: 0.8603 (tt0) cc_final: 0.7844 (tp30) REVERT: A 409 CYS cc_start: 0.8856 (p) cc_final: 0.7912 (m) REVERT: A 508 PHE cc_start: 0.8226 (m-80) cc_final: 0.8002 (m-80) REVERT: A 520 PHE cc_start: 0.7886 (m-80) cc_final: 0.7074 (m-10) REVERT: A 521 ILE cc_start: 0.8301 (tt) cc_final: 0.7989 (pt) REVERT: A 526 GLN cc_start: 0.9433 (tt0) cc_final: 0.8420 (tt0) REVERT: A 527 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8450 (tt0) REVERT: A 604 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9132 (tp) REVERT: A 639 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8269 (tm-30) REVERT: A 664 MET cc_start: 0.8401 (tpp) cc_final: 0.7933 (tpp) REVERT: A 738 SER cc_start: 0.9292 (p) cc_final: 0.8815 (m) REVERT: A 758 MET cc_start: 0.8914 (tpp) cc_final: 0.8529 (tpp) REVERT: A 802 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 831 LYS cc_start: 0.8392 (mttt) cc_final: 0.7711 (mmtp) REVERT: A 987 MET cc_start: 0.8934 (mmm) cc_final: 0.8684 (mmp) REVERT: A 1005 LEU cc_start: 0.8805 (mt) cc_final: 0.8245 (tt) REVERT: B 142 LYS cc_start: 0.9292 (mtmm) cc_final: 0.9087 (pttm) REVERT: B 220 HIS cc_start: 0.8617 (m90) cc_final: 0.7863 (p-80) REVERT: B 239 MET cc_start: 0.9175 (mtm) cc_final: 0.7903 (mmp) REVERT: B 242 ASP cc_start: 0.9272 (m-30) cc_final: 0.8903 (m-30) REVERT: B 253 PHE cc_start: 0.7263 (m-10) cc_final: 0.6620 (m-10) REVERT: B 297 ILE cc_start: 0.7990 (mm) cc_final: 0.7691 (mm) REVERT: B 326 GLU cc_start: 0.7918 (tp30) cc_final: 0.7003 (tt0) REVERT: B 358 LEU cc_start: 0.8396 (tp) cc_final: 0.8012 (tp) REVERT: B 403 GLU cc_start: 0.8570 (tt0) cc_final: 0.7676 (tp30) REVERT: B 409 CYS cc_start: 0.8993 (m) cc_final: 0.8498 (t) REVERT: B 527 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8359 (tt0) REVERT: B 631 PHE cc_start: 0.8461 (m-80) cc_final: 0.8088 (m-80) REVERT: B 639 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8570 (tm-30) REVERT: B 654 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7959 (tm-30) REVERT: B 664 MET cc_start: 0.8577 (mmt) cc_final: 0.8092 (mmm) REVERT: B 669 CYS cc_start: 0.8590 (m) cc_final: 0.7876 (m) REVERT: B 738 SER cc_start: 0.9221 (p) cc_final: 0.8944 (m) REVERT: B 751 ASN cc_start: 0.8305 (m-40) cc_final: 0.8052 (m110) REVERT: B 802 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 831 LYS cc_start: 0.8510 (mttt) cc_final: 0.7933 (mmtp) REVERT: B 989 PHE cc_start: 0.8897 (m-80) cc_final: 0.8615 (m-80) REVERT: B 1005 LEU cc_start: 0.8827 (mt) cc_final: 0.8513 (tt) REVERT: B 1008 MET cc_start: 0.8442 (mmm) cc_final: 0.8119 (mmp) REVERT: C 142 LYS cc_start: 0.8888 (pttm) cc_final: 0.8661 (pttp) REVERT: C 235 LEU cc_start: 0.9414 (tp) cc_final: 0.9099 (tt) REVERT: C 239 MET cc_start: 0.9175 (mtp) cc_final: 0.8944 (mtp) REVERT: C 240 MET cc_start: 0.8655 (mtm) cc_final: 0.8191 (mmt) REVERT: C 242 ASP cc_start: 0.9234 (m-30) cc_final: 0.8955 (m-30) REVERT: C 249 TYR cc_start: 0.8225 (m-80) cc_final: 0.6992 (m-80) REVERT: C 253 PHE cc_start: 0.7603 (m-80) cc_final: 0.3659 (m-10) REVERT: C 379 LYS cc_start: 0.9105 (tttt) cc_final: 0.8785 (tptm) REVERT: C 380 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8559 (pp20) REVERT: C 403 GLU cc_start: 0.8613 (tt0) cc_final: 0.7991 (tp30) REVERT: C 405 LEU cc_start: 0.9457 (tt) cc_final: 0.8997 (tt) REVERT: C 408 MET cc_start: 0.8775 (mtm) cc_final: 0.8448 (mtm) REVERT: C 527 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8430 (tt0) REVERT: C 639 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8695 (tm-30) REVERT: C 730 CYS cc_start: 0.8877 (m) cc_final: 0.8495 (m) REVERT: C 738 SER cc_start: 0.9203 (p) cc_final: 0.8877 (m) REVERT: C 758 MET cc_start: 0.8722 (tpp) cc_final: 0.8472 (tpp) REVERT: C 802 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7243 (mt-10) REVERT: C 831 LYS cc_start: 0.8284 (mttt) cc_final: 0.7594 (mmtp) REVERT: C 940 ASP cc_start: 0.8820 (m-30) cc_final: 0.8235 (t70) REVERT: C 987 MET cc_start: 0.8950 (mmm) cc_final: 0.8733 (mmp) REVERT: C 1001 GLN cc_start: 0.7352 (mm110) cc_final: 0.6902 (mm-40) REVERT: C 1006 SER cc_start: 0.8739 (t) cc_final: 0.7495 (p) REVERT: C 1008 MET cc_start: 0.8315 (mmm) cc_final: 0.7871 (mmm) REVERT: D 220 HIS cc_start: 0.8266 (m90) cc_final: 0.7598 (p-80) REVERT: D 230 ILE cc_start: 0.9162 (pt) cc_final: 0.8958 (pt) REVERT: D 239 MET cc_start: 0.9179 (mtm) cc_final: 0.7957 (mmp) REVERT: D 242 ASP cc_start: 0.9243 (m-30) cc_final: 0.8813 (m-30) REVERT: D 253 PHE cc_start: 0.7525 (m-10) cc_final: 0.7033 (m-10) REVERT: D 381 TYR cc_start: 0.8695 (t80) cc_final: 0.8109 (t80) REVERT: D 403 GLU cc_start: 0.8692 (tt0) cc_final: 0.7621 (tp30) REVERT: D 408 MET cc_start: 0.8252 (mtm) cc_final: 0.7941 (mtm) REVERT: D 415 CYS cc_start: 0.9160 (t) cc_final: 0.8294 (t) REVERT: D 419 CYS cc_start: 0.8169 (m) cc_final: 0.7502 (p) REVERT: D 492 HIS cc_start: 0.8061 (m170) cc_final: 0.7832 (m170) REVERT: D 527 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8483 (tt0) REVERT: D 639 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8710 (tm-30) REVERT: D 654 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7952 (tm-30) REVERT: D 664 MET cc_start: 0.8417 (mmm) cc_final: 0.8199 (tpp) REVERT: D 738 SER cc_start: 0.9260 (p) cc_final: 0.8966 (m) REVERT: D 790 ILE cc_start: 0.8727 (mm) cc_final: 0.7987 (tp) REVERT: D 802 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7613 (mt-10) REVERT: D 831 LYS cc_start: 0.8456 (mttt) cc_final: 0.7819 (mmtp) REVERT: D 989 PHE cc_start: 0.9172 (m-10) cc_final: 0.8719 (m-80) REVERT: D 1005 LEU cc_start: 0.8801 (mt) cc_final: 0.8521 (tt) REVERT: D 1006 SER cc_start: 0.9035 (t) cc_final: 0.8463 (m) REVERT: D 1008 MET cc_start: 0.8298 (mmm) cc_final: 0.7877 (mmm) REVERT: E 235 LEU cc_start: 0.9445 (tt) cc_final: 0.9237 (tt) REVERT: E 239 MET cc_start: 0.9068 (mtm) cc_final: 0.8820 (mtp) REVERT: E 240 MET cc_start: 0.8587 (mtm) cc_final: 0.8115 (mmt) REVERT: E 242 ASP cc_start: 0.9240 (m-30) cc_final: 0.8913 (m-30) REVERT: E 253 PHE cc_start: 0.6951 (m-80) cc_final: 0.5351 (m-10) REVERT: E 298 LEU cc_start: 0.8656 (tp) cc_final: 0.8349 (tp) REVERT: E 403 GLU cc_start: 0.8579 (tt0) cc_final: 0.7792 (tp30) REVERT: E 407 THR cc_start: 0.8775 (m) cc_final: 0.8283 (p) REVERT: E 408 MET cc_start: 0.8741 (mtp) cc_final: 0.8217 (mmm) REVERT: E 415 CYS cc_start: 0.9297 (t) cc_final: 0.8824 (t) REVERT: E 483 LEU cc_start: 0.8783 (mt) cc_final: 0.8581 (pt) REVERT: E 505 MET cc_start: 0.7314 (mtm) cc_final: 0.7059 (mtt) REVERT: E 527 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8462 (tt0) REVERT: E 557 ASP cc_start: 0.7664 (t0) cc_final: 0.6973 (t0) REVERT: E 639 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8687 (tm-30) REVERT: E 664 MET cc_start: 0.8230 (tpp) cc_final: 0.7806 (tpp) REVERT: E 730 CYS cc_start: 0.8776 (p) cc_final: 0.8370 (p) REVERT: E 738 SER cc_start: 0.9149 (p) cc_final: 0.8813 (m) REVERT: E 758 MET cc_start: 0.8623 (tpp) cc_final: 0.8358 (tpp) REVERT: E 764 THR cc_start: 0.9067 (p) cc_final: 0.8816 (p) REVERT: E 802 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7784 (mt-10) REVERT: E 831 LYS cc_start: 0.8427 (mttt) cc_final: 0.7856 (mmtp) REVERT: E 919 LEU cc_start: 0.9026 (mt) cc_final: 0.8745 (mp) REVERT: E 937 LEU cc_start: 0.8377 (mt) cc_final: 0.8071 (pp) REVERT: E 940 ASP cc_start: 0.8776 (m-30) cc_final: 0.8246 (t70) REVERT: E 989 PHE cc_start: 0.9072 (m-10) cc_final: 0.8520 (m-80) REVERT: E 1005 LEU cc_start: 0.8884 (mt) cc_final: 0.8558 (tt) REVERT: F 142 LYS cc_start: 0.9302 (mtmm) cc_final: 0.9008 (pttm) REVERT: F 238 LYS cc_start: 0.8486 (tttt) cc_final: 0.7855 (tttt) REVERT: F 239 MET cc_start: 0.9111 (mtm) cc_final: 0.7844 (mmp) REVERT: F 240 MET cc_start: 0.8360 (mtm) cc_final: 0.8032 (mmt) REVERT: F 242 ASP cc_start: 0.9229 (m-30) cc_final: 0.8945 (m-30) REVERT: F 253 PHE cc_start: 0.7211 (m-80) cc_final: 0.6969 (m-10) REVERT: F 304 PHE cc_start: 0.8578 (t80) cc_final: 0.8230 (t80) REVERT: F 358 LEU cc_start: 0.8352 (tp) cc_final: 0.7975 (tp) REVERT: F 379 LYS cc_start: 0.9045 (tttt) cc_final: 0.8668 (tttt) REVERT: F 381 TYR cc_start: 0.8404 (t80) cc_final: 0.7927 (t80) REVERT: F 407 THR cc_start: 0.8807 (m) cc_final: 0.8388 (p) REVERT: F 415 CYS cc_start: 0.9222 (t) cc_final: 0.8382 (t) REVERT: F 419 CYS cc_start: 0.7973 (m) cc_final: 0.7616 (p) REVERT: F 527 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8268 (tt0) REVERT: F 532 MET cc_start: 0.8347 (tpp) cc_final: 0.8136 (tpp) REVERT: F 576 VAL cc_start: 0.9321 (t) cc_final: 0.9120 (t) REVERT: F 639 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8565 (tm-30) REVERT: F 671 GLU cc_start: 0.8724 (tt0) cc_final: 0.8382 (tm-30) REVERT: F 738 SER cc_start: 0.9274 (p) cc_final: 0.8942 (m) REVERT: F 755 ASP cc_start: 0.8107 (m-30) cc_final: 0.7783 (m-30) REVERT: F 762 CYS cc_start: 0.8643 (m) cc_final: 0.8278 (m) REVERT: F 793 VAL cc_start: 0.8980 (t) cc_final: 0.8699 (t) REVERT: F 802 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7868 (mt-10) REVERT: F 831 LYS cc_start: 0.8506 (mttt) cc_final: 0.7825 (mmtp) REVERT: F 937 LEU cc_start: 0.8380 (mt) cc_final: 0.8105 (pp) REVERT: F 940 ASP cc_start: 0.8880 (m-30) cc_final: 0.8289 (t70) REVERT: F 989 PHE cc_start: 0.9049 (m-10) cc_final: 0.8504 (m-80) outliers start: 8 outliers final: 0 residues processed: 925 average time/residue: 0.2171 time to fit residues: 341.1435 Evaluate side-chains 684 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 682 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 54 optimal weight: 0.6980 chunk 283 optimal weight: 6.9990 chunk 282 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 335 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 397 optimal weight: 0.0570 chunk 246 optimal weight: 6.9990 chunk 258 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 467 optimal weight: 3.9990 overall best weight: 2.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 922 ASN B 495 GLN B 522 HIS B 922 ASN C 495 GLN C 506 ASN C 922 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 GLN D 522 HIS E 260 HIS ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 751 ASN E 922 ASN F 260 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 GLN F 522 HIS F 751 ASN F 922 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.126661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.091814 restraints weight = 95727.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.093666 restraints weight = 62146.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094846 restraints weight = 41998.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095120 restraints weight = 36390.