Starting phenix.real_space_refine on Sat Mar 23 22:24:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgu_14713/03_2024/7zgu_14713_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgu_14713/03_2024/7zgu_14713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgu_14713/03_2024/7zgu_14713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgu_14713/03_2024/7zgu_14713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgu_14713/03_2024/7zgu_14713_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgu_14713/03_2024/7zgu_14713_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 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 12 5.49 5 S 330 5.16 5 C 24810 2.51 5 N 6618 2.21 5 O 7170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 305": "OD1" <-> "OD2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 640": "OE1" <-> "OE2" Residue "B GLU 671": "OE1" <-> "OE2" Residue "B TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 640": "OE1" <-> "OE2" Residue "C GLU 671": "OE1" <-> "OE2" Residue "C TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 305": "OD1" <-> "OD2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 640": "OE1" <-> "OE2" Residue "D GLU 671": "OE1" <-> "OE2" Residue "D TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E GLU 389": "OE1" <-> "OE2" Residue "E TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 640": "OE1" <-> "OE2" Residue "E GLU 671": "OE1" <-> "OE2" Residue "E TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 176": "OE1" <-> "OE2" Residue "F GLU 214": "OE1" <-> "OE2" Residue "F PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 305": "OD1" <-> "OD2" Residue "F GLU 389": "OE1" <-> "OE2" Residue "F TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 640": "OE1" <-> "OE2" Residue "F GLU 671": "OE1" <-> "OE2" Residue "F TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38940 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6463 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 22, 'TRANS': 786} Chain breaks: 5 Chain: "B" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6463 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 22, 'TRANS': 786} Chain breaks: 5 Chain: "C" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6463 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 22, 'TRANS': 786} Chain breaks: 5 Chain: "D" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6463 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 22, 'TRANS': 786} Chain breaks: 5 Chain: "E" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6463 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 22, 'TRANS': 786} Chain breaks: 5 Chain: "F" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6463 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 22, 'TRANS': 786} Chain breaks: 5 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.72, per 1000 atoms: 0.51 Number of scatterers: 38940 At special positions: 0 Unit cell: (157.08, 165.24, 140.76, 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 330 16.00 P 12 15.00 O 7170 8.00 N 6618 7.00 C 24810 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 - 3.50 Amino acid : False - 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: 15.69 Conformation dependent library (CDL) restraints added in 7.3 seconds 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9192 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 222 helices and 18 sheets defined 48.0% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.15 Creating SS restraints... Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.504A pdb=" N ARG A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 No H-bonds generated for 'chain 'A' and resid 164 through 167' Processing helix chain 'A' and resid 232 through 244 removed outlier: 3.628A pdb=" N ALA A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 removed outlier: 3.839A pdb=" N MET A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 278 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 279 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.510A pdb=" N LEU A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU A 356 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 359 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 385 Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.576A pdb=" N ARG A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.246A pdb=" N PHE A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 424 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 462 through 478 removed outlier: 3.622A pdb=" N LEU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 492 Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 523 through 536 removed outlier: 3.728A pdb=" N TYR A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 removed outlier: 4.710A pdb=" N THR A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 560 " --> pdb=" O ARG A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 574 through 585 removed outlier: 3.596A pdb=" N ARG A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN A 585 " --> pdb=" O PHE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 592 No H-bonds generated for 'chain 'A' and resid 590 through 592' Processing helix chain 'A' and resid 598 through 617 Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 640 through 649 removed outlier: 4.465A pdb=" N TYR A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 672 removed outlier: 3.547A pdb=" N CYS A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN A 672 " --> pdb=" O PHE A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 739 removed outlier: 3.615A pdb=" N ARG A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 733 " --> pdb=" O PHE A 729 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 736 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 737 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 738 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 765 Processing helix chain 'A' and resid 784 through 796 removed outlier: 3.710A pdb=" N PHE A 788 " --> pdb=" O GLU A 785 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 791 " --> pdb=" O PHE A 788 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 794 " --> pdb=" O SER A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 823 removed outlier: 3.721A pdb=" N VAL A 820 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 853 removed outlier: 3.843A pdb=" N GLN A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP A 846 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 850 " --> pdb=" O ASP A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 879 removed outlier: 3.704A pdb=" N LYS A 878 " --> pdb=" O ILE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 911 removed outlier: 3.933A pdb=" N ALA A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 936 removed outlier: 3.790A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 removed outlier: 4.331A pdb=" N TRP A 959 " --> pdb=" O HIS A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 994 removed outlier: 3.936A pdb=" N GLU A 991 " --> pdb=" O MET A 987 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 992 " --> pdb=" O MET A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1024 removed outlier: 3.549A pdb=" N SER A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A1023 " --> pdb=" O GLU A1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.505A pdb=" N ARG B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 167 No H-bonds generated for 'chain 'B' and resid 164 through 167' Processing helix chain 'B' and resid 232 through 244 removed outlier: 3.628A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.839A pdb=" N MET B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 278 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 279 " --> pdb=" O ILE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 289 No H-bonds generated for 'chain 'B' and resid 286 through 289' Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 352 through 361 removed outlier: 3.510A pdb=" N LEU B 355 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU B 356 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 359 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 385 Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.576A pdb=" N ARG B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.247A pdb=" N PHE B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 424 Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'B' and resid 462 through 478 removed outlier: 3.621A pdb=" N LEU B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 492 Processing helix chain 'B' and resid 496 through 504 Processing helix chain 'B' and resid 523 through 536 removed outlier: 3.728A pdb=" N TYR B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 563 removed outlier: 4.711A pdb=" N THR B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL B 560 " --> pdb=" O ARG B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 574 through 585 removed outlier: 3.596A pdb=" N ARG B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 584 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN B 585 " --> pdb=" O PHE B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 592 No H-bonds generated for 'chain 'B' and resid 590 through 592' Processing helix chain 'B' and resid 598 through 617 Processing helix chain 'B' and resid 627 through 637 Processing helix chain 'B' and resid 640 through 649 removed outlier: 4.465A pdb=" N TYR B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 672 removed outlier: 3.549A pdb=" N CYS B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN B 672 " --> pdb=" O PHE B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 739 removed outlier: 3.615A pdb=" N ARG B 731 " --> pdb=" O SER B 727 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 733 " --> pdb=" O PHE B 729 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 736 " --> pdb=" O GLY B 732 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 738 " --> pdb=" O PHE B 734 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 765 Processing helix chain 'B' and resid 784 through 796 removed outlier: 3.712A pdb=" N PHE B 788 " --> pdb=" O GLU B 785 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 791 " --> pdb=" O PHE B 788 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 794 " --> pdb=" O SER B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 823 removed outlier: 3.722A pdb=" N VAL B 820 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 853 removed outlier: 3.843A pdb=" N GLN B 845 " --> pdb=" O SER B 841 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP B 846 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 849 " --> pdb=" O GLN B 845 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 850 " --> pdb=" O ASP B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 879 removed outlier: 3.704A pdb=" N LYS B 878 " --> pdb=" O ILE B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 911 removed outlier: 3.932A pdb=" N ALA B 903 " --> pdb=" O VAL B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 936 removed outlier: 3.790A pdb=" N GLY