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095263 restraints weight = 33292.141| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 40266 Z= 0.177 Angle : 0.635 9.138 54372 Z= 0.328 Chirality : 0.040 0.152 6156 Planarity : 0.004 0.079 6810 Dihedral : 11.095 176.659 5544 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.94 % Favored : 94.04 % Rotamer: Outliers : 0.07 % Allowed : 2.52 % Favored : 97.42 % 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: -0.06 (0.12), residues: 4848 helix: 0.79 (0.11), residues: 2298 sheet: -0.63 (0.22), residues: 594 loop : -0.75 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 292 TYR 0.019 0.002 TYR F 443 PHE 0.030 0.002 PHE B 148 TRP 0.017 0.001 TRP D 959 HIS 0.007 0.001 HIS A 916 Details of bonding type rmsd covalent geometry : bond 0.00398 (40266) covalent geometry : angle 0.63523 (54372) hydrogen bonds : bond 0.04406 ( 1721) hydrogen bonds : angle 4.75210 ( 4935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 843 time to evaluate : 1.550 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: 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 142 LYS cc_start: 0.9234 (mttt) cc_final: 0.8937 (pttm) REVERT: A 239 MET cc_start: 0.9171 (mtp) cc_final: 0.8080 (mmp) REVERT: A 240 MET cc_start: 0.8766 (mtm) cc_final: 0.8565 (mmt) REVERT: A 242 ASP cc_start: 0.8869 (m-30) cc_final: 0.8569 (m-30) REVERT: A 253 PHE cc_start: 0.6898 (m-80) cc_final: 0.5786 (m-10) REVERT: A 298 LEU cc_start: 0.8782 (tp) cc_final: 0.8504 (tp) REVERT: A 358 LEU cc_start: 0.8659 (tp) cc_final: 0.8353 (tt) REVERT: A 403 GLU cc_start: 0.8534 (tt0) cc_final: 0.7930 (tp30) REVERT: A 508 PHE cc_start: 0.8492 (m-80) cc_final: 0.8172 (m-80) REVERT: A 521 ILE cc_start: 0.8300 (tt) cc_final: 0.8022 (tt) REVERT: A 527 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8528 (tt0) REVERT: A 557 ASP cc_start: 0.7893 (t0) cc_final: 0.7207 (t0) REVERT: A 738 SER cc_start: 0.9354 (p) cc_final: 0.8923 (m) REVERT: A 764 THR cc_start: 0.9191 (p) cc_final: 0.8962 (p) REVERT: A 802 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 989 PHE cc_start: 0.9108 (m-80) cc_final: 0.8661 (m-80) REVERT: A 1005 LEU cc_start: 0.8869 (mt) cc_final: 0.8641 (tt) REVERT: B 220 HIS cc_start: 0.8494 (m90) cc_final: 0.7773 (p-80) REVERT: B 235 LEU cc_start: 0.9374 (tp) cc_final: 0.9031 (tt) REVERT: B 239 MET cc_start: 0.9142 (mtm) cc_final: 0.8669 (mtp) REVERT: B 240 MET cc_start: 0.8996 (mmm) cc_final: 0.8780 (mmt) REVERT: B 242 ASP cc_start: 0.9253 (m-30) cc_final: 0.8915 (m-30) REVERT: B 253 PHE cc_start: 0.7259 (m-10) cc_final: 0.6622 (m-10) REVERT: B 403 GLU cc_start: 0.8599 (tt0) cc_final: 0.7880 (tp30) REVERT: B 405 LEU cc_start: 0.9589 (tt) cc_final: 0.9291 (tt) REVERT: B 517 PHE cc_start: 0.7360 (p90) cc_final: 0.6925 (p90) REVERT: B 526 GLN cc_start: 0.9390 (tt0) cc_final: 0.8886 (tt0) REVERT: B 527 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8469 (tt0) REVERT: B 631 PHE cc_start: 0.8420 (m-10) cc_final: 0.8183 (m-80) REVERT: B 654 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8081 (tm-30) REVERT: B 669 CYS cc_start: 0.8527 (m) cc_final: 0.7856 (m) REVERT: B 738 SER cc_start: 0.9232 (p) cc_final: 0.8959 (m) REVERT: B 802 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7984 (mt-10) REVERT: B 1005 LEU cc_start: 0.8880 (mt) cc_final: 0.8610 (tt) REVERT: B 1008 MET cc_start: 0.8361 (mmm) cc_final: 0.7767 (mmp) REVERT: C 220 HIS cc_start: 0.8361 (m90) cc_final: 0.8086 (m90) REVERT: C 235 LEU cc_start: 0.9402 (tp) cc_final: 0.9113 (tt) REVERT: C 239 MET cc_start: 0.9143 (mtp) cc_final: 0.8911 (mtp) REVERT: C 240 MET cc_start: 0.8666 (mtm) cc_final: 0.8355 (mmt) REVERT: C 242 ASP cc_start: 0.9216 (m-30) cc_final: 0.8943 (m-30) REVERT: C 249 TYR cc_start: 0.8053 (m-80) cc_final: 0.7351 (m-80) REVERT: C 379 LYS cc_start: 0.9120 (tttt) cc_final: 0.8751 (tptm) REVERT: C 403 GLU cc_start: 0.8721 (tt0) cc_final: 0.7879 (tp30) REVERT: C 408 MET cc_start: 0.8947 (mtm) cc_final: 0.8668 (mmt) REVERT: C 411 ILE cc_start: 0.8737 (mt) cc_final: 0.8516 (mt) REVERT: C 517 PHE cc_start: 0.7289 (p90) cc_final: 0.6903 (p90) REVERT: C 527 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8571 (tt0) REVERT: C 664 MET cc_start: 0.8117 (mmt) cc_final: 0.7899 (tpp) REVERT: C 730 CYS cc_start: 0.8767 (m) cc_final: 0.8401 (m) REVERT: C 738 SER cc_start: 0.9234 (p) cc_final: 0.8970 (m) REVERT: C 758 MET cc_start: 0.8762 (tpp) cc_final: 0.8560 (tpp) REVERT: C 802 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7632 (mt-10) REVERT: C 831 LYS cc_start: 0.8587 (mttt) cc_final: 0.7866 (mttm) REVERT: C 940 ASP cc_start: 0.8787 (m-30) cc_final: 0.8254 (t70) REVERT: C 1006 SER cc_start: 0.8655 (t) cc_final: 0.7365 (p) REVERT: C 1008 MET cc_start: 0.8317 (mmm) cc_final: 0.7946 (mmm) REVERT: D 142 LYS cc_start: 0.9191 (mtmm) cc_final: 0.8948 (pttm) REVERT: D 220 HIS cc_start: 0.8036 (m90) cc_final: 0.7603 (p-80) REVERT: D 232 LYS cc_start: 0.8433 (ptpp) cc_final: 0.8202 (ptpp) REVERT: D 242 ASP cc_start: 0.9237 (m-30) cc_final: 0.8887 (m-30) REVERT: D 253 PHE cc_start: 0.7285 (m-10) cc_final: 0.7038 (m-10) REVERT: D 381 TYR cc_start: 0.8672 (t80) cc_final: 0.7966 (t80) REVERT: D 403 GLU cc_start: 0.8632 (tt0) cc_final: 0.8233 (pm20) REVERT: D 415 CYS cc_start: 0.9110 (t) cc_final: 0.7906 (t) REVERT: D 419 CYS cc_start: 0.8137 (m) cc_final: 0.7747 (m) REVERT: D 526 GLN cc_start: 0.9094 (tt0) cc_final: 0.8322 (tt0) REVERT: D 527 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8652 (mp0) REVERT: D 532 MET cc_start: 0.8314 (tpp) cc_final: 0.8094 (tpp) REVERT: D 654 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8001 (tm-30) REVERT: D 664 MET cc_start: 0.8322 (mmm) cc_final: 0.8119 (tpp) REVERT: D 738 SER cc_start: 0.9253 (p) cc_final: 0.8990 (m) REVERT: D 802 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7196 (mt-10) REVERT: D 831 LYS cc_start: 0.8350 (mttt) cc_final: 0.7482 (mttm) REVERT: D 987 MET cc_start: 0.9002 (mmp) cc_final: 0.8764 (mmm) REVERT: D 989 PHE cc_start: 0.9061 (m-10) cc_final: 0.8685 (m-80) REVERT: D 1005 LEU cc_start: 0.8843 (mt) cc_final: 0.8541 (tt) REVERT: D 1006 SER cc_start: 0.9109 (t) cc_final: 0.8543 (m) REVERT: D 1008 MET cc_start: 0.8357 (mmm) cc_final: 0.7864 (mmm) REVERT: E 239 MET cc_start: 0.9017 (mtm) cc_final: 0.8768 (mtp) REVERT: E 240 MET cc_start: 0.8608 (mtm) cc_final: 0.8272 (mmt) REVERT: E 242 ASP cc_start: 0.9240 (m-30) cc_final: 0.8908 (m-30) REVERT: E 253 PHE cc_start: 0.7273 (m-80) cc_final: 0.5146 (m-10) REVERT: E 298 LEU cc_start: 0.8638 (tp) cc_final: 0.8383 (tp) REVERT: E 403 GLU cc_start: 0.8562 (tt0) cc_final: 0.7777 (tp30) REVERT: E 408 MET cc_start: 0.8510 (mtp) cc_final: 0.7823 (mmm) REVERT: E 409 CYS cc_start: 0.8705 (m) cc_final: 0.8355 (m) REVERT: E 415 CYS cc_start: 0.9226 (t) cc_final: 0.8857 (t) REVERT: E 417 ILE cc_start: 0.9486 (mt) cc_final: 0.9282 (tp) REVERT: E 527 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8430 (tt0) REVERT: E 557 ASP cc_start: 0.7822 (t0) cc_final: 0.7215 (t0) REVERT: E 664 MET cc_start: 0.8197 (tpp) cc_final: 0.7762 (tpp) REVERT: E 738 SER cc_start: 0.9258 (p) cc_final: 0.8913 (m) REVERT: E 764 THR cc_start: 0.9048 (p) cc_final: 0.8829 (p) REVERT: E 802 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7693 (mt-10) REVERT: E 831 LYS cc_start: 0.8544 (mttt) cc_final: 0.7737 (mmtp) REVERT: E 922 ASN cc_start: 0.8308 (m-40) cc_final: 0.7954 (m-40) REVERT: E 940 ASP cc_start: 0.8726 (m-30) cc_final: 0.8200 (t70) REVERT: E 989 PHE cc_start: 0.8958 (m-10) cc_final: 0.8465 (m-80) REVERT: E 1005 LEU cc_start: 0.8803 (mt) cc_final: 0.8454 (tt) REVERT: F 142 LYS cc_start: 0.9293 (mtmm) cc_final: 0.9076 (pttm) REVERT: F 235 LEU cc_start: 0.9369 (tp) cc_final: 0.9161 (tp) REVERT: F 238 LYS cc_start: 0.8449 (tttt) cc_final: 0.8053 (tttt) REVERT: F 239 MET cc_start: 0.9070 (mtm) cc_final: 0.8713 (mtp) REVERT: F 242 ASP cc_start: 0.9197 (m-30) cc_final: 0.8948 (m-30) REVERT: F 253 PHE cc_start: 0.7296 (m-80) cc_final: 0.6998 (m-10) REVERT: F 381 TYR cc_start: 0.8366 (t80) cc_final: 0.8058 (t80) REVERT: F 403 GLU cc_start: 0.8602 (tt0) cc_final: 0.7716 (tp30) REVERT: F 405 LEU cc_start: 0.9473 (tt) cc_final: 0.9268 (mt) REVERT: F 407 THR cc_start: 0.8750 (m) cc_final: 0.8465 (p) REVERT: F 415 CYS cc_start: 0.9240 (t) cc_final: 0.8580 (t) REVERT: F 517 PHE cc_start: 0.7294 (p90) cc_final: 0.6898 (p90) REVERT: F 527 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8493 (tt0) REVERT: F 639 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8591 (tm-30) REVERT: F 664 MET cc_start: 0.8353 (tpp) cc_final: 0.7799 (tpp) REVERT: F 730 CYS cc_start: 0.8851 (p) cc_final: 0.8345 (p) REVERT: F 737 LEU cc_start: 0.9578 (mt) cc_final: 0.9366 (tt) REVERT: F 738 SER cc_start: 0.9325 (p) cc_final: 0.9024 (m) REVERT: F 762 CYS cc_start: 0.8629 (m) cc_final: 0.8234 (m) REVERT: F 764 THR cc_start: 0.9206 (p) cc_final: 0.8990 (p) REVERT: F 793 VAL cc_start: 0.8903 (t) cc_final: 0.8597 (t) REVERT: F 802 GLU cc_start: 0.8263 (mt-10) cc_final: 0.6924 (mt-10) REVERT: F 831 LYS cc_start: 0.8665 (mttt) cc_final: 0.7433 (mttt) REVERT: F 937 LEU cc_start: 0.8428 (mt) cc_final: 0.8045 (pp) REVERT: F 940 ASP cc_start: 0.8864 (m-30) cc_final: 0.8323 (t70) REVERT: F 987 MET cc_start: 0.9228 (mmm) cc_final: 0.8973 (mmm) REVERT: F 989 PHE cc_start: 0.9006 (m-10) cc_final: 0.8450 (m-80) outliers start: 3 outliers final: 0 residues processed: 843 average time/residue: 0.2150 time to fit residues: 309.8544 Evaluate side-chains 617 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 617 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 307 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 347 optimal weight: 8.9990 chunk 458 optimal weight: 0.8980 chunk 476 optimal weight: 7.9990 chunk 180 optimal weight: 0.0870 chunk 191 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 922 ASN B 260 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN B 522 HIS B 751 ASN C 495 GLN C 506 ASN C 522 HIS C 751 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS D 922 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 ASN F 522 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.124765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091561 restraints weight = 97255.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091470 restraints weight = 66932.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092902 restraints weight = 52076.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.093177 restraints weight = 44176.