B 935 " --> pdb=" O LEU B 931 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 967 removed outlier: 4.331A pdb=" N TRP B 959 " --> pdb=" O HIS B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 994 removed outlier: 3.936A pdb=" N GLU B 991 " --> pdb=" O MET B 987 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 992 " --> pdb=" O MET B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1024 removed outlier: 3.549A pdb=" N SER B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA B1017 " --> pdb=" O GLU B1013 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B1018 " --> pdb=" O THR B1014 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B1019 " --> pdb=" O LYS B1015 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B1021 " --> pdb=" O ALA B1017 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU B1023 " --> pdb=" O GLU B1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.505A pdb=" N ARG C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 167 No H-bonds generated for 'chain 'C' and resid 164 through 167' Processing helix chain 'C' and resid 232 through 244 removed outlier: 3.629A pdb=" N ALA C 236 " --> pdb=" O LYS C 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 removed outlier: 3.839A pdb=" N MET C 277 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER C 278 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS C 279 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 289 No H-bonds generated for 'chain 'C' and resid 286 through 289' Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 328 through 337 Processing helix chain 'C' and resid 352 through 361 removed outlier: 3.510A pdb=" N LEU C 355 " --> pdb=" O PRO C 352 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU C 356 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN C 359 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 385 Processing helix chain 'C' and resid 389 through 401 removed outlier: 3.576A pdb=" N ARG C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.247A pdb=" N PHE C 410 " --> pdb=" O PHE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 424 Processing helix chain 'C' and resid 439 through 452 Processing helix chain 'C' and resid 462 through 478 removed outlier: 3.621A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 492 Processing helix chain 'C' and resid 496 through 504 Processing helix chain 'C' and resid 523 through 536 removed outlier: 3.728A pdb=" N TYR C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 563 removed outlier: 4.710A pdb=" N THR C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL C 560 " --> pdb=" O ARG C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 574 through 585 removed outlier: 3.597A pdb=" N ARG C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 584 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN C 585 " --> pdb=" O PHE C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 592 No H-bonds generated for 'chain 'C' and resid 590 through 592' Processing helix chain 'C' and resid 598 through 617 Processing helix chain 'C' and resid 627 through 637 Processing helix chain 'C' and resid 640 through 649 removed outlier: 4.465A pdb=" N TYR C 649 " --> pdb=" O ARG C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.548A pdb=" N CYS C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN C 672 " --> pdb=" O PHE C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 739 removed outlier: 3.615A pdb=" N ARG C 731 " --> pdb=" O SER C 727 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY C 732 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU C 733 " --> pdb=" O PHE C 729 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 736 " --> pdb=" O GLY C 732 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 737 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 738 " --> pdb=" O PHE C 734 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 739 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 765 Processing helix chain 'C' and resid 784 through 796 removed outlier: 3.711A pdb=" N PHE C 788 " --> pdb=" O GLU C 785 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 791 " --> pdb=" O PHE C 788 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 794 " --> pdb=" O SER C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 823 removed outlier: 3.721A pdb=" N VAL C 820 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 853 removed outlier: 3.843A pdb=" N GLN C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP C 846 " --> pdb=" O ALA C 842 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER C 849 " --> pdb=" O GLN C 845 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 850 " --> pdb=" O ASP C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 879 removed outlier: 3.704A pdb=" N LYS C 878 " --> pdb=" O ILE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 911 removed outlier: 3.933A pdb=" N ALA C 903 " --> pdb=" O VAL C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 936 removed outlier: 3.789A pdb=" N GLY C 935 " --> pdb=" O LEU C 931 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 967 removed outlier: 4.331A pdb=" N TRP C 959 " --> pdb=" O HIS C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 994 removed outlier: 3.936A pdb=" N GLU C 991 " --> pdb=" O MET C 987 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 992 " --> pdb=" O MET C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1024 removed outlier: 3.549A pdb=" N SER C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA C1017 " --> pdb=" O GLU C1013 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C1018 " --> pdb=" O THR C1014 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C1019 " --> pdb=" O LYS C1015 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C1021 " --> pdb=" O ALA C1017 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU C1023 " --> pdb=" O GLU C1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.505A pdb=" N ARG D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 146 " --> pdb=" O LYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 167 No H-bonds generated for 'chain 'D' and resid 164 through 167' Processing helix chain 'D' and resid 232 through 244 removed outlier: 3.629A pdb=" N ALA D 236 " --> pdb=" O LYS D 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 removed outlier: 3.839A pdb=" N MET D 277 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER D 278 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS D 279 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 289 No H-bonds generated for 'chain 'D' and resid 286 through 289' Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 328 through 337 Processing helix chain 'D' and resid 352 through 361 removed outlier: 3.510A pdb=" N LEU D 355 " --> pdb=" O PRO D 352 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU D 356 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN D 359 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 385 Processing helix chain 'D' and resid 389 through 401 removed outlier: 3.576A pdb=" N ARG D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA D 394 " --> pdb=" O ALA D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.246A pdb=" N PHE D 410 " --> pdb=" O PHE D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 424 Processing helix chain 'D' and resid 439 through 452 Processing helix chain 'D' and resid 462 through 478 removed outlier: 3.621A pdb=" N LEU D 472 " --> pdb=" O GLY D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 492 Processing helix chain 'D' and resid 496 through 504 Processing helix chain 'D' and resid 523 through 536 removed outlier: 3.729A pdb=" N TYR D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 563 removed outlier: 4.711A pdb=" N THR D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL D 560 " --> pdb=" O ARG D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 570 No H-bonds generated for 'chain 'D' and resid 568 through 570' Processing helix chain 'D' and resid 574 through 585 removed outlier: 3.597A pdb=" N ARG D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 584 " --> pdb=" O LEU D 580 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASN D 585 " --> pdb=" O PHE D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 592 No H-bonds generated for 'chain 'D' and resid 590 through 592' Processing helix chain 'D' and resid 598 through 617 Processing helix chain 'D' and resid 627 through 637 Processing helix chain 'D' and resid 640 through 649 removed outlier: 4.465A pdb=" N TYR D 649 " --> pdb=" O ARG D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 672 removed outlier: 3.548A pdb=" N CYS D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN D 672 " --> pdb=" O PHE D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 739 removed outlier: 3.615A pdb=" N ARG D 731 " --> pdb=" O SER D 727 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY D 732 " --> pdb=" O SER D 728 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D 733 " --> pdb=" O PHE D 729 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER D 738 " --> pdb=" O PHE D 734 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 739 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 765 Processing helix chain 'D' and resid 784 through 796 removed outlier: 3.711A pdb=" N PHE D 788 " --> pdb=" O GLU D 785 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER D 791 " --> pdb=" O PHE D 788 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D 794 " --> pdb=" O SER D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 823 removed outlier: 3.721A pdb=" N VAL D 820 " --> pdb=" O ARG D 816 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY D 821 " --> pdb=" O LEU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 853 removed outlier: 3.843A pdb=" N GLN D 845 " --> pdb=" O SER D 841 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP D 846 " --> pdb=" O ALA D 842 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER D 849 " --> pdb=" O GLN D 845 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL D 850 " --> pdb=" O ASP D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 879 removed outlier: 3.704A pdb=" N LYS D 878 " --> pdb=" O ILE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 911 removed outlier: 3.933A pdb=" N ALA D 903 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 936 removed outlier: 3.789A pdb=" N GLY D 935 " --> pdb=" O LEU D 931 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 936 " --> pdb=" O LEU D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 967 removed outlier: 4.332A pdb=" N TRP D 959 " --> pdb=" O HIS D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 994 removed outlier: 3.936A pdb=" N GLU D 991 " --> pdb=" O MET D 987 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL D 992 " --> pdb=" O MET D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1024 removed outlier: 3.548A pdb=" N SER D1016 " --> pdb=" O TYR D1012 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA D1017 " --> pdb=" O GLU D1013 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D1018 " --> pdb=" O THR D1014 