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093382 restraints weight = 39658.126| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 40266 Z= 0.182 Angle : 0.646 13.196 54372 Z= 0.330 Chirality : 0.040 0.168 6156 Planarity : 0.004 0.061 6810 Dihedral : 11.010 179.788 5544 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.80 % 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: -0.24 (0.12), residues: 4848 helix: 0.66 (0.11), residues: 2322 sheet: -0.85 (0.22), residues: 582 loop : -0.84 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 378 TYR 0.020 0.002 TYR D 518 PHE 0.030 0.002 PHE A 520 TRP 0.025 0.001 TRP F 959 HIS 0.010 0.001 HIS C 916 Details of bonding type rmsd covalent geometry : bond 0.00410 (40266) covalent geometry : angle 0.64559 (54372) hydrogen bonds : bond 0.04242 ( 1721) hydrogen bonds : angle 4.73838 ( 4935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 822 time to evaluate : 1.374 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.9237 (mttt) cc_final: 0.8913 (pttm) REVERT: A 239 MET cc_start: 0.9130 (mtp) cc_final: 0.8072 (mmp) REVERT: A 242 ASP cc_start: 0.8808 (m-30) cc_final: 0.8581 (m-30) REVERT: A 253 PHE cc_start: 0.6940 (m-80) cc_final: 0.5896 (m-10) REVERT: A 298 LEU cc_start: 0.8794 (tp) cc_final: 0.8496 (tp) REVERT: A 403 GLU cc_start: 0.8559 (tt0) cc_final: 0.7983 (tp30) REVERT: A 521 ILE cc_start: 0.8382 (tt) cc_final: 0.7993 (tt) REVERT: A 526 GLN cc_start: 0.9288 (tt0) cc_final: 0.8563 (tt0) REVERT: A 527 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8676 (tt0) REVERT: A 557 ASP cc_start: 0.7985 (t0) cc_final: 0.7374 (t0) REVERT: A 639 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8590 (tm-30) REVERT: A 738 SER cc_start: 0.9390 (p) cc_final: 0.8999 (m) REVERT: A 758 MET cc_start: 0.8703 (tpp) cc_final: 0.8253 (tpp) REVERT: A 762 CYS cc_start: 0.8405 (m) cc_final: 0.7802 (m) REVERT: A 793 VAL cc_start: 0.9001 (t) cc_final: 0.8766 (t) REVERT: A 802 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 831 LYS cc_start: 0.8578 (mttt) cc_final: 0.7291 (mttt) REVERT: A 987 MET cc_start: 0.8832 (mmm) cc_final: 0.8540 (mmp) REVERT: A 989 PHE cc_start: 0.9003 (m-80) cc_final: 0.8693 (m-80) REVERT: B 142 LYS cc_start: 0.8928 (pttm) cc_final: 0.8706 (pttp) REVERT: B 220 HIS cc_start: 0.8448 (m90) cc_final: 0.7688 (p-80) REVERT: B 235 LEU cc_start: 0.9417 (tp) cc_final: 0.9189 (tp) REVERT: B 239 MET cc_start: 0.9179 (mtm) cc_final: 0.8766 (mtp) REVERT: B 240 MET cc_start: 0.9147 (mmm) cc_final: 0.8385 (tpt) REVERT: B 242 ASP cc_start: 0.9211 (m-30) cc_final: 0.8832 (m-30) REVERT: B 253 PHE cc_start: 0.7144 (m-10) cc_final: 0.6553 (m-10) REVERT: B 403 GLU cc_start: 0.8614 (tt0) cc_final: 0.7908 (tp30) REVERT: B 405 LEU cc_start: 0.9517 (tt) cc_final: 0.9215 (tt) REVERT: B 408 MET cc_start: 0.8917 (mtm) cc_final: 0.8689 (mtm) REVERT: B 517 PHE cc_start: 0.7467 (p90) cc_final: 0.6982 (p90) REVERT: B 520 PHE cc_start: 0.7698 (m-80) cc_final: 0.6690 (m-80) REVERT: B 526 GLN cc_start: 0.9344 (tt0) cc_final: 0.8303 (tt0) REVERT: B 527 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8556 (tt0) REVERT: B 631 PHE cc_start: 0.8523 (m-10) cc_final: 0.8219 (m-80) REVERT: B 639 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8595 (tm-30) REVERT: B 654 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8128 (tm-30) REVERT: B 669 CYS cc_start: 0.8496 (m) cc_final: 0.7784 (m) REVERT: B 738 SER cc_start: 0.9232 (p) cc_final: 0.8976 (m) REVERT: B 764 THR cc_start: 0.9128 (p) cc_final: 0.8915 (p) REVERT: B 783 SER cc_start: 0.8625 (t) cc_final: 0.8421 (p) REVERT: B 802 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7277 (mt-10) REVERT: B 831 LYS cc_start: 0.8720 (mttt) cc_final: 0.7504 (mttt) REVERT: B 989 PHE cc_start: 0.8793 (m-80) cc_final: 0.8198 (m-80) REVERT: C 220 HIS cc_start: 0.8450 (m90) cc_final: 0.8195 (m90) REVERT: C 235 LEU cc_start: 0.9428 (tp) cc_final: 0.9093 (tt) REVERT: C 239 MET cc_start: 0.9151 (mtp) cc_final: 0.8933 (mtp) REVERT: C 240 MET cc_start: 0.8668 (mtm) cc_final: 0.8367 (mmt) REVERT: C 242 ASP cc_start: 0.9171 (m-30) cc_final: 0.8880 (m-30) REVERT: C 253 PHE cc_start: 0.7326 (m-80) cc_final: 0.6600 (m-80) REVERT: C 347 LEU cc_start: 0.9388 (tp) cc_final: 0.9102 (mt) REVERT: C 379 LYS cc_start: 0.9112 (tttt) cc_final: 0.8748 (tptm) REVERT: C 403 GLU cc_start: 0.8688 (tt0) cc_final: 0.8365 (pm20) REVERT: C 408 MET cc_start: 0.9042 (mtm) cc_final: 0.8234 (mtm) REVERT: C 413 LEU cc_start: 0.9107 (tt) cc_final: 0.8717 (mt) REVERT: C 436 SER cc_start: 0.8348 (m) cc_final: 0.7565 (t) REVERT: C 517 PHE cc_start: 0.7410 (p90) cc_final: 0.6940 (p90) REVERT: C 527 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8648 (mp0) REVERT: C 639 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8288 (tm-30) REVERT: C 730 CYS cc_start: 0.8741 (m) cc_final: 0.8478 (m) REVERT: C 738 SER cc_start: 0.9214 (p) cc_final: 0.8996 (m) REVERT: C 802 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7644 (mt-10) REVERT: C 940 ASP cc_start: 0.8815 (m-30) cc_final: 0.8336 (t70) REVERT: C 1006 SER cc_start: 0.8701 (t) cc_final: 0.7880 (m) REVERT: C 1008 MET cc_start: 0.8424 (mmm) cc_final: 0.8076 (mmm) REVERT: D 142 LYS cc_start: 0.9193 (mtmm) cc_final: 0.8931 (pttm) REVERT: D 220 HIS cc_start: 0.7971 (m90) cc_final: 0.7470 (p-80) REVERT: D 242 ASP cc_start: 0.9207 (m-30) cc_final: 0.8817 (m-30) REVERT: D 253 PHE cc_start: 0.7347 (m-10) cc_final: 0.6802 (m-10) REVERT: D 381 TYR cc_start: 0.8649 (t80) cc_final: 0.7982 (t80) REVERT: D 403 GLU cc_start: 0.8668 (tt0) cc_final: 0.8303 (pm20) REVERT: D 408 MET cc_start: 0.8570 (mtm) cc_final: 0.8086 (mtm) REVERT: D 409 CYS cc_start: 0.8623 (m) cc_final: 0.8234 (m) REVERT: D 415 CYS cc_start: 0.9106 (t) cc_final: 0.8078 (t) REVERT: D 417 ILE cc_start: 0.9490 (mt) cc_final: 0.9279 (tp) REVERT: D 419 CYS cc_start: 0.8125 (m) cc_final: 0.7774 (m) REVERT: D 532 MET cc_start: 0.8241 (tpp) cc_final: 0.8013 (tpp) REVERT: D 639 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8338 (tm-30) REVERT: D 654 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8033 (tm-30) REVERT: D 661 MET cc_start: 0.8590 (tpt) cc_final: 0.8374 (tpt) REVERT: D 738 SER cc_start: 0.9289 (p) cc_final: 0.8972 (m) REVERT: D 758 MET cc_start: 0.8805 (tpp) cc_final: 0.8568 (tpp) REVERT: D 802 GLU cc_start: 0.8159 (mt-10) cc_final: 0.6931 (mt-10) REVERT: D 831 LYS cc_start: 0.8496 (mttt) cc_final: 0.7199 (mttt) REVERT: D 987 MET cc_start: 0.9119 (mmp) cc_final: 0.8828 (mmm) REVERT: D 989 PHE cc_start: 0.9000 (m-10) cc_final: 0.8648 (m-80) REVERT: D 1006 SER cc_start: 0.9138 (t) cc_final: 0.8583 (m) REVERT: D 1008 MET cc_start: 0.8378 (mmm) cc_final: 0.7906 (mmp) REVERT: E 230 ILE cc_start: 0.9033 (pt) cc_final: 0.8825 (pt) REVERT: E 235 LEU cc_start: 0.9413 (tt) cc_final: 0.9189 (tt) REVERT: E 239 MET cc_start: 0.9014 (mtm) cc_final: 0.8780 (mtp) REVERT: E 240 MET cc_start: 0.8635 (mtm) cc_final: 0.8347 (mmt) REVERT: E 242 ASP cc_start: 0.9231 (m-30) cc_final: 0.8902 (m-30) REVERT: E 253 PHE cc_start: 0.7283 (m-80) cc_final: 0.5206 (m-10) REVERT: E 298 LEU cc_start: 0.8596 (tp) cc_final: 0.8356 (tp) REVERT: E 403 GLU cc_start: 0.8634 (tt0) cc_final: 0.7870 (tp30) REVERT: E 405 LEU cc_start: 0.9533 (tt) cc_final: 0.9298 (mt) REVERT: E 409 CYS cc_start: 0.8684 (m) cc_final: 0.8421 (m) REVERT: E 415 CYS cc_start: 0.9101 (t) cc_final: 0.8759 (t) REVERT: E 417 ILE cc_start: 0.9493 (mt) cc_final: 0.9277 (tp) REVERT: E 527 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8515 (tt0) REVERT: E 557 ASP cc_start: 0.7852 (t0) cc_final: 0.7204 (t0) REVERT: E 738 SER cc_start: 0.9281 (p) cc_final: 0.8955 (m) REVERT: E 758 MET cc_start: 0.8767 (tpp) cc_final: 0.8531 (tpp) REVERT: E 783 SER cc_start: 0.8719 (t) cc_final: 0.8475 (p) REVERT: E 802 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7157 (mt-10) REVERT: E 831 LYS cc_start: 0.8413 (mttt) cc_final: 0.7094 (mttt) REVERT: E 940 ASP cc_start: 0.8742 (m-30) cc_final: 0.8268 (t70) REVERT: E 987 MET cc_start: 0.9070 (mmm) cc_final: 0.8843 (mmm) REVERT: E 989 PHE cc_start: 0.8828 (m-10) cc_final: 0.8294 (m-80) REVERT: F 238 LYS cc_start: 0.8412 (tttt) cc_final: 0.7978 (mmmt) REVERT: F 239 MET cc_start: 0.9068 (mtm) cc_final: 0.7943 (mmp) REVERT: F 253 PHE cc_start: 0.7371 (m-80) cc_final: 0.7046 (m-10) REVERT: F 381 TYR cc_start: 0.8453 (t80) cc_final: 0.7915 (t80) REVERT: F 403 GLU cc_start: 0.8522 (tt0) cc_final: 0.7746 (tp30) REVERT: F 407 THR cc_start: 0.9258 (m) cc_final: 0.8871 (p) REVERT: F 409 CYS cc_start: 0.8955 (m) cc_final: 0.8533 (t) REVERT: F 415 CYS cc_start: 0.9117 (t) cc_final: 0.7620 (t) REVERT: F 517 PHE cc_start: 0.7366 (p90) cc_final: 0.6845 (p90) REVERT: F 527 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8555 (tt0) REVERT: F 730 CYS cc_start: 0.8787 (p) cc_final: 0.8242 (p) REVERT: F 737 LEU cc_start: 0.9628 (mt) cc_final: 0.9405 (tt) REVERT: F 738 SER cc_start: 0.9311 (p) cc_final: 0.9009 (m) REVERT: F 762 CYS cc_start: 0.8584 (m) cc_final: 0.8148 (m) REVERT: F 764 THR cc_start: 0.9264 (p) cc_final: 0.8989 (p) REVERT: F 786 CYS cc_start: 0.7808 (p) cc_final: 0.7418 (p) REVERT: F 793 VAL cc_start: 0.8919 (t) cc_final: 0.8691 (t) REVERT: F 802 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7020 (tt0) REVERT: F 831 LYS cc_start: 0.8716 (mttt) cc_final: 0.7474 (mttt) REVERT: F 937 LEU cc_start: 0.8389 (mt) cc_final: 0.8020 (pp) REVERT: F 940 ASP cc_start: 0.8917 (m-30) cc_final: 0.8397 (t70) REVERT: F 989 PHE cc_start: 0.8923 (m-10) cc_final: 0.8351 (m-80) outliers start: 3 outliers final: 0 residues processed: 822 average time/residue: 0.2087 time to fit residues: 294.9383 Evaluate side-chains 613 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 613 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 405 optimal weight: 20.0000 chunk 4 optimal weight: 0.1980 chunk 111 optimal weight: 20.0000 chunk 318 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 chunk 417 optimal weight: 4.9990 chunk 364 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 419 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 120 optimal weight: 0.1980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 751 ASN A 922 ASN B 260 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS B 922 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS D 922 ASN E 391 GLN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN E 522 HIS E 751 ASN E 922 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 HIS F 751 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.125926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091023 restraints weight = 97030.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092950 restraints weight = 64587.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.094039 restraints weight = 43242.