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D1019 " --> pdb=" O LYS D1015 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D1021 " --> pdb=" O ALA D1017 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU D1023 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.505A pdb=" N ARG E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 167 No H-bonds generated for 'chain 'E' and resid 164 through 167' Processing helix chain 'E' and resid 232 through 244 removed outlier: 3.629A pdb=" N ALA E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 removed outlier: 3.839A pdb=" N MET E 277 " --> pdb=" O ASP E 274 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E 278 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS E 279 " --> pdb=" O ILE E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 289 No H-bonds generated for 'chain 'E' and resid 286 through 289' Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 328 through 337 Processing helix chain 'E' and resid 352 through 361 removed outlier: 3.509A pdb=" N LEU E 355 " --> pdb=" O PRO E 352 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU E 356 " --> pdb=" O VAL E 353 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN E 359 " --> pdb=" O GLU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 385 Processing helix chain 'E' and resid 389 through 401 removed outlier: 3.576A pdb=" N ARG E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA E 394 " --> pdb=" O ALA E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.246A pdb=" N PHE E 410 " --> pdb=" O PHE E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 424 Processing helix chain 'E' and resid 439 through 452 Processing helix chain 'E' and resid 462 through 478 removed outlier: 3.621A pdb=" N LEU E 472 " --> pdb=" O GLY E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 492 Processing helix chain 'E' and resid 496 through 504 Processing helix chain 'E' and resid 523 through 536 removed outlier: 3.728A pdb=" N TYR E 534 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 535 " --> pdb=" O ALA E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 554 through 563 removed outlier: 4.710A pdb=" N THR E 559 " --> pdb=" O SER E 555 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL E 560 " --> pdb=" O ARG E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 570 No H-bonds generated for 'chain 'E' and resid 568 through 570' Processing helix chain 'E' and resid 574 through 585 removed outlier: 3.597A pdb=" N ARG E 578 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 584 " --> pdb=" O LEU E 580 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN E 585 " --> pdb=" O PHE E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 592 No H-bonds generated for 'chain 'E' and resid 590 through 592' Processing helix chain 'E' and resid 598 through 617 Processing helix chain 'E' and resid 627 through 637 Processing helix chain 'E' and resid 640 through 649 removed outlier: 4.465A pdb=" N TYR E 649 " --> pdb=" O ARG E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 672 removed outlier: 3.549A pdb=" N CYS E 669 " --> pdb=" O VAL E 665 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN E 672 " --> pdb=" O PHE E 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 727 through 739 removed outlier: 3.615A pdb=" N ARG E 731 " --> pdb=" O SER E 727 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY E 732 " --> pdb=" O SER E 728 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU E 733 " --> pdb=" O PHE E 729 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL E 736 " --> pdb=" O GLY E 732 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 737 " --> pdb=" O LEU E 733 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER E 738 " --> pdb=" O PHE E 734 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR E 739 " --> pdb=" O SER E 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 765 Processing helix chain 'E' and resid 784 through 796 removed outlier: 3.711A pdb=" N PHE E 788 " --> pdb=" O GLU E 785 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER E 791 " --> pdb=" O PHE E 788 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU E 794 " --> pdb=" O SER E 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 812 through 823 removed outlier: 3.721A pdb=" N VAL E 820 " --> pdb=" O ARG E 816 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY E 821 " --> pdb=" O LEU E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 841 through 853 removed outlier: 3.842A pdb=" N GLN E 845 " --> pdb=" O SER E 841 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP E 846 " --> pdb=" O ALA E 842 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER E 849 " --> pdb=" O GLN E 845 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 850 " --> pdb=" O ASP E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 869 through 879 removed outlier: 3.704A pdb=" N LYS E 878 " --> pdb=" O ILE E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 899 through 911 removed outlier: 3.933A pdb=" N ALA E 903 " --> pdb=" O VAL E 899 " (cutoff:3.500A) Processing helix chain 'E' and resid 928 through 936 removed outlier: 3.790A pdb=" N GLY E 935 " --> pdb=" O LEU E 931 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 936 " --> pdb=" O LEU E 932 " (cutoff:3.500A) Processing helix chain 'E' and resid 955 through 967 removed outlier: 4.331A pdb=" N TRP E 959 " --> pdb=" O HIS E 956 " (cutoff:3.500A) Processing helix chain 'E' and resid 983 through 994 removed outlier: 3.937A pdb=" N GLU E 991 " --> pdb=" O MET E 987 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL E 992 " --> pdb=" O MET E 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 1012 through 1024 removed outlier: 3.549A pdb=" N SER E1016 " --> pdb=" O TYR E1012 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA E1017 " --> pdb=" O GLU E1013 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU E1018 " --> pdb=" O THR E1014 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E1019 " --> pdb=" O LYS E1015 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU E1021 " --> pdb=" O ALA E1017 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU E1023 " --> pdb=" O GLU E1019 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 147 removed outlier: 3.505A pdb=" N ARG F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 167 No H-bonds generated for 'chain 'F' and resid 164 through 167' Processing helix chain 'F' and resid 232 through 244 removed outlier: 3.629A pdb=" N ALA F 236 " --> pdb=" O LYS F 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG F 237 " --> pdb=" O THR F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 removed outlier: 3.839A pdb=" N MET F 277 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER F 278 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS F 279 " --> pdb=" O ILE F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 289 No H-bonds generated for 'chain 'F' and resid 286 through 289' Processing helix chain 'F' and resid 294 through 296 No H-bonds generated for 'chain 'F' and resid 294 through 296' Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 328 through 337 Processing helix chain 'F' and resid 352 through 361 removed outlier: 3.510A pdb=" N LEU F 355 " --> pdb=" O PRO F 352 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU F 356 " --> pdb=" O VAL F 353 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN F 359 " --> pdb=" O GLU F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 385 Processing helix chain 'F' and resid 389 through 401 removed outlier: 3.576A pdb=" N ARG F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 410 removed outlier: 4.246A pdb=" N PHE F 410 " --> pdb=" O PHE F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 424 Processing helix chain 'F' and resid 439 through 452 Processing helix chain 'F' and resid 462 through 478 removed outlier: 3.622A pdb=" N LEU F 472 " --> pdb=" O GLY F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 492 Processing helix chain 'F' and resid 496 through 504 Processing helix chain 'F' and resid 523 through 536 removed outlier: 3.728A pdb=" N TYR F 534 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 535 " --> pdb=" O ALA F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 563 removed outlier: 4.711A pdb=" N THR F 559 " --> pdb=" O SER F 555 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL F 560 " --> pdb=" O ARG F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 570 No H-bonds generated for 'chain 'F' and resid 568 through 570' Processing helix chain 'F' and resid 574 through 585 removed outlier: 3.597A pdb=" N ARG F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL F 584 " --> pdb=" O LEU F 580 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASN F 585 " --> pdb=" O PHE F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 592 No H-bonds generated for 'chain 'F' and resid 590 through 592' Processing helix chain 'F' and resid 598 through 617 Processing helix chain 'F' and resid 627 through 637 Processing helix chain 'F' and resid 640 through 649 removed outlier: 4.465A pdb=" N TYR F 649 " --> pdb=" O ARG F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 660 through 672 removed outlier: 3.548A pdb=" N CYS F 669 " --> pdb=" O VAL F 665 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN F 672 " --> pdb=" O PHE F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 727 through 739 removed outlier: 3.616A pdb=" N ARG F 731 " --> pdb=" O SER F 727 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLY F 732 " --> pdb=" O SER F 728 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU F 733 " --> pdb=" O PHE F 729 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 736 " --> pdb=" O GLY F 732 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 737 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER F 738 " --> pdb=" O PHE F 734 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR F 739 " --> pdb=" O SER F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 755 through 765 Processing helix chain 'F' and resid 784 through 796 removed outlier: 3.711A pdb=" N PHE F 788 " --> pdb=" O GLU F 785 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER F 791 " --> pdb=" O PHE F 788 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU F 794 " --> pdb=" O SER F 791 " (cutoff:3.500A) Processing helix chain 'F' and resid 812 through 823 removed outlier: 3.721A pdb=" N VAL F 820 " --> pdb=" O ARG F 816 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY F 821 " --> pdb=" O LEU F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 841 through 853 removed outlier: 3.843A pdb=" N GLN F 845 " --> pdb=" O SER F 841 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP F 846 " --> pdb=" O ALA F 842 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER F 849 " --> pdb=" O GLN F 845 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL F 850 " --> pdb=" O ASP F 846 " (cutoff:3.500A) Processing helix chain 'F' and resid 869 through 879 removed outlier: 3.703A pdb=" N LYS F 878 " --> pdb=" O ILE F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 899 through 911 removed outlier: 3.933A pdb=" N