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.094311 restraints weight = 37061.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.094451 restraints weight = 34279.886| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40266 Z= 0.135 Angle : 0.627 12.536 54372 Z= 0.313 Chirality : 0.040 0.180 6156 Planarity : 0.003 0.041 6810 Dihedral : 10.931 178.447 5544 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.09 % Allowed : 1.50 % Favored : 98.41 % 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: -0.22 (0.12), residues: 4848 helix: 0.70 (0.11), residues: 2334 sheet: -0.92 (0.22), residues: 582 loop : -0.83 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 351 TYR 0.018 0.001 TYR B 533 PHE 0.021 0.002 PHE B 813 TRP 0.023 0.001 TRP A 959 HIS 0.010 0.001 HIS F 916 Details of bonding type rmsd covalent geometry : bond 0.00306 (40266) covalent geometry : angle 0.62655 (54372) hydrogen bonds : bond 0.03920 ( 1721) hydrogen bonds : angle 4.60035 ( 4935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 822 time to evaluate : 1.469 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.9283 (mttt) cc_final: 0.8976 (pttm) REVERT: A 232 LYS cc_start: 0.8570 (ptpp) cc_final: 0.8262 (ptpp) REVERT: A 239 MET cc_start: 0.9174 (mtp) cc_final: 0.8219 (mmp) REVERT: A 242 ASP cc_start: 0.8829 (m-30) cc_final: 0.8569 (m-30) REVERT: A 251 ASP cc_start: 0.8517 (p0) cc_final: 0.8151 (m-30) REVERT: A 253 PHE cc_start: 0.6849 (m-80) cc_final: 0.5787 (m-10) REVERT: A 298 LEU cc_start: 0.8815 (tp) cc_final: 0.8589 (tp) REVERT: A 393 ARG cc_start: 0.9435 (ttm-80) cc_final: 0.8963 (ttm-80) REVERT: A 403 GLU cc_start: 0.8587 (tt0) cc_final: 0.8009 (tp30) REVERT: A 517 PHE cc_start: 0.7719 (p90) cc_final: 0.7295 (p90) REVERT: A 521 ILE cc_start: 0.8302 (tt) cc_final: 0.7895 (tt) REVERT: A 527 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8604 (tt0) REVERT: A 532 MET cc_start: 0.8419 (tpt) cc_final: 0.8163 (tpt) REVERT: A 557 ASP cc_start: 0.8020 (t0) cc_final: 0.7362 (t70) REVERT: A 576 VAL cc_start: 0.9583 (t) cc_final: 0.9381 (t) REVERT: A 639 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8583 (tm-30) REVERT: A 737 LEU cc_start: 0.9589 (mt) cc_final: 0.9371 (tt) REVERT: A 738 SER cc_start: 0.9352 (p) cc_final: 0.9008 (m) REVERT: A 762 CYS cc_start: 0.8415 (m) cc_final: 0.7934 (m) REVERT: A 793 VAL cc_start: 0.9005 (t) cc_final: 0.8765 (t) REVERT: A 802 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7064 (mt-10) REVERT: A 831 LYS cc_start: 0.8602 (mttt) cc_final: 0.7353 (mttt) REVERT: A 940 ASP cc_start: 0.8654 (m-30) cc_final: 0.8355 (m-30) REVERT: A 987 MET cc_start: 0.9073 (mmm) cc_final: 0.8805 (mmp) REVERT: A 1005 LEU cc_start: 0.8926 (mt) cc_final: 0.8648 (tt) REVERT: B 220 HIS cc_start: 0.8581 (m90) cc_final: 0.7684 (p-80) REVERT: B 232 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8378 (ptpp) REVERT: B 235 LEU cc_start: 0.9368 (tp) cc_final: 0.9036 (tt) REVERT: B 239 MET cc_start: 0.9157 (mtm) cc_final: 0.8679 (mtp) REVERT: B 240 MET cc_start: 0.9145 (mmm) cc_final: 0.8437 (tpt) REVERT: B 242 ASP cc_start: 0.9165 (m-30) cc_final: 0.8819 (m-30) REVERT: B 253 PHE cc_start: 0.7173 (m-10) cc_final: 0.6516 (m-10) REVERT: B 403 GLU cc_start: 0.8663 (tt0) cc_final: 0.7945 (tp30) REVERT: B 405 LEU cc_start: 0.9567 (tt) cc_final: 0.9240 (tt) REVERT: B 517 PHE cc_start: 0.7458 (p90) cc_final: 0.6912 (p90) REVERT: B 532 MET cc_start: 0.8228 (tpp) cc_final: 0.7919 (tpp) REVERT: B 557 ASP cc_start: 0.7629 (t0) cc_final: 0.7031 (t0) REVERT: B 654 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8115 (tm-30) REVERT: B 738 SER cc_start: 0.9198 (p) cc_final: 0.8977 (m) REVERT: B 802 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7227 (mt-10) REVERT: B 822 LEU cc_start: 0.9033 (mt) cc_final: 0.8828 (mt) REVERT: B 831 LYS cc_start: 0.8735 (mttt) cc_final: 0.7522 (mttt) REVERT: B 940 ASP cc_start: 0.8828 (m-30) cc_final: 0.8522 (m-30) REVERT: B 989 PHE cc_start: 0.8884 (m-80) cc_final: 0.8200 (m-80) REVERT: C 235 LEU cc_start: 0.9421 (tp) cc_final: 0.9066 (tt) REVERT: C 239 MET cc_start: 0.9160 (mtp) cc_final: 0.8928 (mtp) REVERT: C 240 MET cc_start: 0.8625 (mtm) cc_final: 0.8369 (mmt) REVERT: C 242 ASP cc_start: 0.9167 (m-30) cc_final: 0.8870 (m-30) REVERT: C 253 PHE cc_start: 0.7295 (m-80) cc_final: 0.6655 (m-80) REVERT: C 379 LYS cc_start: 0.9092 (tttt) cc_final: 0.8713 (tptm) REVERT: C 403 GLU cc_start: 0.8603 (tt0) cc_final: 0.7845 (tp30) REVERT: C 408 MET cc_start: 0.9192 (mtm) cc_final: 0.8807 (mmt) REVERT: C 413 LEU cc_start: 0.9044 (tt) cc_final: 0.8805 (tp) REVERT: C 517 PHE cc_start: 0.7467 (p90) cc_final: 0.6846 (p90) REVERT: C 527 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8646 (mp0) REVERT: C 557 ASP cc_start: 0.7633 (t0) cc_final: 0.6861 (t0) REVERT: C 576 VAL cc_start: 0.9464 (t) cc_final: 0.9245 (t) REVERT: C 730 CYS cc_start: 0.8781 (m) cc_final: 0.8512 (m) REVERT: C 783 SER cc_start: 0.8665 (t) cc_final: 0.8420 (p) REVERT: C 802 GLU cc_start: 0.8228 (mt-10) cc_final: 0.6796 (mt-10) REVERT: C 831 LYS cc_start: 0.8689 (mttt) cc_final: 0.7522 (mttt) REVERT: C 940 ASP cc_start: 0.8797 (m-30) cc_final: 0.8274 (t0) REVERT: C 987 MET cc_start: 0.9269 (mmp) cc_final: 0.9066 (mmp) REVERT: C 1006 SER cc_start: 0.8725 (t) cc_final: 0.8145 (m) REVERT: C 1008 MET cc_start: 0.8450 (mmm) cc_final: 0.8052 (mmm) REVERT: D 142 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8954 (pttm) REVERT: D 220 HIS cc_start: 0.8146 (m90) cc_final: 0.7468 (p-80) REVERT: D 232 LYS cc_start: 0.8475 (ptpp) cc_final: 0.8267 (ptpp) REVERT: D 242 ASP cc_start: 0.9181 (m-30) cc_final: 0.8878 (m-30) REVERT: D 253 PHE cc_start: 0.7441 (m-10) cc_final: 0.6960 (m-10) REVERT: D 381 TYR cc_start: 0.8633 (t80) cc_final: 0.8036 (t80) REVERT: D 403 GLU cc_start: 0.8688 (tt0) cc_final: 0.8398 (pm20) REVERT: D 409 CYS cc_start: 0.8644 (m) cc_final: 0.8072 (t) REVERT: D 415 CYS cc_start: 0.9141 (t) cc_final: 0.7999 (t) REVERT: D 419 CYS cc_start: 0.8191 (m) cc_final: 0.7862 (m) REVERT: D 532 MET cc_start: 0.8283 (tpp) cc_final: 0.8056 (tpp) REVERT: D 654 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8066 (tm-30) REVERT: D 738 SER cc_start: 0.9276 (p) cc_final: 0.9015 (m) REVERT: D 802 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7050 (mt-10) REVERT: D 831 LYS cc_start: 0.8681 (mttt) cc_final: 0.7464 (mttt) REVERT: D 987 MET cc_start: 0.9189 (mmp) cc_final: 0.8899 (mmm) REVERT: D 989 PHE cc_start: 0.9031 (m-10) cc_final: 0.8740 (m-80) REVERT: D 1006 SER cc_start: 0.8790 (t) cc_final: 0.8129 (m) REVERT: D 1008 MET cc_start: 0.8396 (mmm) cc_final: 0.7918 (mmp) REVERT: E 232 LYS cc_start: 0.7826 (ptmt) cc_final: 0.7357 (ptpp) REVERT: E 235 LEU cc_start: 0.9406 (tt) cc_final: 0.9140 (tt) REVERT: E 239 MET cc_start: 0.8979 (mtm) cc_final: 0.8710 (mtp) REVERT: E 240 MET cc_start: 0.8637 (mtm) cc_final: 0.8375 (mmt) REVERT: E 242 ASP cc_start: 0.9174 (m-30) cc_final: 0.8839 (m-30) REVERT: E 253 PHE cc_start: 0.7312 (m-80) cc_final: 0.5213 (m-10) REVERT: E 298 LEU cc_start: 0.8648 (tp) cc_final: 0.8403 (tp) REVERT: E 341 LEU cc_start: 0.8890 (tp) cc_final: 0.8686 (tp) REVERT: E 403 GLU cc_start: 0.8741 (tt0) cc_final: 0.7962 (tp30) REVERT: E 405 LEU cc_start: 0.9541 (tt) cc_final: 0.9249 (mt) REVERT: E 408 MET cc_start: 0.8796 (mmm) cc_final: 0.7981 (mmm) REVERT: E 415 CYS cc_start: 0.9138 (t) cc_final: 0.8818 (t) REVERT: E 417 ILE cc_start: 0.9478 (mt) cc_final: 0.9265 (tp) REVERT: E 520 PHE cc_start: 0.7884 (m-80) cc_final: 0.7538 (m-10) REVERT: E 526 GLN cc_start: 0.9338 (tt0) cc_final: 0.8482 (tt0) REVERT: E 527 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8451 (tt0) REVERT: E 532 MET cc_start: 0.8465 (tpt) cc_final: 0.8180 (tpt) REVERT: E 557 ASP cc_start: 0.7879 (t0) cc_final: 0.7184 (t0) REVERT: E 575 PHE cc_start: 0.8536 (m-80) cc_final: 0.8244 (m-80) REVERT: E 576 VAL cc_start: 0.9508 (t) cc_final: 0.9282 (t) REVERT: E 730 CYS cc_start: 0.8597 (p) cc_final: 0.8266 (p) REVERT: E 738 SER cc_start: 0.9245 (p) cc_final: 0.9004 (m) REVERT: E 790 ILE cc_start: 0.8860 (mm) cc_final: 0.8097 (tp) REVERT: E 802 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7307 (mt-10) REVERT: E 831 LYS cc_start: 0.8654 (mttt) cc_final: 0.7362 (mttt) REVERT: E 940 ASP cc_start: 0.8726 (m-30) cc_final: 0.8167 (t70) REVERT: E 989 PHE cc_start: 0.8816 (m-10) cc_final: 0.8285 (m-80) REVERT: F 142 LYS cc_start: 0.8946 (pttm) cc_final: 0.8746 (pttm) REVERT: F 238 LYS cc_start: 0.8400 (tttt) cc_final: 0.7900 (mmmt) REVERT: F 239 MET cc_start: 0.9106 (mtm) cc_final: 0.7866 (mmp) REVERT: F 242 ASP cc_start: 0.9223 (m-30) cc_final: 0.8991 (m-30) REVERT: F 253 PHE cc_start: 0.7517 (m-80) cc_final: 0.7164 (m-10) REVERT: F 381 TYR cc_start: 0.8398 (t80) cc_final: 0.7984 (t80) REVERT: F 403 GLU cc_start: 0.8624 (tt0) cc_final: 0.7835 (tp30) REVERT: F 407 THR cc_start: 0.9319 (m) cc_final: 0.8961 (p) REVERT: F 409 CYS cc_start: 0.9016 (m) cc_final: 0.8729 (t) REVERT: F 415 CYS cc_start: 0.9115 (t) cc_final: 0.8052 (t) REVERT: F 419 CYS cc_start: 0.7981 (m) cc_final: 0.7736 (m) REVERT: F 517 PHE cc_start: 0.7498 (p90) cc_final: 0.6975 (p90) REVERT: F 527 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8507 (mp0) REVERT: F 532 MET cc_start: 0.8323 (tpp) cc_final: 0.8075 (tpp) REVERT: F 557 ASP cc_start: 0.7716 (t0) cc_final: 0.7044 (t0) REVERT: F 730 CYS cc_start: 0.8639 (p) cc_final: 0.7987 (p) REVERT: F 738 SER cc_start: 0.9278 (p) cc_final: 0.9006 (m) REVERT: F 762 CYS cc_start: 0.8641 (m) cc_final: 0.8366 (p) REVERT: F 764 THR cc_start: 0.9226 (p) cc_final: 0.8970 (p) REVERT: F 802 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7024 (tt0) REVERT: F 831 LYS cc_start: 0.8724 (mttt) cc_final: 0.7617 (mttt) REVERT: F 937 LEU cc_start: 0.8386 (mt) cc_final: 0.8004 (pp) REVERT: F 940 ASP cc_start: 0.8928 (m-30) cc_final: 0.8366 (t70) REVERT: F 989 PHE cc_start: 0.8944 (m-10) cc_final: 0.8419 (m-80) outliers start: 4 outliers final: 2 residues processed: 823 average time/residue: 0.2083 time to fit residues: 295.3522 Evaluate side-chains 616 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 614 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 168 optimal weight: 5.9990 chunk 416 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 345 optimal weight: 5.9990 chunk 456 optimal weight: 4.9990 chunk 346 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 429 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 ASN B 506 ASN B 522 HIS ** B 663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 922 ASN C 220 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS D 922 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 922 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 HIS F 922 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.122188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.090579 restraints weight = 97327.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090900 restraints weight = 66664.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.092323 restraints weight = 60599.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092625 restraints weight = 44163.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.093038 restraints weight = 40751.717| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.6777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 40266 Z= 0.223 Angle : 0.696 12.304 54372 Z= 0.355 Chirality : 0.042 0.281 6156 Planarity : 0.004 0.056 6810 Dihedral : 10.910 175.526 5544 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.69 % Favored : 92.29 % Rotamer: Outliers : 0.02 % Allowed : 2.02 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.36 (0.12), residues: 4848 helix: 0.71 (0.11), residues: 2316 sheet: -1.41 (0.22), residues: 558 loop : -0.92 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 327 TYR 0.025 0.002 TYR E 861 PHE 0.047 0.002 PHE A 989 TRP 0.028 0.002 TRP A 959 HIS 0.010 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00496 (40266) covalent geometry : angle 0.69569 (54372) hydrogen bonds : bond 0.04281 ( 1721) hydrogen bonds : angle 4.81814 ( 4935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 768 time to evaluate : 1.639 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.9245 (mttt) cc_final: 0.8967 (pttm) REVERT: A 232 LYS cc_start: 0.8771 (ptpp) cc_final: 0.8469 (ptpp) REVERT: A 239 MET cc_start: 0.9205 (mtp) cc_final: 0.8277 (mmp) REVERT: A 242 ASP cc_start: 0.8849 (m-30) cc_final: 0.8632 (m-30) REVERT: A 253 PHE cc_start: 0.6807 (m-80) cc_final: 0.6516 (m-10) REVERT: A 275 LEU cc_start: 0.9111 (mp) cc_final: 0.8650 (mt) REVERT: A 393 ARG cc_start: 0.9417 (ttm-80) cc_final: 0.9101 (ttm-80) REVERT: A 403 GLU cc_start: 0.8556 (tt0) cc_final: 0.8001 (tp30) REVERT: A 521 ILE cc_start: 0.8260 (tt) cc_final: 0.7632 (tt) REVERT: A 526 GLN cc_start: 0.9271 (tt0) cc_final: 0.8718 (tt0) REVERT: A 527 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8782 (tt0) REVERT: A 532 MET cc_start: 0.8452 (tpt) cc_final: 0.8161 (tpt) REVERT: A 557 ASP cc_start: 0.8186 (t0) cc_final: 0.7467 (t0) REVERT: A 637 MET cc_start: 0.8945 (tmm) cc_final: 0.8603 (tmm) REVERT: A 738 SER cc_start: 0.9368 (p) cc_final: 0.9014 (m) REVERT: A 764 THR cc_start: 0.9264 (p) cc_final: 0.9052 (p) REVERT: A 802 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7212 (mt-10) REVERT: A 831 LYS cc_start: 0.8475 (mttt) cc_final: 0.7340 (mttt) REVERT: A 940 ASP cc_start: 0.8703 (m-30) cc_final: 0.8394 (m-30) REVERT: B 220 HIS cc_start: 0.8518 (m90) cc_final: 0.7709 (p-80) REVERT: B 235 LEU cc_start: 0.9420 (tp) cc_final: 0.9043 (tt) REVERT: B 239 MET cc_start: 0.9168 (mtm) cc_final: 0.8670 (mtp) REVERT: B 240 MET cc_start: 0.9188 (mmm) cc_final: 0.8540 (tpt) REVERT: B 242 ASP cc_start: 0.9121 (m-30) cc_final: 0.8796 (m-30) REVERT: B 253 PHE cc_start: 0.6970 (m-10) cc_final: 0.6379 (m-10) REVERT: B 403 GLU cc_start: 0.8584 (tt0) cc_final: 0.7918 (tp30) REVERT: B 518 TYR cc_start: 0.7095 (m-10) cc_final: 0.6677 (m-10) REVERT: B 532 MET cc_start: 0.8196 (tpp) cc_final: 0.7901 (tpp) REVERT: B 557 ASP cc_start: 0.7790 (t0) cc_final: 0.7151 (t0) REVERT: B 631 PHE cc_start: 0.8485 (m-80) cc_final: 0.8100 (m-80) REVERT: B 654 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8164 (tm-30) REVERT: B 669 CYS cc_start: 0.8529 (m) cc_final: 0.7993 (m) REVERT: B 802 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7172 (mt-10) REVERT: B 831 LYS cc_start: 0.8575 (mttt) cc_final: 0.7397 (mttt) REVERT: B 940 ASP cc_start: 0.8854 (m-30) cc_final: 0.8539 (m-30) REVERT: B 989 PHE cc_start: 0.8810 (m-80) cc_final: 0.8226 (m-80) REVERT: B 1008 MET cc_start: 0.8538 (mmm) cc_final: 0.8091 (mmp) REVERT: C 151 ILE cc_start: 0.8611 (mm) cc_final: 0.8206 (mt) REVERT: C 239 MET cc_start: 0.9142 (mtp) cc_final: 0.8046 (mmp) REVERT: C 240 MET cc_start: 0.8678 (mtm) cc_final: 0.8405 (mmt) REVERT: C 242 ASP cc_start: 0.9133 (m-30) cc_final: 0.8748 (m-30) REVERT: C 253 PHE cc_start: 0.7315 (m-80) cc_final: 0.6459 (m-80) REVERT: C 403 GLU cc_start: 0.8564 (tt0) cc_final: 0.7892 (tp30) REVERT: C 413 LEU cc_start: 0.9106 (tt) cc_final: 0.8856 (tp) REVERT: C 557 ASP cc_start: 0.7739 (t0) cc_final: 0.6988 (t0) REVERT: C 639 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8321 (tm-30) REVERT: C 730 CYS cc_start: 0.8671 (m) cc_final: 0.8423 (m) REVERT: C 802 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7585 (mt-10) REVERT: C 940 ASP cc_start: 0.8847 (m-30) cc_final: 0.8615 (m-30) REVERT: C 1008 MET cc_start: 0.8448 (mmm) cc_final: 0.8021 (mmm) REVERT: D 142 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8937 (pttm) REVERT: D 220 HIS cc_start: 0.8070 (m90) cc_final: 0.7829 (m90) REVERT: D 239 MET cc_start: 0.9202 (mtp) cc_final: 0.8240 (mmp) REVERT: D 242 ASP cc_start: 0.9111 (m-30) cc_final: 0.8713 (m-30) REVERT: D 253 PHE cc_start: 0.7312 (m-10) cc_final: 0.6839 (m-10) REVERT: D 381 TYR cc_start: 0.8665 (t80) cc_final: 0.7996 (t80) REVERT: D 403 GLU cc_start: 0.8645 (tt0) cc_final: 0.7642 (tp30) REVERT: D 409 CYS cc_start: 0.8909 (m) cc_final: 0.8192 (t) REVERT: D 415 CYS cc_start: 0.9019 (t) cc_final: 0.7919 (t) REVERT: D 419 CYS cc_start: 0.8067 (m) cc_final: 0.7622 (m) REVERT: D 518 TYR cc_start: 0.7293 (m-10) cc_final: 0.7019 (m-10) REVERT: D 526 GLN cc_start: 0.9097 (tt0) cc_final: 0.8511 (tt0) REVERT: D 532 MET cc_start: 0.8361 (tpp) cc_final: 0.8069 (tpp) REVERT: D 557 ASP cc_start: 0.7904 (t0) cc_final: 0.7162 (t0) REVERT: D 639 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8365 (tm-30) REVERT: D 654 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8073 (tm-30) REVERT: D 664 MET cc_start: 0.8044 (tpp) cc_final: 0.7592 (tpp) REVERT: D 802 GLU cc_start: 0.8246 (mt-10) cc_final: 0.6930 (mt-10) REVERT: D 831 LYS cc_start: 0.8620 (mttt) cc_final: 0.7437 (mttt) REVERT: D 940 ASP cc_start: 0.8859 (m-30) cc_final: 0.8572 (m-30) REVERT: D 987 MET cc_start: 0.9247 (mmp) cc_final: 0.8987 (mmm) REVERT: D 989 PHE cc_start: 0.8974 (m-10) cc_final: 0.8581 (m-80) REVERT: D 1008 MET cc_start: 0.8446 (mmm) cc_final: 0.7992 (mmm) REVERT: E 151 ILE cc_start: 0.8275 (mt) cc_final: 0.7901 (pt) REVERT: E 230 ILE cc_start: 0.9021 (pt) cc_final: 0.8758 (pt) REVERT: E 235 LEU cc_start: 0.9407 (tt) cc_final: 0.9113 (tt) REVERT: E 239 MET cc_start: 0.8957 (mtm) cc_final: 0.8700 (mtp) REVERT: E 242 ASP cc_start: 0.9167 (m-30) cc_final: 0.8845 (m-30) REVERT: E 253 PHE cc_start: 0.7257 (m-80) cc_final: 0.5949 (m-10) REVERT: E 255 TYR cc_start: 0.7377 (m-80) cc_final: 0.7068 (m-80) REVERT: E 275 LEU cc_start: 0.9073 (mp) cc_final: 0.8151 (mt) REVERT: E 403 GLU cc_start: 0.8696 (tt0) cc_final: 0.7936 (tp30) REVERT: E 405 LEU cc_start: 0.9523 (tt) cc_final: 0.9319 (mt) REVERT: E 408 MET cc_start: 0.9205 (mmm) cc_final: 0.8920 (mmm) REVERT: E 409 CYS cc_start: 0.8775 (m) cc_final: 0.8364 (t) REVERT: E 415 CYS cc_start: 0.8980 (t) cc_final: 0.8453 (t) REVERT: E 527 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8684 (mt-10) REVERT: E 557 ASP cc_start: 0.8044 (t0) cc_final: 0.7357 (t0) REVERT: E 661 MET cc_start: 0.8334 (tpp) cc_final: 0.7989 (tpt) REVERT: E 802 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7355 (mt-10) REVERT: E 831 LYS cc_start: 0.8504 (mttt) cc_final: 0.7243 (mttt) REVERT: E 940 ASP cc_start: 0.8769 (m-30) cc_final: 0.8208 (t70) REVERT: E 987 MET cc_start: 0.9087 (mmm) cc_final: 0.8874 (mmm) REVERT: E 989 PHE cc_start: 0.8719 (m-10) cc_final: 0.8263 (m-80) REVERT: F 238 LYS cc_start: 0.8390 (tttt) cc_final: 0.7928 (mmmt) REVERT: F 239 MET cc_start: 0.9110 (mtm) cc_final: 0.7916 (mmp) REVERT: F 253 PHE cc_start: 0.7284 (m-80) cc_final: 0.6904 (m-10) REVERT: F 403 GLU cc_start: 0.8565 (tt0) cc_final: 0.7885 (tp30) REVERT: F 407 THR cc_start: 0.9363 (m) cc_final: 0.8762 (p) REVERT: F 409 CYS cc_start: 0.9087 (m) cc_final: 0.8797 (t) REVERT: F 415 CYS cc_start: 0.8963 (t) cc_final: 0.8435 (t) REVERT: F 527 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8523 (mp0) REVERT: F 557 ASP cc_start: 0.7761 (t0) cc_final: 0.7115 (t0) REVERT: F 647 MET cc_start: 0.8524 (mmp) cc_final: 0.8262 (mmp) REVERT: F 762 CYS cc_start: 0.8615 (m) cc_final: 0.8134 (m) REVERT: F 793 VAL cc_start: 0.8879 (t) cc_final: 0.8638 (t) REVERT: F 802 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7005 (tt0) REVERT: F 831 LYS cc_start: 0.8526 (mttt) cc_final: 0.7250 (mttt) REVERT: F 940 ASP cc_start: 0.8961 (m-30) cc_final: 0.8402 (t0) REVERT: F 950 ASN cc_start: 0.8543 (t0) cc_final: 0.8246 (t0) REVERT: F 989 PHE cc_start: 0.8874 (m-10) cc_final: 0.8359 (m-80) outliers start: 1 outliers final: 0 residues processed: 768 average time/residue: 0.2063 time to fit residues: 274.5978 Evaluate side-chains 577 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 577 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 418 optimal weight: 0.0470 chunk 258 optimal weight: 9.9990 chunk 482 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 214 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 361 optimal weight: 3.9990 chunk 336 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 chunk 408 optimal weight: 5.9990 chunk 438 optimal weight: 10.0000 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 922 ASN ** B 663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 922 ASN C 506 ASN D 367 HIS ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS D 922 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 HIS E 922 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 HIS F 751 ASN F 922 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.123651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.091672 restraints weight = 97297.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091440 restraints weight = 63843.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092887 restraints weight = 56309.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093231 restraints weight = 42193.