ALA F 903 " --> pdb=" O VAL F 899 " (cutoff:3.500A) Processing helix chain 'F' and resid 928 through 936 removed outlier: 3.789A pdb=" N GLY F 935 " --> pdb=" O LEU F 931 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 936 " --> pdb=" O LEU F 932 " (cutoff:3.500A) Processing helix chain 'F' and resid 955 through 967 removed outlier: 4.332A pdb=" N TRP F 959 " --> pdb=" O HIS F 956 " (cutoff:3.500A) Processing helix chain 'F' and resid 983 through 994 removed outlier: 3.936A pdb=" N GLU F 991 " --> pdb=" O MET F 987 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL F 992 " --> pdb=" O MET F 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 1012 through 1024 removed outlier: 3.548A pdb=" N SER F1016 " --> pdb=" O TYR F1012 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA F1017 " --> pdb=" O GLU F1013 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU F1018 " --> pdb=" O THR F1014 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU F1019 " --> pdb=" O LYS F1015 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU F1021 " --> pdb=" O ALA F1017 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU F1023 " --> pdb=" O GLU F1019 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 173 through 175 removed outlier: 6.044A pdb=" N LEU A 346 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE A 224 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 348 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 345 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TYR A 255 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU A 300 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 257 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP A 302 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A 259 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 652 through 654 removed outlier: 6.414A pdb=" N SER A 678 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A 745 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG A 774 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU A 802 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS A 831 " --> pdb=" O LEU A 803 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 916 through 920 removed outlier: 6.622A pdb=" N VAL A 945 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU A 919 " --> pdb=" O VAL A 945 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU A 947 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS A 973 " --> pdb=" O LEU A 946 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU A 948 " --> pdb=" O LYS A 973 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER A 975 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN A1002 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR A1029 " --> pdb=" O LEU A1003 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU A1005 " --> pdb=" O THR A1029 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A1031 " --> pdb=" O LEU A1005 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 173 through 175 removed outlier: 6.044A pdb=" N LEU B 346 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE B 224 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 348 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 345 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TYR B 255 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU B 300 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE B 257 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP B 302 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE B 259 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 652 through 654 removed outlier: 6.414A pdb=" N SER B 678 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU B 745 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG B 774 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU B 802 " --> pdb=" O LEU B 775 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS B 831 " --> pdb=" O LEU B 803 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 916 through 920 removed outlier: 6.622A pdb=" N VAL B 945 " --> pdb=" O LEU B 917 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU B 919 " --> pdb=" O VAL B 945 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU B 947 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS B 973 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU B 948 " --> pdb=" O LYS B 973 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER B 975 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN B1002 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR B1029 " --> pdb=" O LEU B1003 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU B1005 " --> pdb=" O THR B1029 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1031 " --> pdb=" O LEU B1005 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.044A pdb=" N LEU C 346 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE C 224 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE C 348 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C 345 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TYR C 255 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU C 300 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE C 257 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP C 302 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 259 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 652 through 654 removed outlier: 6.413A pdb=" N SER C 678 " --> pdb=" O ILE C 653 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU C 745 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG C 774 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU C 802 " --> pdb=" O LEU C 775 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS C 831 " --> pdb=" O LEU C 803 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 916 through 920 removed outlier: 6.621A pdb=" N VAL C 945 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU C 919 " --> pdb=" O VAL C 945 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU C 947 " --> pdb=" O LEU C 919 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS C 973 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU C 948 " --> pdb=" O LYS C 973 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER C 975 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN C1002 " --> pdb=" O LEU C 974 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR C1029 " --> pdb=" O LEU C1003 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU C1005 " --> pdb=" O THR C1029 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C1031 " --> pdb=" O LEU C1005 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.044A pdb=" N LEU D 346 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N PHE D 224 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE D 348 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER D 345 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TYR D 255 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU D 300 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE D 257 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP D 302 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE D 259 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 652 through 654 removed outlier: 6.413A pdb=" N SER D 678 " --> pdb=" O ILE D 653 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU D 745 " --> pdb=" O LEU D 679 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG D 774 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU D 802 " --> pdb=" O LEU D 775 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS D 831 " --> pdb=" O LEU D 803 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 916 through 920 removed outlier: 6.621A pdb=" N VAL D 945 " --> pdb=" O LEU D 917 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU D 919 " --> pdb=" O VAL D 945 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU D 947 " --> pdb=" O LEU D 919 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS D 973 " --> pdb=" O LEU D 946 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU D 948 " --> pdb=" O LYS D 973 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER D 975 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN D1002 " --> pdb=" O LEU D 974 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR D1029 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU D1005 " --> pdb=" O THR D1029 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL D1031 " --> pdb=" O LEU D1005 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 173 through 175 removed outlier: 6.043A pdb=" N LEU E 346 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE E 224 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE E 348 " --> pdb=" O PHE E 224 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER E 345 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TYR E 255 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU E 300 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE E 257 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASP E 302 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE E 259 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 652 through 654 removed outlier: 6.414A pdb=" N SER E 678 " --> pdb=" O ILE E 653 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU E 745 " --> pdb=" O LEU E 679 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG E 774 " --> pdb=" O LEU E 746 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU E 802 " --> pdb=" O LEU E 775 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS E 831 " --> pdb=" O LEU E 803 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 916 through 920 removed outlier: 6.622A pdb=" N VAL E 945 " --> pdb=" O LEU E 917 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU E 919 " --> pdb=" O VAL E 945 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU E 947 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS E 973 " --> pdb=" O LEU E 946 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU E 948 " --> pdb=" O LYS E 973 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER E 975 " --> pdb=" O LEU E 948 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN E1002 " --> pdb=" O LEU E 974 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR E1029 " --> pdb=" O LEU E1003 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU E1005 " --> pdb=" O THR E1029 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL E1031 " --> pdb=" O LEU E1005 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 173 through 175 removed outlier: 6.044A pdb=" N LEU F 346 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE F 224 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE F 348 " --> pdb=" O PHE F 224 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER F 345 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TYR F 255 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU F 300 " --> pdb=" O TYR F 255 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE F 257 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP F 302 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE F 259 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 652 through 654 removed outlier: 6.414A pdb=" N SER F 678 " --> pdb=" O ILE F 653 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU F 745 " --> pdb=" O LEU F 679 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG F 774 " --> pdb=" O LEU F 746 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU F 802 " --> pdb=" O LEU F 775 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS F 831 " --> pdb=" O LEU F 803 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 916 through 920 removed outlier: 6.622A pdb=" N VAL F 945 " --> pdb=" O LEU F 917 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU F 919 " --> pdb=" O VAL F 945 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU F 947 " --> pdb=" O LEU F 919 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS F 973 " --> pdb=" O LEU F 946 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU F 948 " --> pdb=" O LYS F 973 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER F 975 " --> pdb=" O LEU F 948 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN F1002 " --> pdb=" O LEU F 974 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR F1029 " --> pdb=" O LEU F1003 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU F1005 " --> pdb=" O THR F1029 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL F1031 " --> pdb=" O LEU F1005 " (cutoff:3.500A) No H-bonds generated for sheet with id= R 1236 hydrogen bonds defined for protein. 