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093877 restraints weight = 39114.346| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40266 Z= 0.154 Angle : 0.659 14.118 54372 Z= 0.330 Chirality : 0.041 0.200 6156 Planarity : 0.004 0.087 6810 Dihedral : 10.884 178.007 5544 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.14 % Favored : 92.84 % Rotamer: Outliers : 0.04 % Allowed : 1.06 % Favored : 98.90 % 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: -0.44 (0.12), residues: 4848 helix: 0.64 (0.11), residues: 2322 sheet: -1.49 (0.22), residues: 558 loop : -0.96 (0.15), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 675 TYR 0.018 0.001 TYR F1009 PHE 0.029 0.002 PHE D 508 TRP 0.027 0.002 TRP B 959 HIS 0.007 0.001 HIS F 916 Details of bonding type rmsd covalent geometry : bond 0.00350 (40266) covalent geometry : angle 0.65895 (54372) hydrogen bonds : bond 0.03939 ( 1721) hydrogen bonds : angle 4.70502 ( 4935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 775 time to evaluate : 1.508 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.9249 (mttt) cc_final: 0.8954 (pttm) REVERT: A 151 ILE cc_start: 0.8572 (mm) cc_final: 0.8047 (mt) REVERT: A 239 MET cc_start: 0.9201 (mtp) cc_final: 0.8233 (mmp) REVERT: A 242 ASP cc_start: 0.8822 (m-30) cc_final: 0.8599 (m-30) REVERT: A 253 PHE cc_start: 0.6838 (m-80) cc_final: 0.6523 (m-10) REVERT: A 393 ARG cc_start: 0.9433 (ttm-80) cc_final: 0.9105 (ttm-80) REVERT: A 403 GLU cc_start: 0.8559 (tt0) cc_final: 0.8039 (tp30) REVERT: A 517 PHE cc_start: 0.7770 (p90) cc_final: 0.7362 (p90) REVERT: A 521 ILE cc_start: 0.8335 (tt) cc_final: 0.7813 (tt) REVERT: A 526 GLN cc_start: 0.9268 (tt0) cc_final: 0.8765 (tt0) REVERT: A 527 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8772 (tt0) REVERT: A 532 MET cc_start: 0.8521 (tpt) cc_final: 0.8178 (tpt) REVERT: A 557 ASP cc_start: 0.8062 (t0) cc_final: 0.7430 (t0) REVERT: A 639 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8242 (tm-30) REVERT: A 738 SER cc_start: 0.9379 (p) cc_final: 0.9015 (m) REVERT: A 764 THR cc_start: 0.9173 (p) cc_final: 0.8960 (p) REVERT: A 790 ILE cc_start: 0.8980 (mm) cc_final: 0.8659 (mm) REVERT: A 802 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7120 (mt-10) REVERT: A 831 LYS cc_start: 0.8653 (mttt) cc_final: 0.7577 (mttt) REVERT: A 940 ASP cc_start: 0.8704 (m-30) cc_final: 0.8388 (m-30) REVERT: A 989 PHE cc_start: 0.8991 (m-10) cc_final: 0.8636 (m-80) REVERT: B 151 ILE cc_start: 0.8676 (mm) cc_final: 0.8322 (mt) REVERT: B 220 HIS cc_start: 0.8344 (m90) cc_final: 0.7818 (p-80) REVERT: B 232 LYS cc_start: 0.8567 (ptpp) cc_final: 0.8270 (pttt) REVERT: B 235 LEU cc_start: 0.9386 (tp) cc_final: 0.9057 (tp) REVERT: B 239 MET cc_start: 0.9174 (mtm) cc_final: 0.8707 (mtp) REVERT: B 240 MET cc_start: 0.9183 (mmm) cc_final: 0.8522 (tpt) REVERT: B 242 ASP cc_start: 0.9113 (m-30) cc_final: 0.8752 (m-30) REVERT: B 347 LEU cc_start: 0.9534 (tt) cc_final: 0.9228 (mt) REVERT: B 403 GLU cc_start: 0.8645 (tt0) cc_final: 0.7982 (tp30) REVERT: B 518 TYR cc_start: 0.7141 (m-10) cc_final: 0.6730 (m-10) REVERT: B 526 GLN cc_start: 0.9251 (tt0) cc_final: 0.8701 (tt0) REVERT: B 532 MET cc_start: 0.8240 (tpp) cc_final: 0.7920 (tpp) REVERT: B 557 ASP cc_start: 0.7813 (t0) cc_final: 0.7119 (t0) REVERT: B 631 PHE cc_start: 0.8394 (m-80) cc_final: 0.8139 (m-10) REVERT: B 654 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8226 (tm-30) REVERT: B 802 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7139 (mt-10) REVERT: B 831 LYS cc_start: 0.8588 (mttt) cc_final: 0.7574 (mttt) REVERT: B 940 ASP cc_start: 0.8859 (m-30) cc_final: 0.8549 (m-30) REVERT: B 989 PHE cc_start: 0.8837 (m-80) cc_final: 0.8248 (m-80) REVERT: B 1006 SER cc_start: 0.8428 (m) cc_final: 0.7589 (m) REVERT: B 1008 MET cc_start: 0.8480 (mmm) cc_final: 0.8083 (mmp) REVERT: C 151 ILE cc_start: 0.8676 (mm) cc_final: 0.8322 (mt) REVERT: C 239 MET cc_start: 0.9049 (mtp) cc_final: 0.8005 (mmp) REVERT: C 240 MET cc_start: 0.8630 (mtm) cc_final: 0.8425 (mmt) REVERT: C 242 ASP cc_start: 0.9158 (m-30) cc_final: 0.8756 (m-30) REVERT: C 253 PHE cc_start: 0.7167 (m-80) cc_final: 0.6563 (m-80) REVERT: C 403 GLU cc_start: 0.8650 (tt0) cc_final: 0.7876 (tp30) REVERT: C 413 LEU cc_start: 0.9049 (tt) cc_final: 0.8822 (mt) REVERT: C 557 ASP cc_start: 0.7667 (t0) cc_final: 0.6865 (t0) REVERT: C 639 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8331 (tm-30) REVERT: C 730 CYS cc_start: 0.8675 (m) cc_final: 0.8387 (m) REVERT: C 802 GLU cc_start: 0.8239 (mt-10) cc_final: 0.6762 (mt-10) REVERT: C 831 LYS cc_start: 0.8731 (mttt) cc_final: 0.7603 (mttt) REVERT: C 1008 MET cc_start: 0.8425 (mmm) cc_final: 0.8073 (mmm) REVERT: D 142 LYS cc_start: 0.9187 (mtmm) cc_final: 0.8951 (pttm) REVERT: D 151 ILE cc_start: 0.8461 (mm) cc_final: 0.8132 (mt) REVERT: D 220 HIS cc_start: 0.8106 (m90) cc_final: 0.7854 (m90) REVERT: D 232 LYS cc_start: 0.8581 (ptpp) cc_final: 0.8380 (ptpp) REVERT: D 239 MET cc_start: 0.9192 (mtp) cc_final: 0.8223 (mmp) REVERT: D 242 ASP cc_start: 0.9107 (m-30) cc_final: 0.8679 (m-30) REVERT: D 253 PHE cc_start: 0.7320 (m-10) cc_final: 0.6829 (m-10) REVERT: D 381 TYR cc_start: 0.8601 (t80) cc_final: 0.8030 (t80) REVERT: D 403 GLU cc_start: 0.8539 (tt0) cc_final: 0.7587 (tp30) REVERT: D 409 CYS cc_start: 0.8914 (m) cc_final: 0.8105 (t) REVERT: D 415 CYS cc_start: 0.9064 (t) cc_final: 0.7747 (t) REVERT: D 419 CYS cc_start: 0.8144 (m) cc_final: 0.7298 (p) REVERT: D 508 PHE cc_start: 0.7964 (m-80) cc_final: 0.7678 (m-80) REVERT: D 518 TYR cc_start: 0.7322 (m-10) cc_final: 0.7093 (m-10) REVERT: D 532 MET cc_start: 0.8287 (tpp) cc_final: 0.8041 (tpp) REVERT: D 557 ASP cc_start: 0.7757 (t0) cc_final: 0.6997 (t0) REVERT: D 639 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8388 (tm-30) REVERT: D 654 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8036 (tm-30) REVERT: D 664 MET cc_start: 0.8039 (tpp) cc_final: 0.7475 (tpp) REVERT: D 802 GLU cc_start: 0.8178 (mt-10) cc_final: 0.6855 (mt-10) REVERT: D 831 LYS cc_start: 0.8620 (mttt) cc_final: 0.7362 (mttt) REVERT: D 987 MET cc_start: 0.9279 (mmp) cc_final: 0.9057 (mmm) REVERT: D 988 MET cc_start: 0.8684 (tpp) cc_final: 0.8456 (tpp) REVERT: D 989 PHE cc_start: 0.9009 (m-10) cc_final: 0.8609 (m-80) REVERT: E 239 MET cc_start: 0.9011 (mtm) cc_final: 0.7802 (mmp) REVERT: E 242 ASP cc_start: 0.9150 (m-30) cc_final: 0.8740 (m-30) REVERT: E 253 PHE cc_start: 0.7365 (m-80) cc_final: 0.5947 (m-10) REVERT: E 256 LEU cc_start: 0.8640 (tp) cc_final: 0.8221 (mp) REVERT: E 275 LEU cc_start: 0.9041 (mp) cc_final: 0.8714 (mt) REVERT: E 298 LEU cc_start: 0.8526 (tp) cc_final: 0.8102 (tp) REVERT: E 326 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6714 (mt-10) REVERT: E 350 THR cc_start: 0.8303 (t) cc_final: 0.7880 (t) REVERT: E 403 GLU cc_start: 0.8742 (tt0) cc_final: 0.7970 (tp30) REVERT: E 405 LEU cc_start: 0.9499 (tt) cc_final: 0.9216 (mt) REVERT: E 408 MET cc_start: 0.9060 (mmm) cc_final: 0.8691 (mmm) REVERT: E 415 CYS cc_start: 0.9098 (t) cc_final: 0.8648 (t) REVERT: E 520 PHE cc_start: 0.8006 (m-80) cc_final: 0.7495 (m-80) REVERT: E 526 GLN cc_start: 0.9321 (tt0) cc_final: 0.8490 (tt0) REVERT: E 527 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8656 (mt-10) REVERT: E 532 MET cc_start: 0.8345 (tpp) cc_final: 0.8055 (tpp) REVERT: E 557 ASP cc_start: 0.8000 (t0) cc_final: 0.7348 (t0) REVERT: E 661 MET cc_start: 0.8258 (tpp) cc_final: 0.7860 (tpt) REVERT: E 730 CYS cc_start: 0.8485 (p) cc_final: 0.8122 (p) REVERT: E 790 ILE cc_start: 0.8787 (mm) cc_final: 0.8071 (tp) REVERT: E 802 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7247 (mt-10) REVERT: E 831 LYS cc_start: 0.8527 (mttt) cc_final: 0.7266 (mttt) REVERT: E 940 ASP cc_start: 0.8746 (m-30) cc_final: 0.8191 (t70) REVERT: E 987 MET cc_start: 0.9150 (mmm) cc_final: 0.8938 (mmm) REVERT: E 989 PHE cc_start: 0.8732 (m-10) cc_final: 0.8245 (m-80) REVERT: E 1006 SER cc_start: 0.8449 (m) cc_final: 0.7641 (m) REVERT: E 1008 MET cc_start: 0.8476 (mmm) cc_final: 0.8177 (mmm) REVERT: F 238 LYS cc_start: 0.8352 (tttt) cc_final: 0.7912 (mmmt) REVERT: F 239 MET cc_start: 0.9144 (mtm) cc_final: 0.7884 (mmp) REVERT: F 242 ASP cc_start: 0.9150 (m-30) cc_final: 0.8943 (m-30) REVERT: F 253 PHE cc_start: 0.7520 (m-80) cc_final: 0.7080 (m-80) REVERT: F 403 GLU cc_start: 0.8594 (tt0) cc_final: 0.7901 (tp30) REVERT: F 405 LEU cc_start: 0.9522 (tt) cc_final: 0.9296 (mt) REVERT: F 407 THR cc_start: 0.9350 (m) cc_final: 0.8703 (p) REVERT: F 409 CYS cc_start: 0.9153 (m) cc_final: 0.8911 (t) REVERT: F 415 CYS cc_start: 0.8962 (t) cc_final: 0.8734 (p) REVERT: F 526 GLN cc_start: 0.9279 (tt0) cc_final: 0.8663 (tt0) REVERT: F 527 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8501 (mt-10) REVERT: F 532 MET cc_start: 0.8320 (tpp) cc_final: 0.8040 (tpp) REVERT: F 557 ASP cc_start: 0.7805 (t0) cc_final: 0.7151 (t0) REVERT: F 647 MET cc_start: 0.8577 (mmp) cc_final: 0.8228 (mmp) REVERT: F 738 SER cc_start: 0.9371 (p) cc_final: 0.9060 (m) REVERT: F 764 THR cc_start: 0.9260 (p) cc_final: 0.9005 (p) REVERT: F 802 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7012 (tt0) REVERT: F 831 LYS cc_start: 0.8588 (mttt) cc_final: 0.7273 (mttt) REVERT: F 989 PHE cc_start: 0.8920 (m-10) cc_final: 0.8367 (m-80) outliers start: 2 outliers final: 0 residues processed: 775 average time/residue: 0.2082 time to fit residues: 278.0506 Evaluate side-chains 599 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 599 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 339 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 355 optimal weight: 0.9990 chunk 359 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 364 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 433 optimal weight: 3.9990 chunk 382 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 922 ASN B 522 HIS B 922 ASN C 922 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS D 922 ASN E 367 HIS ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 HIS ** E 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 922 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 HIS F 922 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.123786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.091772 restraints weight = 97237.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091779 restraints weight = 63950.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092844 restraints weight = 56700.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093834 restraints weight = 43020.