3294 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: 15.29 Time building geometry restraints manager: 16.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 12552 1.35 - 1.47: 9144 1.47 - 1.59: 17544 1.59 - 1.71: 18 1.71 - 1.83: 432 Bond restraints: 39690 Sorted by residual: bond pdb=" CB GLU D1013 " pdb=" CG GLU D1013 " ideal model delta sigma weight residual 1.520 1.583 -0.063 3.00e-02 1.11e+03 4.45e+00 bond pdb=" CB GLU F1013 " pdb=" CG GLU F1013 " ideal model delta sigma weight residual 1.520 1.583 -0.063 3.00e-02 1.11e+03 4.37e+00 bond pdb=" CB GLU A1013 " pdb=" CG GLU A1013 " ideal model delta sigma weight residual 1.520 1.583 -0.063 3.00e-02 1.11e+03 4.36e+00 bond pdb=" CB GLU B1013 " pdb=" CG GLU B1013 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.33e+00 bond pdb=" CB GLU C1013 " pdb=" CG GLU C1013 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.33e+00 ... (remaining 39685 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.84: 550 105.84 - 113.38: 22205 113.38 - 120.93: 19839 120.93 - 128.47: 10632 128.47 - 136.02: 318 Bond angle restraints: 53544 Sorted by residual: angle pdb=" CA GLU D1013 " pdb=" CB GLU D1013 " pdb=" CG GLU D1013 " ideal model delta sigma weight residual 114.10 126.60 -12.50 2.00e+00 2.50e-01 3.91e+01 angle pdb=" CA GLU A1013 " pdb=" CB GLU A1013 " pdb=" CG GLU A1013 " ideal model delta sigma weight residual 114.10 126.58 -12.48 2.00e+00 2.50e-01 3.90e+01 angle pdb=" CA GLU B1013 " pdb=" CB GLU B1013 " pdb=" CG GLU B1013 " ideal model delta sigma weight residual 114.10 126.57 -12.47 2.00e+00 2.50e-01 3.89e+01 angle pdb=" CA GLU F1013 " pdb=" CB GLU F1013 " pdb=" CG GLU F1013 " ideal model delta sigma weight residual 114.10 126.57 -12.47 2.00e+00 2.50e-01 3.89e+01 angle pdb=" CA GLU E1013 " pdb=" CB GLU E1013 " pdb=" CG GLU E1013 " ideal model delta sigma weight residual 114.10 126.55 -12.45 2.00e+00 2.50e-01 3.87e+01 ... (remaining 53539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.23: 22953 29.23 - 58.46: 930 58.46 - 87.69: 78 87.69 - 116.92: 0 116.92 - 146.16: 9 Dihedral angle restraints: 23970 sinusoidal: 9822 harmonic: 14148 Sorted by residual: dihedral pdb=" C5' ADP C1101 " pdb=" O5' ADP C1101 " pdb=" PA ADP C1101 " pdb=" O2A ADP C1101 " ideal model delta sinusoidal sigma weight residual -60.00 86.16 -146.16 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP B1101 " pdb=" O5' ADP B1101 " pdb=" PA ADP B1101 " pdb=" O2A ADP B1101 " ideal model delta sinusoidal sigma weight residual -60.00 86.15 -146.15 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP A1101 " pdb=" O5' ADP A1101 " pdb=" PA ADP A1101 " pdb=" O2A ADP A1101 " ideal model delta sinusoidal sigma weight residual -60.00 86.13 -146.13 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 23967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3997 0.033 - 0.067: 1527 0.067 - 0.100: 370 0.100 - 0.133: 159 0.133 - 0.166: 25 Chirality restraints: 6078 Sorted by residual: chirality pdb=" CB ILE C 276 " pdb=" CA ILE C 276 " pdb=" CG1 ILE C 276 " pdb=" CG2 ILE C 276 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CB ILE D 276 " pdb=" CA ILE D 276 " pdb=" CG1 ILE D 276 " pdb=" CG2 ILE D 276 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CB ILE A 276 " pdb=" CA ILE A 276 " pdb=" CG1 ILE A 276 " pdb=" CG2 ILE A 276 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 6075 not shown) Planarity restraints: 6714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 284 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO B 285 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 285 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 285 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 284 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO F 285 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO F 285 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 285 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 284 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO D 285 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 285 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 285 " 0.037 5.00e-02 4.00e+02 ... (remaining 6711 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3063 2.74 - 3.28: 41410 3.28 - 3.82: 64676 3.82 - 4.36: 78170 4.36 - 4.90: 129836 Nonbonded interactions: 317155 Sorted by model distance: nonbonded pdb=" OH TYR B 632 " pdb=" OD1 ASP B 662 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR F 632 " pdb=" OD1 ASP F 662 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR A 632 " pdb=" OD1 ASP A 662 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR C 632 " pdb=" OD1 ASP C 662 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR D 632 " pdb=" OD1 ASP D 662 " model vdw 2.202 2.440 ... (remaining 317150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 22.180 Check model and map are aligned: 0.670 Set scattering table: 0.320 Process input model: 103.370 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.260 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 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 : 0.003 0.063 39690 Z= 0.176 Angle : 0.678 12.501 53544 Z= 0.348 Chirality : 0.040 0.166 6078 Planarity : 0.004 0.067 6714 Dihedral : 14.945 146.155 14778 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.55 % Allowed : 0.52 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 4782 helix: 0.25 (0.12), residues: 2052 sheet: -0.77 (0.25), residues: 438 loop : -1.33 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 243 HIS 0.004 0.001 HIS E 522 PHE 0.012 0.001 PHE E 299 TYR 0.013 0.001 TYR B 249 ARG 0.006 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1109 time to evaluate : 4.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ILE cc_start: 0.8091 (tp) cc_final: 0.7881 (tp) REVERT: A 239 MET cc_start: 0.6788 (ttp) cc_final: 0.6528 (ttp) REVERT: A 276 ILE cc_start: 0.5810 (OUTLIER) cc_final: 0.5587 (mp) REVERT: A 282 ASP cc_start: 0.5810 (p0) cc_final: 0.5595 (p0) REVERT: A 301 MET cc_start: 0.6952 (ttm) cc_final: 0.6602 (ttm) REVERT: A 322 TRP cc_start: 0.7313 (t60) cc_final: 0.6390 (t60) REVERT: A 329 ASP cc_start: 0.7600 (m-30) cc_final: 0.7310 (m-30) REVERT: A 353 VAL cc_start: 0.8778 (p) cc_final: 0.8501 (t) REVERT: A 369 GLU cc_start: 0.6914 (tt0) cc_final: 0.6710 (tt0) REVERT: A 563 GLU cc_start: 0.6576 (pp20) cc_final: 0.6117 (tm-30) REVERT: A 603 GLN cc_start: 0.7920 (tp40) cc_final: 0.7169 (tm-30) REVERT: A 607 GLU cc_start: 0.7609 (tp30) cc_final: 0.7408 (tp30) REVERT: A 611 TRP cc_start: 0.7188 (t60) cc_final: 0.6554 (t60) REVERT: A 631 PHE cc_start: 0.7510 (m-10) cc_final: 0.7234 (m-80) REVERT: A 637 MET cc_start: 0.6915 (tpp) cc_final: 0.6556 (tpp) REVERT: A 645 ARG cc_start: 0.7104 (mtm110) cc_final: 0.6399 (mtm110) REVERT: A 648 ASP cc_start: 0.7533 (m-30) cc_final: 0.7224 (t0) REVERT: A 649 TYR cc_start: 0.7430 (m-80) cc_final: 0.7166 (m-10) REVERT: A 759 ARG cc_start: 0.7864 (ttt180) cc_final: 0.7650 (ttt180) REVERT: A 815 ILE cc_start: 0.8210 (mm) cc_final: 0.7872 (mm) REVERT: A 922 ASN cc_start: 0.5723 (m110) cc_final: 0.5104 (m110) REVERT: A 990 CYS cc_start: 0.7550 (m) cc_final: 0.6781 (m) REVERT: A 1006 SER cc_start: 0.8304 (m) cc_final: 0.7777 (t) REVERT: A 1022 GLN cc_start: 0.7782 (tm-30) cc_final: 0.7581 (tm-30) REVERT: B 174 ILE cc_start: 0.7363 (mt) cc_final: 0.7071 (mt) REVERT: B 239 MET cc_start: 0.6488 (ttp) cc_final: 0.6273 (ttp) REVERT: B 240 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.6200 (ttp) REVERT: B 250 GLN cc_start: 0.6804 (tp40) cc_final: 0.6585 (mm-40) REVERT: B 276 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5673 (mp) REVERT: B 282 ASP cc_start: 0.6123 (p0) cc_final: 0.5923 (p0) REVERT: B 288 HIS cc_start: 0.7627 (m90) cc_final: 0.7328 (m90) REVERT: B 367 HIS cc_start: 0.6850 (m-70) cc_final: 0.6613 (m-70) REVERT: B 488 ASP cc_start: 0.7482 (m-30) cc_final: 0.7269 (m-30) REVERT: B 563 GLU cc_start: 0.6705 (pp20) cc_final: 0.5484 (tm-30) REVERT: B 603 GLN cc_start: 0.7768 (tp40) cc_final: 0.7055 (tm-30) REVERT: B 613 GLU cc_start: 0.7477 (tt0) cc_final: 0.7247 (tt0) REVERT: B 629 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6226 (mm-30) REVERT: B 644 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7447 (mm-40) REVERT: B 649 TYR cc_start: 0.7330 (m-80) cc_final: 0.6380 (m-80) REVERT: B 652 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7886 (ttmm) REVERT: B 800 LEU cc_start: 0.8261 (mm) cc_final: 0.7997 (mt) REVERT: B 802 GLU cc_start: 0.6509 (mt-10) cc_final: 0.6241 (mt-10) REVERT: B 815 ILE cc_start: 0.8353 (mm) cc_final: 0.7527 (mm) REVERT: B 816 ARG cc_start: 0.7695 (ttt180) cc_final: 0.7329 (ttt90) REVERT: B 831 LYS cc_start: 0.7920 (mttt) cc_final: 0.7042 (mttm) REVERT: B 934 GLU cc_start: 0.6481 (tm-30) cc_final: 0.5998 (tm-30) REVERT: B 973 LYS cc_start: 0.8165 (ptmt) cc_final: 0.7713 (ptpt) REVERT: B 988 MET cc_start: 0.7536 (mmm) cc_final: 0.7068 (mmm) REVERT: B 989 PHE cc_start: 0.7755 (m-10) cc_final: 0.7412 (m-80) REVERT: B 1006 SER cc_start: 0.8165 (m) cc_final: 0.7702 (p) REVERT: B 1008 MET cc_start: 0.6391 (mmm) cc_final: 0.6067 (ttt) REVERT: B 1025 LYS cc_start: 0.6958 (mmtt) cc_final: 0.6697 (mptt) REVERT: C 239 MET cc_start: 0.6532 (ttp) cc_final: 0.6323 (ttp) REVERT: C 269 GLN cc_start: 0.4153 (mp10) cc_final: 0.3894 (mp10) REVERT: C 276 ILE cc_start: 0.5948 (OUTLIER) cc_final: 0.5656 (mt) REVERT: C 282 ASP cc_start: 0.6116 (p0) cc_final: 0.5812 (p0) REVERT: C 301 MET cc_start: 0.7028 (ttm) cc_final: 0.6780 (ttt) REVERT: C 322 TRP cc_start: 0.7525 (t60) cc_final: 0.7208 (t60) REVERT: C 367 HIS cc_start: 0.6847 (m-70) cc_final: 0.6285 (m-70) REVERT: C 419 CYS cc_start: 0.7753 (m) cc_final: 0.7201 (m) REVERT: C 488 ASP cc_start: 0.7643 (m-30) cc_final: 0.7223 (m-30) REVERT: C 603 GLN cc_start: 0.7934 (tp40) cc_final: 0.7308 (tm-30) REVERT: C 606 LEU cc_start: 0.7612 (mm) cc_final: 0.7298 (mp) REVERT: C 613 GLU cc_start: 0.7183 (tt0) cc_final: 0.6953 (tt0) REVERT: C 638 GLN cc_start: 0.7297 (mm-40) cc_final: 0.7049 (tp40) REVERT: C 649 TYR cc_start: 0.7255 (m-80) cc_final: 0.6997 (m-80) REVERT: C 743 LEU cc_start: 0.7732 (tp) cc_final: 0.7492 (tp) REVERT: C 774 ARG cc_start: 0.7250 (mtm110) cc_final: 0.6677 (mtm110) REVERT: C 853 THR cc_start: 0.8321 (t) cc_final: 0.8015 (p) REVERT: C 859 ARG cc_start: 0.7221 (mtt-85) cc_final: 0.7006 (mtt-85) REVERT: C 912 GLN cc_start: 0.7418 (tt0) cc_final: 0.7146 (tt0) REVERT: C 991 GLU cc_start: 0.7073 (pm20) cc_final: 0.6778 (pm20) REVERT: C 1022 GLN cc_start: 0.8283 (tm-30) cc_final: 0.8029 (tm-30) REVERT: D 142 LYS cc_start: 0.7238 (tttm) cc_final: 0.7031 (tmtt) REVERT: D 171 LEU cc_start: 0.8064 (mt) cc_final: 0.7855 (mp) REVERT: D 238 LYS cc_start: 0.7455 (tptt) cc_final: 0.6978 (tptp) REVERT: D 239 MET cc_start: 0.6639 (ttp) cc_final: 0.6337 (ttp) REVERT: D 240 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6371 (mtm) REVERT: D 250 GLN cc_start: 0.7245 (tp40) cc_final: 0.6928 (tp40) REVERT: D 258 TYR cc_start: 0.7437 (t80) cc_final: 0.7121 (t80) REVERT: D 271 SER cc_start: 0.6948 (p) cc_final: 0.6738 (t) REVERT: D 322 TRP cc_start: 0.7506 (t60) cc_final: 0.6873 (t60) REVERT: D 329 ASP cc_start: 0.7021 (m-30) cc_final: 0.6751 (t70) REVERT: D 348 ILE cc_start: 0.7391 (pt) cc_final: 0.6904 (mt) REVERT: D 367 HIS cc_start: 0.6879 (m-70) cc_final: 0.6489 (m-70) REVERT: D 533 TYR cc_start: 0.6540 (t80) cc_final: 0.6240 (t80) REVERT: D 563 GLU cc_start: 0.6149 (pp20) cc_final: 0.5295 (tm-30) REVERT: D 607 GLU cc_start: 0.7290 (tp30) cc_final: 0.7022 (tp30) REVERT: D 611 TRP cc_start: 0.6985 (t60) cc_final: 0.6338 (t60) REVERT: D 627 GLN cc_start: 0.7437 (mt0) cc_final: 0.7046 (mt0) REVERT: D 637 MET cc_start: 0.7014 (tpp) cc_final: 0.6797 (tpt) REVERT: D 640 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6435 (mm-30) REVERT: D 641 ASP cc_start: 0.7064 (p0) cc_final: 0.6491 (t0) REVERT: D 644 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7492 (mm-40) REVERT: D 645 ARG cc_start: 0.7121 (mtm110) cc_final: 0.6240 (mtm180) REVERT: D 748 LEU cc_start: 0.7745 (mt) cc_final: 0.7528 (mt) REVERT: D 767 HIS cc_start: 0.7231 (t-90) cc_final: 0.6946 (t-90) REVERT: D 787 CYS cc_start: 0.7368 (m) cc_final: 0.7127 (m) REVERT: D 806 SER cc_start: 0.7619 (p) cc_final: 0.7399 (m) REVERT: D 853 THR cc_start: 0.8287 (t) cc_final: 0.8043 (p) REVERT: D 859 ARG cc_start: 0.7228 (mtt-85) cc_final: 0.7013 (mtt-85) REVERT: D 933 CYS cc_start: 0.6831 (m) cc_final: 0.6545 (m) REVERT: D 973 LYS cc_start: 0.8232 (ptmt) cc_final: 0.7820 (ptpp) REVERT: D 990 CYS cc_start: 0.7714 (m) cc_final: 0.7099 (m) REVERT: D 1019 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7586 (tp30) REVERT: D 1022 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7469 (tm-30) REVERT: D 1030 VAL cc_start: 0.7758 (p) cc_final: 0.7495 (t) REVERT: E 172 ARG cc_start: 0.6796 (mtt90) cc_final: 0.6530 (mtt90) REVERT: E 175 LYS cc_start: 0.7980 (tttt) cc_final: 0.7673 (tttt) REVERT: E 238 LYS cc_start: 0.7604 (tptt) cc_final: 0.7364 (tptt) REVERT: E 282 ASP cc_start: 0.5908 (p0) cc_final: 0.5703 (p0) REVERT: E 289 LYS cc_start: 0.7596 (pttt) cc_final: 0.7392 (pttp) REVERT: E 311 PHE cc_start: 0.7409 (t80) cc_final: 0.7070 (t80) REVERT: E 322 TRP cc_start: 0.6792 (t60) cc_final: 0.6530 (t60) REVERT: E 367 HIS cc_start: 0.6620 (m-70) cc_final: 0.6388 (m-70) REVERT: E 375 GLU cc_start: 0.7077 (tt0) cc_final: 0.6800 (tt0) REVERT: E 384 LYS cc_start: 0.7819 (mttt) cc_final: 0.7583 (mtmm) REVERT: E 404 VAL cc_start: 0.7796 (t) cc_final: 0.7413 (p) REVERT: E 409 CYS cc_start: 0.7404 (m) cc_final: 0.6905 (t) REVERT: E 413 LEU cc_start: 0.8166 (tp) cc_final: 0.7932 (tt) REVERT: E 415 CYS cc_start: 0.6342 (m) cc_final: 0.4396 (m) REVERT: E 419 CYS cc_start: 0.7602 (m) cc_final: 0.7067 (m) REVERT: E 563 GLU cc_start: 0.6018 (pp20) cc_final: 0.5178 (tm-30) REVERT: E 629 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6846 (tp30) REVERT: E 631 PHE cc_start: 0.7619 (m-10) cc_final: 0.7326 (m-80) REVERT: E 637 MET cc_start: 0.7010 (tpp) cc_final: 0.6770 (tpp) REVERT: E 645 ARG cc_start: 0.7048 (mtm110) cc_final: 0.6639 (mtm110) REVERT: E 648 ASP cc_start: 0.7501 (m-30) cc_final: 0.6993 (t0) REVERT: E 649 TYR cc_start: 0.7296 (m-80) cc_final: 0.7083 (m-80) REVERT: E 741 GLN cc_start: 0.7412 (mm110) cc_final: 0.7099 (mp10) REVERT: E 844 CYS cc_start: 0.7089 (m) cc_final: 0.6885 (m) REVERT: E 853 THR cc_start: 0.8406 (t) cc_final: 0.8037 (p) REVERT: E 859 ARG cc_start: 0.7360 (mtt-85) cc_final: 0.7084 (mtt-85) REVERT: E 878 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8094 (tppt) REVERT: E 880 LYS cc_start: 0.7597 (pttp) cc_final: 0.7392 (ptmt) REVERT: E 933 CYS cc_start: 0.7184 (m) cc_final: 0.6880 (m) REVERT: E 973 LYS cc_start: 0.8298 (ptmt) cc_final: 0.7789 (ptpp) REVERT: E 1006 SER cc_start: 0.7930 (m) cc_final: 0.7348 (t) REVERT: E 1019 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7368 (tp30) REVERT: E 1022 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7005 (tm-30) REVERT: F 144 VAL cc_start: 0.7247 (t) cc_final: 0.7006 (m) REVERT: F 234 ILE cc_start: 0.7392 (pt) cc_final: 0.7181 (pt) REVERT: F 238 LYS cc_start: 0.7456 (tptt) cc_final: 0.7198 (tptp) REVERT: F 239 MET cc_start: 0.6541 (ttp) cc_final: 0.6332 (ttp) REVERT: F 258 TYR cc_start: 0.7497 (t80) cc_final: 0.7240 (t80) REVERT: F 301 MET cc_start: 0.7265 (ttm) cc_final: 0.6809 (ttm) REVERT: F 342 PRO cc_start: 0.7758 (Cg_exo) cc_final: 0.7510 (Cg_endo) REVERT: F 370 ILE cc_start: 0.7444 (mm) cc_final: 0.7218 (tp) REVERT: F 526 GLN cc_start: 0.7001 (tt0) cc_final: 0.6764 (tt0) REVERT: F 533 TYR cc_start: 0.6862 (t80) cc_final: 0.6560 (t80) REVERT: F 563 GLU cc_start: 0.6070 (pp20) cc_final: 0.5115 (tm-30) REVERT: F 569 GLU cc_start: 0.6695 (tp30) cc_final: 0.6047 (tp30) REVERT: F 607 GLU cc_start: 0.7158 (tp30) cc_final: 0.6819 (tp30) REVERT: F 611 TRP cc_start: 0.7011 (t60) cc_final: 0.6498 (t60) REVERT: F 613 GLU cc_start: 0.7200 (tt0) cc_final: 0.6980 (tt0) REVERT: F 644 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7418 (mm-40) REVERT: F 645 ARG cc_start: 0.6963 (mtm110) cc_final: 0.6252 (mpp80) REVERT: F 649 TYR cc_start: 0.7106 (m-80) cc_final: 0.6762 (m-80) REVERT: F 806 SER cc_start: 0.7827 (p) cc_final: 0.7539 (m) REVERT: F 831 LYS cc_start: 0.7850 (mttt) cc_final: 0.7390 (mttt) REVERT: F 853 THR cc_start: 0.8073 (t) cc_final: 0.7718 (p) REVERT: F 876 CYS cc_start: 0.7400 (m) cc_final: 0.6955 (m) REVERT: F 927 LYS cc_start: 0.7804 (ptmt) cc_final: 0.7530 (ptmm) REVERT: F 929 ILE cc_start: 0.8477 (mt) cc_final: 0.8053 (mp) REVERT: F 933 CYS cc_start: 0.7033 (m) cc_final: 0.6774 (m) REVERT: F 1019 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7606 (mm-30) REVERT: F 1022 GLN cc_start: 0.7466 (tm-30) cc_final: 0.7175 (tm-30) REVERT: F 1023 GLU cc_start: 0.6897 (mp0) cc_final: 0.6515 (mp0) REVERT: F 1029 THR cc_start: 0.8025 (m) cc_final: 0.7700 (t) outliers start: 24 outliers final: 11 residues processed: 1121 average time/residue: 0.5156 time to fit residues: 926.8132 Evaluate side-chains 916 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 900 time to evaluate : 4.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 1013 GLU Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain E residue 240 MET Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 1013 GLU Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 1013 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 4.9990 chunk 363 optimal weight: 0.0370 chunk 201 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 376 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 280 optimal weight: 0.6980 chunk 435 optimal weight: 3.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 ASN C 674 HIS C 824 HIS ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 GLN D 771 ASN D 824 HIS D 893 ASN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 GLN E 638 GLN E 741 GLN E 824 HIS E 893 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 741 GLN ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 39690 Z= 0.282 Angle : 0.709 11.851 53544 Z= 0.352 Chirality : 0.044 0.248 6078 Planarity : 0.005 0.066 6714 Dihedral : 7.843 161.629 5298 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.43 % Allowed : 11.78 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.12), residues: 4782 helix: -0.32 (0.10), residues: 2166 sheet: -0.86 (0.22), residues: 498 loop : -1.54 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 322 HIS 0.008 0.001 HIS E 938 PHE 0.025 0.002 PHE B 568 TYR 0.023 0.002 TYR E 635 ARG 0.013 0.001 ARG E 779 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 950 time to evaluate : 4.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.7329 (t80) cc_final: 0.7072 (t80) REVERT: A 239 MET cc_start: 0.6733 (ttp) cc_final: 0.6431 (ttp) REVERT: A 301 MET cc_start: 0.6815 (ttm) cc_final: 0.6571 (ttp) REVERT: A 326 GLU cc_start: 0.7267 (tp30) cc_final: 0.6574 (tm-30) REVERT: A 329 ASP cc_start: 0.7838 (m-30) cc_final: 0.7586 (m-30) REVERT: A 348 ILE cc_start: 0.7440 (pt) cc_final: 0.7150 (mt) REVERT: A 351 ARG cc_start: 0.7488 (mtm180) cc_final: 0.7245 (mtm180) REVERT: A 369 GLU cc_start: 0.7075 (tt0) cc_final: 0.6845 (tt0) REVERT: A 419 CYS cc_start: 0.7717 (m) cc_final: 0.7359 (m) REVERT: A 523 MET cc_start: 0.7106 (tpp) cc_final: 0.6762 (mmm) REVERT: A 603 GLN cc_start: 0.7785 (tp40) cc_final: 0.7033 (tm-30) REVERT: A 607 GLU cc_start: 0.7674 (tp30) cc_final: 0.7451 (tp30) REVERT: A 613 GLU cc_start: 0.7464 (tt0) cc_final: 0.6868 (tt0) REVERT: A 631 PHE cc_start: 0.7573 (m-10) cc_final: 0.7308 (m-80) REVERT: A 637 MET cc_start: 0.6985 (tpp) cc_final: 0.6717 (tpt) REVERT: A 652 LYS cc_start: 0.8047 (ttmt) cc_final: 0.7764 (ttmm) REVERT: A 660 ARG cc_start: 0.6971 (tpp80) cc_final: 0.6550 (ttm-80) REVERT: A 661 MET cc_start: 0.7681 (tpt) cc_final: 0.7470 (tpt) REVERT: A 669 CYS cc_start: 0.7181 (m) cc_final: 0.6388 (m) REVERT: A 759 ARG cc_start: 0.7803 (ttt180) cc_final: 0.7550 (ttt-90) REVERT: A 840 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7942 (p) REVERT: A 930 LYS cc_start: 0.8046 (mttt) cc_final: 0.7602 (mttt) REVERT: A 973 LYS cc_start: 0.8212 (ptmt) cc_final: 0.7625 (ptpp) REVERT: A 990 CYS cc_start: 0.7312 (m) cc_final: 0.6656 (m) REVERT: A 1006 SER cc_start: 0.8443 (m) cc_final: 0.7872 (t) REVERT: A 1009 TYR cc_start: 0.6509 (m-80) cc_final: 0.6267 (m-10) REVERT: B 239 MET cc_start: 0.6379 (ttp) cc_final: 0.6171 (ttp) REVERT: B 250 GLN cc_start: 0.6888 (tp40) cc_final: 0.6630 (mm-40) REVERT: B 288 HIS cc_start: 0.7597 (m90) cc_final: 0.7354 (m90) REVERT: B 306 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6103 (mm-30) REVERT: B 337 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6990 (mpp80) REVERT: B 367 HIS cc_start: 0.7048 (m-70) cc_final: 0.6738 (m-70) REVERT: B 369 GLU cc_start: 0.6820 (tt0) cc_final: 0.6565 (tt0) REVERT: B 409 CYS cc_start: 0.7586 (m) cc_final: 