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.094414 restraints weight = 38437.144| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.7216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40266 Z= 0.143 Angle : 0.649 13.818 54372 Z= 0.324 Chirality : 0.040 0.209 6156 Planarity : 0.004 0.066 6810 Dihedral : 10.810 176.538 5544 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.59 % Favored : 92.39 % Rotamer: Outliers : 0.07 % Allowed : 0.43 % Favored : 99.51 % 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: -0.41 (0.12), residues: 4848 helix: 0.62 (0.11), residues: 2358 sheet: -1.46 (0.22), residues: 558 loop : -0.90 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 675 TYR 0.017 0.001 TYR F1009 PHE 0.042 0.002 PHE E 406 TRP 0.028 0.001 TRP B 959 HIS 0.008 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00323 (40266) covalent geometry : angle 0.64891 (54372) hydrogen bonds : bond 0.03801 ( 1721) hydrogen bonds : angle 4.68679 ( 4935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 759 time to evaluate : 1.513 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: 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 142 LYS cc_start: 0.9264 (mttt) cc_final: 0.8956 (pttm) REVERT: A 151 ILE cc_start: 0.8574 (mm) cc_final: 0.8087 (mt) REVERT: A 239 MET cc_start: 0.9193 (mtp) cc_final: 0.8217 (mmp) REVERT: A 242 ASP cc_start: 0.8810 (m-30) cc_final: 0.8561 (m-30) REVERT: A 253 PHE cc_start: 0.6834 (m-80) cc_final: 0.6198 (m-10) REVERT: A 393 ARG cc_start: 0.9442 (ttm-80) cc_final: 0.9113 (ttm-80) REVERT: A 403 GLU cc_start: 0.8597 (tt0) cc_final: 0.8082 (tp30) REVERT: A 517 PHE cc_start: 0.7814 (p90) cc_final: 0.7388 (p90) REVERT: A 521 ILE cc_start: 0.8249 (tt) cc_final: 0.7750 (tt) REVERT: A 526 GLN cc_start: 0.9257 (tt0) cc_final: 0.8657 (tt0) REVERT: A 527 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8558 (mt-10) REVERT: A 532 MET cc_start: 0.8499 (tpt) cc_final: 0.8142 (tpt) REVERT: A 557 ASP cc_start: 0.8015 (t0) cc_final: 0.7362 (t0) REVERT: A 738 SER cc_start: 0.9386 (p) cc_final: 0.8954 (m) REVERT: A 764 THR cc_start: 0.9121 (p) cc_final: 0.8888 (p) REVERT: A 790 ILE cc_start: 0.8754 (mm) cc_final: 0.8444 (mm) REVERT: A 802 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7015 (mt-10) REVERT: A 831 LYS cc_start: 0.8466 (mttt) cc_final: 0.7294 (mttt) REVERT: A 989 PHE cc_start: 0.9025 (m-10) cc_final: 0.8701 (m-80) REVERT: B 151 ILE cc_start: 0.8690 (mm) cc_final: 0.8384 (mt) REVERT: B 235 LEU cc_start: 0.9383 (tp) cc_final: 0.9059 (tt) REVERT: B 239 MET cc_start: 0.9129 (mtm) cc_final: 0.8643 (mtp) REVERT: B 240 MET cc_start: 0.9194 (mmm) cc_final: 0.8554 (tpt) REVERT: B 242 ASP cc_start: 0.9110 (m-30) cc_final: 0.8754 (m-30) REVERT: B 253 PHE cc_start: 0.6985 (m-10) cc_final: 0.6709 (m-10) REVERT: B 275 LEU cc_start: 0.9166 (mt) cc_final: 0.8915 (mt) REVERT: B 403 GLU cc_start: 0.8606 (tt0) cc_final: 0.7987 (tp30) REVERT: B 518 TYR cc_start: 0.7154 (m-10) cc_final: 0.6752 (m-10) REVERT: B 532 MET cc_start: 0.8233 (tpp) cc_final: 0.7898 (tpp) REVERT: B 533 TYR cc_start: 0.8182 (t80) cc_final: 0.7944 (t80) REVERT: B 557 ASP cc_start: 0.7753 (t0) cc_final: 0.7103 (t0) REVERT: B 631 PHE cc_start: 0.8379 (m-80) cc_final: 0.8022 (m-10) REVERT: B 654 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8225 (tm-30) REVERT: B 802 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7085 (mt-10) REVERT: B 831 LYS cc_start: 0.8503 (mttt) cc_final: 0.7431 (mttt) REVERT: B 940 ASP cc_start: 0.8869 (m-30) cc_final: 0.8566 (m-30) REVERT: B 989 PHE cc_start: 0.8820 (m-80) cc_final: 0.8264 (m-80) REVERT: C 151 ILE cc_start: 0.8710 (mm) cc_final: 0.8370 (mt) REVERT: C 239 MET cc_start: 0.9076 (mtp) cc_final: 0.8046 (mmp) REVERT: C 240 MET cc_start: 0.8645 (mtm) cc_final: 0.8427 (mmt) REVERT: C 242 ASP cc_start: 0.9153 (m-30) cc_final: 0.8768 (m-30) REVERT: C 253 PHE cc_start: 0.7229 (m-80) cc_final: 0.6720 (m-80) REVERT: C 403 GLU cc_start: 0.8568 (tt0) cc_final: 0.8066 (tp30) REVERT: C 413 LEU cc_start: 0.9042 (tt) cc_final: 0.8828 (mt) REVERT: C 557 ASP cc_start: 0.7570 (t0) cc_final: 0.6800 (t0) REVERT: C 730 CYS cc_start: 0.8641 (m) cc_final: 0.8361 (m) REVERT: C 802 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7300 (mt-10) REVERT: C 831 LYS cc_start: 0.8735 (mttt) cc_final: 0.7814 (mttm) REVERT: C 940 ASP cc_start: 0.8845 (m-30) cc_final: 0.8621 (m-30) REVERT: C 989 PHE cc_start: 0.8780 (m-80) cc_final: 0.8376 (m-80) REVERT: C 1008 MET cc_start: 0.8498 (mmm) cc_final: 0.8063 (mmm) REVERT: D 142 LYS cc_start: 0.9193 (mtmm) cc_final: 0.8958 (pttm) REVERT: D 151 ILE cc_start: 0.8475 (mm) cc_final: 0.8253 (mt) REVERT: D 220 HIS cc_start: 0.8189 (m90) cc_final: 0.7928 (m90) REVERT: D 239 MET cc_start: 0.9165 (mtp) cc_final: 0.8188 (mmp) REVERT: D 242 ASP cc_start: 0.9087 (m-30) cc_final: 0.8673 (m-30) REVERT: D 253 PHE cc_start: 0.7317 (m-10) cc_final: 0.6783 (m-10) REVERT: D 381 TYR cc_start: 0.8598 (t80) cc_final: 0.8060 (t80) REVERT: D 403 GLU cc_start: 0.8479 (tt0) cc_final: 0.7514 (tp30) REVERT: D 408 MET cc_start: 0.8907 (mmm) cc_final: 0.8472 (mmm) REVERT: D 409 CYS cc_start: 0.8920 (m) cc_final: 0.8061 (t) REVERT: D 415 CYS cc_start: 0.9051 (t) cc_final: 0.7893 (t) REVERT: D 419 CYS cc_start: 0.8137 (m) cc_final: 0.7724 (m) REVERT: D 508 PHE cc_start: 0.8143 (m-80) cc_final: 0.7851 (m-10) REVERT: D 526 GLN cc_start: 0.9046 (tt0) cc_final: 0.8513 (tt0) REVERT: D 532 MET cc_start: 0.8328 (tpp) cc_final: 0.7976 (tpp) REVERT: D 557 ASP cc_start: 0.7690 (t0) cc_final: 0.6999 (t0) REVERT: D 654 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8041 (tm-30) REVERT: D 661 MET cc_start: 0.8632 (tpt) cc_final: 0.8281 (tpt) REVERT: D 664 MET cc_start: 0.8048 (tpp) cc_final: 0.7484 (tpp) REVERT: D 802 GLU cc_start: 0.8141 (mt-10) cc_final: 0.6804 (mt-10) REVERT: D 831 LYS cc_start: 0.8602 (mttt) cc_final: 0.7542 (mttt) REVERT: D 987 MET cc_start: 0.9282 (mmp) cc_final: 0.9045 (mmm) REVERT: D 989 PHE cc_start: 0.9002 (m-10) cc_final: 0.8581 (m-80) REVERT: E 235 LEU cc_start: 0.9377 (tt) cc_final: 0.9085 (tt) REVERT: E 239 MET cc_start: 0.9068 (mtm) cc_final: 0.8809 (mtp) REVERT: E 242 ASP cc_start: 0.9145 (m-30) cc_final: 0.8862 (m-30) REVERT: E 253 PHE cc_start: 0.7322 (m-80) cc_final: 0.5898 (m-10) REVERT: E 326 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7211 (mt-10) REVERT: E 403 GLU cc_start: 0.8703 (tt0) cc_final: 0.7968 (tp30) REVERT: E 409 CYS cc_start: 0.8960 (m) cc_final: 0.8352 (t) REVERT: E 415 CYS cc_start: 0.9122 (t) cc_final: 0.8495 (t) REVERT: E 520 PHE cc_start: 0.7984 (m-80) cc_final: 0.7415 (m-10) REVERT: E 526 GLN cc_start: 0.9312 (tt0) cc_final: 0.8503 (tt0) REVERT: E 527 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8579 (mp0) REVERT: E 557 ASP cc_start: 0.7928 (t0) cc_final: 0.7267 (t0) REVERT: E 661 MET cc_start: 0.8181 (tpp) cc_final: 0.7934 (tpt) REVERT: E 730 CYS cc_start: 0.8356 (p) cc_final: 0.7969 (p) REVERT: E 802 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7252 (mt-10) REVERT: E 831 LYS cc_start: 0.8696 (mttt) cc_final: 0.7488 (mttt) REVERT: E 940 ASP cc_start: 0.8764 (m-30) cc_final: 0.8201 (t70) REVERT: E 987 MET cc_start: 0.9198 (mmm) cc_final: 0.8961 (mmm) REVERT: E 989 PHE cc_start: 0.8704 (m-10) cc_final: 0.8248 (m-80) REVERT: F 238 LYS cc_start: 0.8272 (tttt) cc_final: 0.7837 (mmmt) REVERT: F 239 MET cc_start: 0.9098 (mtm) cc_final: 0.7837 (mmp) REVERT: F 242 ASP cc_start: 0.9134 (m-30) cc_final: 0.8866 (m-30) REVERT: F 253 PHE cc_start: 0.7497 (m-80) cc_final: 0.7088 (m-80) REVERT: F 403 GLU cc_start: 0.8555 (tt0) cc_final: 0.7890 (tp30) REVERT: F 405 LEU cc_start: 0.9583 (tt) cc_final: 0.9308 (mt) REVERT: F 407 THR cc_start: 0.9272 (m) cc_final: 0.8643 (p) REVERT: F 408 MET cc_start: 0.9310 (mtm) cc_final: 0.8919 (mmm) REVERT: F 409 CYS cc_start: 0.9165 (m) cc_final: 0.8887 (t) REVERT: F 527 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8526 (mt-10) REVERT: F 532 MET cc_start: 0.8319 (tpp) cc_final: 0.8015 (tpp) REVERT: F 557 ASP cc_start: 0.7929 (t0) cc_final: 0.7275 (t0) REVERT: F 647 MET cc_start: 0.8534 (mmp) cc_final: 0.8195 (mmp) REVERT: F 654 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8225 (tm-30) REVERT: F 738 SER cc_start: 0.9388 (p) cc_final: 0.9066 (m) REVERT: F 762 CYS cc_start: 0.8790 (m) cc_final: 0.8453 (p) REVERT: F 764 THR cc_start: 0.9214 (p) cc_final: 0.8916 (p) REVERT: F 802 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7097 (tt0) REVERT: F 831 LYS cc_start: 0.8551 (mttt) cc_final: 0.7268 (mttt) REVERT: F 950 ASN cc_start: 0.8457 (t0) cc_final: 0.8144 (m-40) REVERT: F 989 PHE cc_start: 0.8870 (m-10) cc_final: 0.8367 (m-80) outliers start: 3 outliers final: 0 residues processed: 759 average time/residue: 0.2011 time to fit residues: 263.1528 Evaluate side-chains 580 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 chunk 395 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 437 optimal weight: 2.9990 chunk 454 optimal weight: 1.9990 chunk 389 optimal weight: 3.9990 chunk 193 optimal weight: 0.0070 chunk 300 optimal weight: 0.3980 chunk 399 optimal weight: 9.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 751 ASN A 922 ASN B 220 HIS B 522 HIS B 922 ASN C 391 GLN C 922 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS D 922 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 ASN E 522 HIS E 751 ASN ** E 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 922 ASN ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 HIS F 751 ASN F 922 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.124856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.090522 restraints weight = 96377.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.092412 restraints weight = 66270.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.093100 restraints weight = 46351.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.093358 restraints weight = 38592.