0.6624 (p) REVERT: B 523 MET cc_start: 0.7386 (tpt) cc_final: 0.6127 (tpt) REVERT: B 563 GLU cc_start: 0.7055 (pp20) cc_final: 0.6649 (tm-30) REVERT: B 599 LYS cc_start: 0.7529 (tptt) cc_final: 0.6876 (tptt) REVERT: B 603 GLN cc_start: 0.7589 (tp40) cc_final: 0.6927 (tm-30) REVERT: B 644 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7808 (mm-40) REVERT: B 647 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8140 (mtm) REVERT: B 652 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7925 (ttmm) REVERT: B 785 GLU cc_start: 0.7778 (pt0) cc_final: 0.7396 (pt0) REVERT: B 826 LEU cc_start: 0.7643 (tp) cc_final: 0.7342 (tt) REVERT: B 831 LYS cc_start: 0.7963 (mttt) cc_final: 0.7315 (mttm) REVERT: B 929 ILE cc_start: 0.8386 (mp) cc_final: 0.7924 (mt) REVERT: B 934 GLU cc_start: 0.6713 (tm-30) cc_final: 0.6044 (tm-30) REVERT: B 973 LYS cc_start: 0.8197 (ptmt) cc_final: 0.7947 (ptmm) REVERT: B 988 MET cc_start: 0.7550 (mmm) cc_final: 0.7090 (tmm) REVERT: B 1006 SER cc_start: 0.8231 (m) cc_final: 0.7883 (p) REVERT: B 1008 MET cc_start: 0.6493 (mmm) cc_final: 0.6033 (ttt) REVERT: B 1013 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7301 (tm-30) REVERT: B 1019 GLU cc_start: 0.8287 (tp30) cc_final: 0.7915 (mm-30) REVERT: B 1023 GLU cc_start: 0.7266 (mp0) cc_final: 0.6943 (mp0) REVERT: B 1025 LYS cc_start: 0.6824 (mmtt) cc_final: 0.6413 (mmtt) REVERT: C 213 ASP cc_start: 0.7494 (t0) cc_final: 0.7277 (t0) REVERT: C 224 PHE cc_start: 0.7872 (m-10) cc_final: 0.7648 (m-10) REVERT: C 239 MET cc_start: 0.6544 (ttp) cc_final: 0.6299 (ttp) REVERT: C 311 PHE cc_start: 0.7500 (t80) cc_final: 0.7211 (t80) REVERT: C 337 ARG cc_start: 0.7407 (mtt180) cc_final: 0.7204 (mtm180) REVERT: C 351 ARG cc_start: 0.7242 (mtm180) cc_final: 0.6965 (mtm180) REVERT: C 367 HIS cc_start: 0.7106 (m-70) cc_final: 0.6560 (m-70) REVERT: C 369 GLU cc_start: 0.7010 (tt0) cc_final: 0.6669 (tt0) REVERT: C 385 TYR cc_start: 0.8072 (t80) cc_final: 0.7758 (t80) REVERT: C 419 CYS cc_start: 0.7876 (m) cc_final: 0.7268 (m) REVERT: C 488 ASP cc_start: 0.7606 (m-30) cc_final: 0.7253 (m-30) REVERT: C 603 GLN cc_start: 0.7782 (tp40) cc_final: 0.7167 (tm-30) REVERT: C 607 GLU cc_start: 0.7479 (tp30) cc_final: 0.7267 (tp30) REVERT: C 637 MET cc_start: 0.7029 (tpp) cc_final: 0.6517 (tpt) REVERT: C 640 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6775 (mt-10) REVERT: C 645 ARG cc_start: 0.7333 (mtm110) cc_final: 0.7009 (mtm-85) REVERT: C 649 TYR cc_start: 0.7319 (m-80) cc_final: 0.7034 (m-80) REVERT: C 802 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6314 (mt-10) REVERT: C 853 THR cc_start: 0.8258 (t) cc_final: 0.7893 (p) REVERT: C 933 CYS cc_start: 0.7666 (p) cc_final: 0.7428 (p) REVERT: C 938 HIS cc_start: 0.7713 (t-90) cc_final: 0.7321 (t-170) REVERT: C 991 GLU cc_start: 0.7098 (pm20) cc_final: 0.6827 (pm20) REVERT: C 1009 TYR cc_start: 0.6758 (m-80) cc_final: 0.6377 (m-80) REVERT: D 142 LYS cc_start: 0.7234 (tttm) cc_final: 0.6957 (tmtt) REVERT: D 238 LYS cc_start: 0.7463 (tptt) cc_final: 0.7053 (tptp) REVERT: D 239 MET cc_start: 0.6583 (ttp) cc_final: 0.6304 (ttp) REVERT: D 240 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6485 (mtm) REVERT: D 250 GLN cc_start: 0.7224 (tp40) cc_final: 0.6936 (tp40) REVERT: D 301 MET cc_start: 0.7145 (ttp) cc_final: 0.6577 (ttp) REVERT: D 329 ASP cc_start: 0.7234 (m-30) cc_final: 0.6973 (t70) REVERT: D 348 ILE cc_start: 0.7720 (pt) cc_final: 0.7464 (mt) REVERT: D 378 ARG cc_start: 0.6734 (mtt180) cc_final: 0.6288 (mtt180) REVERT: D 415 CYS cc_start: 0.6396 (m) cc_final: 0.6150 (m) REVERT: D 637 MET cc_start: 0.6977 (tpp) cc_final: 0.6558 (tpp) REVERT: D 640 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6465 (mm-30) REVERT: D 641 ASP cc_start: 0.7071 (p0) cc_final: 0.6850 (t0) REVERT: D 644 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7810 (mm-40) REVERT: D 741 GLN cc_start: 0.7267 (mm110) cc_final: 0.6958 (mm110) REVERT: D 800 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8236 (mp) REVERT: D 806 SER cc_start: 0.7625 (p) cc_final: 0.7389 (m) REVERT: D 853 THR cc_start: 0.8363 (t) cc_final: 0.8029 (p) REVERT: D 880 LYS cc_start: 0.7743 (pttt) cc_final: 0.7319 (ptmt) REVERT: D 883 GLN cc_start: 0.6184 (pm20) cc_final: 0.5849 (pm20) REVERT: D 929 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7942 (mp) REVERT: D 933 CYS cc_start: 0.7314 (m) cc_final: 0.6980 (m) REVERT: D 973 LYS cc_start: 0.8277 (ptmt) cc_final: 0.7861 (ptpp) REVERT: D 990 CYS cc_start: 0.7528 (m) cc_final: 0.6821 (m) REVERT: D 1006 SER cc_start: 0.8178 (m) cc_final: 0.7705 (t) REVERT: D 1019 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7596 (mm-30) REVERT: D 1022 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7706 (tm-30) REVERT: D 1023 GLU cc_start: 0.6199 (mp0) cc_final: 0.5718 (mp0) REVERT: E 138 LYS cc_start: 0.7401 (tmmt) cc_final: 0.7060 (tmmt) REVERT: E 172 ARG cc_start: 0.6828 (mtt90) cc_final: 0.6538 (mtt90) REVERT: E 175 LYS cc_start: 0.8005 (tttt) cc_final: 0.7725 (tttt) REVERT: E 210 ASP cc_start: 0.8057 (p0) cc_final: 0.7728 (p0) REVERT: E 269 GLN cc_start: 0.5432 (mp10) cc_final: 0.4042 (mp10) REVERT: E 272 LEU cc_start: 0.7791 (mt) cc_final: 0.7365 (tt) REVERT: E 289 LYS cc_start: 0.7694 (pttt) cc_final: 0.7452 (pttp) REVERT: E 326 GLU cc_start: 0.7164 (tp30) cc_final: 0.6463 (pp20) REVERT: E 351 ARG cc_start: 0.7342 (mtp180) cc_final: 0.7116 (mtm180) REVERT: E 367 HIS cc_start: 0.6856 (m-70) cc_final: 0.6474 (m-70) REVERT: E 383 PHE cc_start: 0.7698 (m-10) cc_final: 0.7396 (m-10) REVERT: E 404 VAL cc_start: 0.7868 (t) cc_final: 0.7457 (p) REVERT: E 409 CYS cc_start: 0.7729 (m) cc_final: 0.7044 (t) REVERT: E 415 CYS cc_start: 0.6631 (m) cc_final: 0.4802 (m) REVERT: E 419 CYS cc_start: 0.7637 (m) cc_final: 0.7207 (m) REVERT: E 610 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8066 (ttmm) REVERT: E 611 TRP cc_start: 0.7409 (t60) cc_final: 0.6652 (t60) REVERT: E 613 GLU cc_start: 0.7405 (tt0) cc_final: 0.7019 (tt0) REVERT: E 630 LEU cc_start: 0.8592 (tt) cc_final: 0.8265 (tt) REVERT: E 631 PHE cc_start: 0.7683 (m-10) cc_final: 0.7430 (m-80) REVERT: E 634 LEU cc_start: 0.8799 (mm) cc_final: 0.8474 (mm) REVERT: E 647 MET cc_start: 0.8047 (ttp) cc_final: 0.7715 (mtm) REVERT: E 648 ASP cc_start: 0.7718 (m-30) cc_final: 0.7411 (t0) REVERT: E 649 TYR cc_start: 0.7272 (m-80) cc_final: 0.6276 (m-80) REVERT: E 660 ARG cc_start: 0.6492 (tpp80) cc_final: 0.6273 (ttm-80) REVERT: E 741 GLN cc_start: 0.7306 (mm-40) cc_final: 0.6956 (mp10) REVERT: E 785 GLU cc_start: 0.7715 (pt0) cc_final: 0.7429 (pt0) REVERT: E 831 LYS cc_start: 0.8406 (mttt) cc_final: 0.7907 (mttp) REVERT: E 853 THR cc_start: 0.8432 (t) cc_final: 0.8024 (p) REVERT: E 859 ARG cc_start: 0.7456 (mtt-85) cc_final: 0.7222 (mtt-85) REVERT: E 878 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8143 (tppt) REVERT: E 880 LYS cc_start: 0.7750 (pttp) cc_final: 0.7489 (ptmt) REVERT: E 893 ASN cc_start: 0.8040 (t160) cc_final: 0.7824 (t0) REVERT: E 933 CYS cc_start: 0.7641 (m) cc_final: 0.7347 (p) REVERT: E 973 LYS cc_start: 0.8363 (ptmt) cc_final: 0.7808 (ptpp) REVERT: E 987 MET cc_start: 0.5799 (mmt) cc_final: 0.5166 (mmm) REVERT: E 1006 SER cc_start: 0.8134 (m) cc_final: 0.7526 (t) REVERT: E 1019 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7153 (tp30) REVERT: E 1022 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7244 (tm-30) REVERT: E 1023 GLU cc_start: 0.6173 (mp0) cc_final: 0.4655 (mp0) REVERT: F 172 ARG cc_start: 0.6520 (mtt90) cc_final: 0.5905 (mtt90) REVERT: F 238 LYS cc_start: 0.7484 (tptt) cc_final: 0.7249 (tptp) REVERT: F 239 MET cc_start: 0.6560 (ttp) cc_final: 0.6340 (ttp) REVERT: F 301 MET cc_start: 0.6852 (ttm) cc_final: 0.6124 (ttp) REVERT: F 337 ARG cc_start: 0.6807 (mpp80) cc_final: 0.6587 (mpp80) REVERT: F 338 LYS cc_start: 0.7965 (mtmm) cc_final: 0.7449 (mtmt) REVERT: F 348 ILE cc_start: 0.7377 (pt) cc_final: 0.7105 (mt) REVERT: F 369 GLU cc_start: 0.6924 (tt0) cc_final: 0.6449 (tt0) REVERT: F 415 CYS cc_start: 0.6414 (m) cc_final: 0.6206 (m) REVERT: F 569 GLU cc_start: 0.6827 (tp30) cc_final: 0.6183 (tp30) REVERT: F 607 GLU cc_start: 0.7190 (tp30) cc_final: 0.6920 (tp30) REVERT: F 613 GLU cc_start: 0.7353 (tt0) cc_final: 0.7085 (tt0) REVERT: F 637 MET cc_start: 0.7269 (tpt) cc_final: 0.6849 (tpt) REVERT: F 644 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7553 (mm-40) REVERT: F 649 TYR cc_start: 0.7252 (m-80) cc_final: 0.6675 (m-80) REVERT: F 806 SER cc_start: 0.7765 (p) cc_final: 0.7518 (m) REVERT: F 831 LYS cc_start: 0.7821 (mttt) cc_final: 0.7612 (mttp) REVERT: F 853 THR cc_start: 0.8214 (t) cc_final: 0.7776 (p) REVERT: F 876 CYS cc_start: 0.7651 (m) cc_final: 0.7127 (m) REVERT: F 929 ILE cc_start: 0.8635 (mt) cc_final: 0.8133 (mp) REVERT: F 1006 SER cc_start: 0.8122 (m) cc_final: 0.7717 (t) REVERT: F 1019 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7695 (mm-30) REVERT: F 1029 THR cc_start: 0.8259 (m) cc_final: 0.7874 (t) outliers start: 107 outliers final: 73 residues processed: 990 average time/residue: 0.5374 time to fit residues: 862.4346 Evaluate side-chains 963 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 885 time to evaluate : 4.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 828 ASN Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 812 ASP Chi-restraints excluded: chain B residue 828 ASN Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 897 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 987 MET Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 783 SER Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 771 ASN Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 849 SER Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 897 THR Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 792 LEU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 874 ILE Chi-restraints excluded: chain E residue 899 VAL Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 970 SER Chi-restraints excluded: chain E residue 1028 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 812 ASP Chi-restraints excluded: chain F residue 828 ASN Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 910 THR Chi-restraints excluded: chain F residue 948 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 362 optimal weight: 0.8980 chunk 296 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 436 optimal weight: 5.9990 chunk 471 optimal weight: 1.9990 chunk 388 optimal weight: 0.0870 chunk 433 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 350 optimal weight: 4.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN B 225 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 845 GLN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 912 GLN ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 952 ASN ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 938 HIS E 952 ASN E1002 ASN F 269 GLN ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 GLN ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 952 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 39690 Z= 0.194 Angle : 0.626 11.796 53544 Z= 0.306 Chirality : 0.041 0.189 6078 Planarity : 0.005 0.069 6714 Dihedral : 7.392 156.311 5259 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.75 % Allowed : 15.37 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.12), residues: 4782 helix: -0.20 (0.11), residues: 2178 sheet: -1.52 (0.21), residues: 600 loop : -1.31 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 243 HIS 0.023 0.001 HIS B 938 PHE 0.026 0.002 PHE D 729 TYR 0.021 0.002 TYR B 635 ARG 0.011 0.000 ARG C 731 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 917 time to evaluate : 4.