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.093578 restraints weight = 35860.582| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.7329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 40266 Z= 0.125 Angle : 0.650 14.308 54372 Z= 0.321 Chirality : 0.040 0.225 6156 Planarity : 0.003 0.050 6810 Dihedral : 10.796 175.943 5544 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.10 % Favored : 92.88 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % 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: -0.38 (0.12), residues: 4848 helix: 0.64 (0.11), residues: 2358 sheet: -1.41 (0.22), residues: 558 loop : -0.89 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 327 TYR 0.019 0.001 TYR C 533 PHE 0.029 0.002 PHE A 508 TRP 0.029 0.001 TRP B 959 HIS 0.006 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00284 (40266) covalent geometry : angle 0.64957 (54372) hydrogen bonds : bond 0.03689 ( 1721) hydrogen bonds : angle 4.67939 ( 4935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 752 time to evaluate : 1.465 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: 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 142 LYS cc_start: 0.9299 (mttt) cc_final: 0.8972 (pttm) REVERT: A 151 ILE cc_start: 0.8544 (mm) cc_final: 0.8134 (mt) REVERT: A 239 MET cc_start: 0.9202 (mtp) cc_final: 0.8201 (mmp) REVERT: A 242 ASP cc_start: 0.8823 (m-30) cc_final: 0.8550 (m-30) REVERT: A 251 ASP cc_start: 0.8446 (p0) cc_final: 0.8066 (m-30) REVERT: A 253 PHE cc_start: 0.6808 (m-80) cc_final: 0.6468 (m-10) REVERT: A 393 ARG cc_start: 0.9460 (ttm-80) cc_final: 0.9110 (ttm-80) REVERT: A 403 GLU cc_start: 0.8607 (tt0) cc_final: 0.8082 (tp30) REVERT: A 405 LEU cc_start: 0.9607 (tp) cc_final: 0.9239 (mm) REVERT: A 517 PHE cc_start: 0.7802 (p90) cc_final: 0.7385 (p90) REVERT: A 521 ILE cc_start: 0.8241 (tt) cc_final: 0.7754 (tt) REVERT: A 526 GLN cc_start: 0.9254 (tt0) cc_final: 0.8646 (tt0) REVERT: A 527 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8517 (mt-10) REVERT: A 532 MET cc_start: 0.8498 (tpt) cc_final: 0.8147 (tpt) REVERT: A 557 ASP cc_start: 0.8126 (t0) cc_final: 0.7455 (t0) REVERT: A 738 SER cc_start: 0.9374 (p) cc_final: 0.8970 (m) REVERT: A 762 CYS cc_start: 0.8687 (m) cc_final: 0.8123 (p) REVERT: A 764 THR cc_start: 0.9103 (p) cc_final: 0.8834 (p) REVERT: A 789 ASP cc_start: 0.7437 (m-30) cc_final: 0.7124 (m-30) REVERT: A 790 ILE cc_start: 0.8875 (mm) cc_final: 0.8193 (tp) REVERT: A 802 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7566 (mt-10) REVERT: A 831 LYS cc_start: 0.8691 (mttt) cc_final: 0.7688 (mttm) REVERT: A 989 PHE cc_start: 0.9034 (m-10) cc_final: 0.8606 (m-80) REVERT: B 232 LYS cc_start: 0.8477 (ptpp) cc_final: 0.8235 (pttt) REVERT: B 235 LEU cc_start: 0.9341 (tp) cc_final: 0.9087 (tp) REVERT: B 239 MET cc_start: 0.9131 (mtm) cc_final: 0.8666 (mtp) REVERT: B 240 MET cc_start: 0.9189 (mmm) cc_final: 0.8584 (tpt) REVERT: B 242 ASP cc_start: 0.9128 (m-30) cc_final: 0.8767 (m-30) REVERT: B 253 PHE cc_start: 0.6899 (m-10) cc_final: 0.6363 (m-10) REVERT: B 275 LEU cc_start: 0.9128 (mt) cc_final: 0.8926 (mt) REVERT: B 403 GLU cc_start: 0.8703 (tt0) cc_final: 0.8050 (tp30) REVERT: B 507 LEU cc_start: 0.8771 (tt) cc_final: 0.8006 (tt) REVERT: B 518 TYR cc_start: 0.7201 (m-10) cc_final: 0.6826 (m-10) REVERT: B 526 GLN cc_start: 0.9092 (tt0) cc_final: 0.8552 (tt0) REVERT: B 532 MET cc_start: 0.8266 (tpp) cc_final: 0.7911 (tpp) REVERT: B 533 TYR cc_start: 0.8156 (t80) cc_final: 0.7902 (t80) REVERT: B 557 ASP cc_start: 0.7723 (t0) cc_final: 0.7149 (t0) REVERT: B 631 PHE cc_start: 0.8435 (m-80) cc_final: 0.8076 (m-10) REVERT: B 654 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8162 (tm-30) REVERT: B 730 CYS cc_start: 0.8858 (m) cc_final: 0.8652 (m) REVERT: B 802 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7101 (mt-10) REVERT: B 822 LEU cc_start: 0.8953 (mt) cc_final: 0.8740 (mt) REVERT: B 831 LYS cc_start: 0.8753 (mttt) cc_final: 0.7676 (mttt) REVERT: B 929 ILE cc_start: 0.9546 (tt) cc_final: 0.9330 (tt) REVERT: B 959 TRP cc_start: 0.8219 (t60) cc_final: 0.7932 (t60) REVERT: B 989 PHE cc_start: 0.8824 (m-80) cc_final: 0.8255 (m-80) REVERT: C 151 ILE cc_start: 0.8747 (mm) cc_final: 0.8512 (mt) REVERT: C 232 LYS cc_start: 0.8008 (pttt) cc_final: 0.7584 (ptpp) REVERT: C 239 MET cc_start: 0.9094 (mtp) cc_final: 0.8041 (mmp) REVERT: C 240 MET cc_start: 0.8629 (mtm) cc_final: 0.8411 (mmt) REVERT: C 242 ASP cc_start: 0.9137 (m-30) cc_final: 0.8778 (m-30) REVERT: C 253 PHE cc_start: 0.7089 (m-80) cc_final: 0.6738 (m-80) REVERT: C 350 THR cc_start: 0.8240 (t) cc_final: 0.7807 (t) REVERT: C 403 GLU cc_start: 0.8756 (tt0) cc_final: 0.7994 (tp30) REVERT: C 526 GLN cc_start: 0.9055 (tt0) cc_final: 0.8471 (tt0) REVERT: C 527 GLU cc_start: 0.8858 (pm20) cc_final: 0.7942 (pt0) REVERT: C 557 ASP cc_start: 0.7643 (t0) cc_final: 0.6925 (t0) REVERT: C 639 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8283 (tm-30) REVERT: C 730 CYS cc_start: 0.8746 (m) cc_final: 0.8412 (m) REVERT: C 802 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7335 (mt-10) REVERT: C 831 LYS cc_start: 0.8753 (mttt) cc_final: 0.7725 (mttp) REVERT: C 1008 MET cc_start: 0.8442 (mmm) cc_final: 0.7967 (mmm) REVERT: D 151 ILE cc_start: 0.8533 (mm) cc_final: 0.8305 (mt) REVERT: D 220 HIS cc_start: 0.8218 (m90) cc_final: 0.7938 (m90) REVERT: D 239 MET cc_start: 0.9160 (mtp) cc_final: 0.8191 (mmp) REVERT: D 242 ASP cc_start: 0.9113 (m-30) cc_final: 0.8667 (m-30) REVERT: D 253 PHE cc_start: 0.7359 (m-10) cc_final: 0.6803 (m-10) REVERT: D 302 ASP cc_start: 0.7373 (t0) cc_final: 0.6893 (t0) REVERT: D 381 TYR cc_start: 0.8574 (t80) cc_final: 0.8078 (t80) REVERT: D 403 GLU cc_start: 0.8522 (tt0) cc_final: 0.7575 (tp30) REVERT: D 408 MET cc_start: 0.8871 (mmm) cc_final: 0.8374 (mmm) REVERT: D 415 CYS cc_start: 0.9109 (t) cc_final: 0.8009 (t) REVERT: D 419 CYS cc_start: 0.8177 (m) cc_final: 0.7276 (p) REVERT: D 508 PHE cc_start: 0.8140 (m-80) cc_final: 0.7856 (m-10) REVERT: D 526 GLN cc_start: 0.9045 (tt0) cc_final: 0.8540 (tt0) REVERT: D 532 MET cc_start: 0.8343 (tpp) cc_final: 0.7970 (tpp) REVERT: D 557 ASP cc_start: 0.7635 (t0) cc_final: 0.6939 (t0) REVERT: D 630 LEU cc_start: 0.9055 (mp) cc_final: 0.8682 (mp) REVERT: D 639 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8326 (tm-30) REVERT: D 654 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8071 (tm-30) REVERT: D 661 MET cc_start: 0.8601 (tpt) cc_final: 0.8285 (tpt) REVERT: D 664 MET cc_start: 0.8071 (tpp) cc_final: 0.7510 (tpp) REVERT: D 802 GLU cc_start: 0.8141 (mt-10) cc_final: 0.6954 (mt-10) REVERT: D 831 LYS cc_start: 0.8774 (mttt) cc_final: 0.7875 (mttt) REVERT: D 987 MET cc_start: 0.9297 (mmp) cc_final: 0.9056 (mmm) REVERT: D 989 PHE cc_start: 0.8995 (m-10) cc_final: 0.8573 (m-80) REVERT: E 235 LEU cc_start: 0.9338 (tt) cc_final: 0.9066 (tt) REVERT: E 239 MET cc_start: 0.8924 (mtm) cc_final: 0.8693 (mtp) REVERT: E 242 ASP cc_start: 0.9150 (m-30) cc_final: 0.8850 (m-30) REVERT: E 253 PHE cc_start: 0.7343 (m-80) cc_final: 0.5829 (m-10) REVERT: E 275 LEU cc_start: 0.8948 (mp) cc_final: 0.8143 (mt) REVERT: E 403 GLU cc_start: 0.8673 (tt0) cc_final: 0.7973 (tp30) REVERT: E 408 MET cc_start: 0.8965 (mmm) cc_final: 0.8674 (mmm) REVERT: E 415 CYS cc_start: 0.9080 (t) cc_final: 0.8652 (t) REVERT: E 520 PHE cc_start: 0.7965 (m-80) cc_final: 0.7413 (m-10) REVERT: E 526 GLN cc_start: 0.9314 (tt0) cc_final: 0.8510 (tt0) REVERT: E 527 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8562 (mp0) REVERT: E 532 MET cc_start: 0.8382 (tpp) cc_final: 0.8158 (tpp) REVERT: E 557 ASP cc_start: 0.7987 (t0) cc_final: 0.7341 (t0) REVERT: E 730 CYS cc_start: 0.8306 (p) cc_final: 0.8020 (p) REVERT: E 802 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7184 (mt-10) REVERT: E 831 LYS cc_start: 0.8736 (mttt) cc_final: 0.7575 (mttt) REVERT: E 987 MET cc_start: 0.9219 (mmm) cc_final: 0.8963 (mmm) REVERT: E 989 PHE cc_start: 0.8723 (m-10) cc_final: 0.8288 (m-80) REVERT: E 1006 SER cc_start: 0.8493 (m) cc_final: 0.7831 (p) REVERT: F 151 ILE cc_start: 0.8544 (mm) cc_final: 0.8251 (mt) REVERT: F 238 LYS cc_start: 0.8258 (tttt) cc_final: 0.7809 (mmmt) REVERT: F 239 MET cc_start: 0.9101 (mtm) cc_final: 0.7828 (mmp) REVERT: F 242 ASP cc_start: 0.9125 (m-30) cc_final: 0.8848 (m-30) REVERT: F 253 PHE cc_start: 0.7454 (m-80) cc_final: 0.7055 (m-80) REVERT: F 255 TYR cc_start: 0.7228 (m-80) cc_final: 0.7021 (m-80) REVERT: F 403 GLU cc_start: 0.8593 (tt0) cc_final: 0.8039 (tp30) REVERT: F 407 THR cc_start: 0.9197 (m) cc_final: 0.8576 (p) REVERT: F 408 MET cc_start: 0.9253 (mtm) cc_final: 0.8826 (mmm) REVERT: F 527 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8492 (mt-10) REVERT: F 532 MET cc_start: 0.8331 (tpp) cc_final: 0.8015 (tpp) REVERT: F 557 ASP cc_start: 0.7928 (t0) cc_final: 0.7192 (t0) REVERT: F 647 MET cc_start: 0.8448 (mmp) cc_final: 0.8139 (mmp) REVERT: F 654 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8219 (tm-30) REVERT: F 738 SER cc_start: 0.9354 (p) cc_final: 0.9032 (m) REVERT: F 751 ASN cc_start: 0.8568 (m-40) cc_final: 0.8366 (m110) REVERT: F 762 CYS cc_start: 0.8747 (m) cc_final: 0.8404 (p) REVERT: F 764 THR cc_start: 0.9195 (p) cc_final: 0.8885 (p) REVERT: F 802 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7020 (mt-10) REVERT: F 831 LYS cc_start: 0.8731 (mttt) cc_final: 0.7413 (mttt) REVERT: F 989 PHE cc_start: 0.8878 (m-10) cc_final: 0.8373 (m-80) REVERT: F 1008 MET cc_start: 0.7448 (mmp) cc_final: 0.7234 (mmp) outliers start: 4 outliers final: 0 residues processed: 752 average time/residue: 0.2050 time to fit residues: 265.6269 Evaluate side-chains 603 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 603 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 241 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 86 optimal weight: 0.0870 chunk 59 optimal weight: 0.8980 chunk 305 optimal weight: 1.9990 chunk 428 optimal weight: 4.9990 chunk 455 optimal weight: 6.9990 chunk 254 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 chunk 283 optimal weight: 0.0030 overall best weight: 0.5970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 922 ASN B 522 HIS B 751 ASN ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS C 367 HIS C 922 ASN D 391 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 GLN D 522 HIS D 922 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 HIS ** E 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 922 ASN F 480 GLN F 522 HIS F 922 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.126081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.090731 restraints weight = 96779.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.092601 restraints weight = 63588.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093992 restraints weight = 42459.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.094321 restraints weight = 36581.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.094441 restraints weight = 33882.238| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40266 Z= 0.117 Angle : 0.641 13.380 54372 Z= 0.318 Chirality : 0.040 0.162 6156 Planarity : 0.003 0.042 6810 Dihedral : 10.756 176.021 5544 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.14 % Favored : 92.84 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % 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: -0.37 (0.13), residues: 4848 helix: 0.64 (0.11), residues: 2364 sheet: -1.34 (0.22), residues: 564 loop : -0.90 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 675 TYR 0.012 0.001 TYR F1009 PHE 0.035 0.002 PHE B 508 TRP 0.036 0.001 TRP E 959 HIS 0.007 0.001 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.00259 (40266) covalent geometry : angle 0.64089 (54372) hydrogen bonds : bond 0.03569 ( 1721) hydrogen bonds : angle 4.64981 ( 4935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7814.78 seconds wall clock time: 136 minutes 25.09 seconds (8185.09 seconds total)