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.7312 (t80) cc_final: 0.6989 (t80) REVERT: A 239 MET cc_start: 0.6643 (ttp) cc_final: 0.6356 (ttp) REVERT: A 301 MET cc_start: 0.6785 (ttm) cc_final: 0.6353 (ttp) REVERT: A 326 GLU cc_start: 0.7279 (tp30) cc_final: 0.7041 (tp30) REVERT: A 329 ASP cc_start: 0.7886 (m-30) cc_final: 0.7663 (m-30) REVERT: A 351 ARG cc_start: 0.7478 (mtm180) cc_final: 0.7260 (mtm180) REVERT: A 369 GLU cc_start: 0.7010 (tt0) cc_final: 0.6794 (tt0) REVERT: A 419 CYS cc_start: 0.7699 (m) cc_final: 0.7323 (m) REVERT: A 563 GLU cc_start: 0.6941 (pp20) cc_final: 0.6630 (tm-30) REVERT: A 603 GLN cc_start: 0.7727 (tp40) cc_final: 0.6981 (tm-30) REVERT: A 607 GLU cc_start: 0.7617 (tp30) cc_final: 0.7397 (tp30) REVERT: A 613 GLU cc_start: 0.7411 (tt0) cc_final: 0.6831 (tt0) REVERT: A 631 PHE cc_start: 0.7567 (m-10) cc_final: 0.7361 (m-80) REVERT: A 652 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7840 (ttmm) REVERT: A 669 CYS cc_start: 0.7130 (m) cc_final: 0.6455 (m) REVERT: A 930 LYS cc_start: 0.8021 (mttt) cc_final: 0.7576 (mttt) REVERT: A 973 LYS cc_start: 0.8218 (ptmt) cc_final: 0.7643 (ptpp) REVERT: A 990 CYS cc_start: 0.7271 (m) cc_final: 0.6572 (m) REVERT: A 1006 SER cc_start: 0.8432 (m) cc_final: 0.7909 (t) REVERT: A 1009 TYR cc_start: 0.6458 (m-80) cc_final: 0.6206 (m-80) REVERT: B 168 TYR cc_start: 0.7615 (t80) cc_final: 0.7318 (t80) REVERT: B 238 LYS cc_start: 0.7318 (tptt) cc_final: 0.6948 (tptp) REVERT: B 239 MET cc_start: 0.6386 (ttp) cc_final: 0.6172 (ttp) REVERT: B 250 GLN cc_start: 0.6847 (tp40) cc_final: 0.6533 (mp10) REVERT: B 272 LEU cc_start: 0.7545 (tp) cc_final: 0.7157 (tt) REVERT: B 306 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6639 (mm-30) REVERT: B 337 ARG cc_start: 0.7220 (mtt180) cc_final: 0.6959 (mpp80) REVERT: B 367 HIS cc_start: 0.7052 (m-70) cc_final: 0.6771 (m-70) REVERT: B 409 CYS cc_start: 0.7602 (m) cc_final: 0.6620 (p) REVERT: B 527 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6678 (mm-30) REVERT: B 563 GLU cc_start: 0.7051 (pp20) cc_final: 0.6793 (tm-30) REVERT: B 603 GLN cc_start: 0.7537 (tp40) cc_final: 0.6863 (tm-30) REVERT: B 613 GLU cc_start: 0.7533 (tt0) cc_final: 0.7163 (tt0) REVERT: B 632 TYR cc_start: 0.7391 (m-80) cc_final: 0.6704 (m-80) REVERT: B 637 MET cc_start: 0.7128 (tpt) cc_final: 0.6910 (tpt) REVERT: B 644 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7657 (mm-40) REVERT: B 758 MET cc_start: 0.6866 (tpt) cc_final: 0.6586 (tpt) REVERT: B 785 GLU cc_start: 0.7703 (pt0) cc_final: 0.7292 (pt0) REVERT: B 826 LEU cc_start: 0.7698 (tp) cc_final: 0.7378 (tt) REVERT: B 934 GLU cc_start: 0.6580 (tm-30) cc_final: 0.5988 (tm-30) REVERT: B 988 MET cc_start: 0.7455 (mmm) cc_final: 0.6964 (tmm) REVERT: B 1008 MET cc_start: 0.6466 (mmm) cc_final: 0.5970 (ttt) REVERT: B 1013 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7273 (tm-30) REVERT: C 224 PHE cc_start: 0.7855 (m-10) cc_final: 0.7650 (m-10) REVERT: C 239 MET cc_start: 0.6461 (ttp) cc_final: 0.6230 (ttp) REVERT: C 282 ASP cc_start: 0.6152 (p0) cc_final: 0.5934 (p0) REVERT: C 301 MET cc_start: 0.6879 (ttm) cc_final: 0.6367 (ttp) REVERT: C 311 PHE cc_start: 0.7556 (t80) cc_final: 0.7246 (t80) REVERT: C 329 ASP cc_start: 0.7737 (m-30) cc_final: 0.7507 (m-30) REVERT: C 348 ILE cc_start: 0.7695 (pt) cc_final: 0.7494 (mt) REVERT: C 351 ARG cc_start: 0.7257 (mtm180) cc_final: 0.6974 (mtm180) REVERT: C 367 HIS cc_start: 0.7091 (m-70) cc_final: 0.6503 (m-70) REVERT: C 385 TYR cc_start: 0.8088 (t80) cc_final: 0.7879 (t80) REVERT: C 409 CYS cc_start: 0.7602 (m) cc_final: 0.7301 (t) REVERT: C 419 CYS cc_start: 0.7905 (m) cc_final: 0.7359 (m) REVERT: C 488 ASP cc_start: 0.7576 (m-30) cc_final: 0.7218 (m-30) REVERT: C 599 LYS cc_start: 0.7663 (tptt) cc_final: 0.7062 (tptt) REVERT: C 603 GLN cc_start: 0.7706 (tp40) cc_final: 0.7130 (tm-30) REVERT: C 607 GLU cc_start: 0.7462 (tp30) cc_final: 0.7239 (tp30) REVERT: C 637 MET cc_start: 0.6998 (tpp) cc_final: 0.6738 (tpt) REVERT: C 640 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6801 (mt-10) REVERT: C 659 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7460 (t) REVERT: C 774 ARG cc_start: 0.7436 (mtm110) cc_final: 0.6815 (mtm-85) REVERT: C 853 THR cc_start: 0.8244 (t) cc_final: 0.7845 (p) REVERT: C 864 GLU cc_start: 0.7144 (tp30) cc_final: 0.6808 (tp30) REVERT: C 930 LYS cc_start: 0.7983 (mttt) cc_final: 0.7693 (mttt) REVERT: C 933 CYS cc_start: 0.7702 (p) cc_final: 0.7455 (p) REVERT: C 991 GLU cc_start: 0.7071 (pm20) cc_final: 0.6721 (pm20) REVERT: C 1006 SER cc_start: 0.8296 (m) cc_final: 0.7752 (t) REVERT: C 1009 TYR cc_start: 0.6701 (m-80) cc_final: 0.6338 (m-80) REVERT: D 142 LYS cc_start: 0.7157 (tttm) cc_final: 0.6863 (tmtt) REVERT: D 238 LYS cc_start: 0.7406 (tptt) cc_final: 0.7021 (tptp) REVERT: D 239 MET cc_start: 0.6499 (ttp) cc_final: 0.6243 (ttp) REVERT: D 250 GLN cc_start: 0.7203 (tp40) cc_final: 0.6935 (tp40) REVERT: D 301 MET cc_start: 0.7165 (ttp) cc_final: 0.6686 (ttp) REVERT: D 329 ASP cc_start: 0.7275 (m-30) cc_final: 0.6988 (t70) REVERT: D 367 HIS cc_start: 0.7096 (m-70) cc_final: 0.6721 (m-70) REVERT: D 369 GLU cc_start: 0.6808 (tt0) cc_final: 0.6486 (tt0) REVERT: D 384 LYS cc_start: 0.8004 (mtmm) cc_final: 0.7799 (mtmm) REVERT: D 415 CYS cc_start: 0.6263 (m) cc_final: 0.5980 (m) REVERT: D 532 MET cc_start: 0.7866 (tpt) cc_final: 0.7062 (tpt) REVERT: D 563 GLU cc_start: 0.6442 (pp20) cc_final: 0.6162 (tm-30) REVERT: D 603 GLN cc_start: 0.7480 (tp40) cc_final: 0.7140 (tp40) REVERT: D 627 GLN cc_start: 0.7482 (mt0) cc_final: 0.7055 (mt0) REVERT: D 640 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6510 (mm-30) REVERT: D 641 ASP cc_start: 0.7098 (p0) cc_final: 0.6850 (t0) REVERT: D 644 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7814 (mm-40) REVERT: D 645 ARG cc_start: 0.7264 (mtm110) cc_final: 0.6395 (mtm110) REVERT: D 741 GLN cc_start: 0.7176 (mm110) cc_final: 0.6870 (mm110) REVERT: D 853 THR cc_start: 0.8382 (t) cc_final: 0.8018 (p) REVERT: D 880 LYS cc_start: 0.7824 (pttt) cc_final: 0.7372 (ptmt) REVERT: D 883 GLN cc_start: 0.6165 (pm20) cc_final: 0.5827 (pm20) REVERT: D 929 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7990 (mp) REVERT: D 933 CYS cc_start: 0.7308 (m) cc_final: 0.6983 (m) REVERT: D 973 LYS cc_start: 0.8284 (ptmt) cc_final: 0.7854 (ptpp) REVERT: D 990 CYS cc_start: 0.7449 (m) cc_final: 0.6741 (m) REVERT: D 1005 LEU cc_start: 0.7078 (mp) cc_final: 0.6747 (mp) REVERT: D 1006 SER cc_start: 0.8209 (m) cc_final: 0.7754 (t) REVERT: D 1019 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7196 (tp30) REVERT: D 1022 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7620 (tm-30) REVERT: D 1023 GLU cc_start: 0.6180 (mp0) cc_final: 0.4442 (mp0) REVERT: E 138 LYS cc_start: 0.7340 (tmmt) cc_final: 0.6998 (tmmt) REVERT: E 172 ARG cc_start: 0.6803 (mtt90) cc_final: 0.6418 (mtt90) REVERT: E 175 LYS cc_start: 0.7986 (tttt) cc_final: 0.7705 (tttt) REVERT: E 272 LEU cc_start: 0.7726 (mt) cc_final: 0.7450 (tt) REVERT: E 289 LYS cc_start: 0.7648 (pttt) cc_final: 0.7410 (pttp) REVERT: E 351 ARG cc_start: 0.7378 (mtp180) cc_final: 0.7176 (mtm180) REVERT: E 369 GLU cc_start: 0.7139 (tt0) cc_final: 0.6604 (tt0) REVERT: E 404 VAL cc_start: 0.7859 (t) cc_final: 0.7386 (p) REVERT: E 409 CYS cc_start: 0.7723 (m) cc_final: 0.7000 (t) REVERT: E 415 CYS cc_start: 0.6491 (m) cc_final: 0.4623 (m) REVERT: E 417 ILE cc_start: 0.7422 (mt) cc_final: 0.7222 (mm) REVERT: E 419 CYS cc_start: 0.7617 (m) cc_final: 0.7182 (m) REVERT: E 563 GLU cc_start: 0.6391 (pp20) cc_final: 0.6069 (tm-30) REVERT: E 610 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8066 (ttmm) REVERT: E 611 TRP cc_start: 0.7437 (t60) cc_final: 0.6782 (t60) REVERT: E 613 GLU cc_start: 0.7337 (tt0) cc_final: 0.6979 (tt0) REVERT: E 630 LEU cc_start: 0.8580 (tt) cc_final: 0.8256 (tt) REVERT: E 634 LEU cc_start: 0.8764 (mm) cc_final: 0.8368 (mm) REVERT: E 637 MET cc_start: 0.7015 (tpp) cc_final: 0.6759 (tpp) REVERT: E 645 ARG cc_start: 0.7681 (mmm160) cc_final: 0.7223 (mmm160) REVERT: E 648 ASP cc_start: 0.7722 (m-30) cc_final: 0.7413 (t0) REVERT: E 649 TYR cc_start: 0.7204 (m-80) cc_final: 0.6406 (m-80) REVERT: E 731 ARG cc_start: 0.6745 (ttm170) cc_final: 0.6522 (ttm110) REVERT: E 741 GLN cc_start: 0.7170 (mm-40) cc_final: 0.6859 (mp10) REVERT: E 785 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: E 826 LEU cc_start: 0.7670 (tp) cc_final: 0.7264 (tt) REVERT: E 831 LYS cc_start: 0.8362 (mttt) cc_final: 0.8049 (mttp) REVERT: E 853 THR cc_start: 0.8476 (t) cc_final: 0.8060 (p) REVERT: E 859 ARG cc_start: 0.7414 (mtt-85) cc_final: 0.7183 (mtt-85) REVERT: E 864 GLU cc_start: 0.7270 (tp30) cc_final: 0.7046 (tp30) REVERT: E 878 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8140 (tppt) REVERT: E 880 LYS cc_start: 0.7810 (pttp) cc_final: 0.7594 (ptmt) REVERT: E 933 CYS cc_start: 0.7606 (m) cc_final: 0.7314 (p) REVERT: E 973 LYS cc_start: 0.8366 (ptmt) cc_final: 0.7793 (ptpp) REVERT: E 987 MET cc_start: 0.5773 (mmt) cc_final: 0.5225 (mmm) REVERT: E 1003 LEU cc_start: 0.7945 (tt) cc_final: 0.7733 (tt) REVERT: E 1006 SER cc_start: 0.8145 (m) cc_final: 0.7587 (t) REVERT: E 1009 TYR cc_start: 0.6432 (m-80) cc_final: 0.6100 (m-80) REVERT: E 1019 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7091 (tp30) REVERT: E 1022 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7179 (tm-30) REVERT: E 1023 GLU cc_start: 0.6171 (mp0) cc_final: 0.4491 (mp0) REVERT: F 143 TYR cc_start: 0.6637 (t80) cc_final: 0.6392 (t80) REVERT: F 238 LYS cc_start: 0.7530 (tptt) cc_final: 0.7278 (tptp) REVERT: F 301 MET cc_start: 0.6926 (ttm) cc_final: 0.6286 (ttp) REVERT: F 337 ARG cc_start: 0.6787 (mpp80) cc_final: 0.6546 (mpp80) REVERT: F 338 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7433 (mtmt) REVERT: F 369 GLU cc_start: 0.6796 (tt0) cc_final: 0.6561 (tt0) REVERT: F 410 PHE cc_start: 0.7322 (p90) cc_final: 0.7056 (p90) REVERT: F 415 CYS cc_start: 0.6387 (m) cc_final: 0.6149 (m) REVERT: F 563 GLU cc_start: 0.6282 (pp20) cc_final: 0.5753 (tm-30) REVERT: F 569 GLU cc_start: 0.6819 (tp30) cc_final: 0.6363 (tp30) REVERT: F 585 ASN cc_start: 0.7881 (t0) cc_final: 0.7489 (t0) REVERT: F 603 GLN cc_start: 0.6977 (tp40) cc_final: 0.6185 (tm-30) REVERT: F 607 GLU cc_start: 0.7159 (tp30) cc_final: 0.6765 (tp30) REVERT: F 613 GLU cc_start: 0.7336 (tt0) cc_final: 0.7043 (tt0) REVERT: F 637 MET cc_start: 0.7338 (tpt) cc_final: 0.6954 (tpt) REVERT: F 644 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7441 (mm-40) REVERT: F 647 MET cc_start: 0.8110 (ttp) cc_final: 0.7620 (mtm) REVERT: F 649 TYR cc_start: 0.7194 (m-80) cc_final: 0.6660 (m-80) REVERT: F 831 LYS cc_start: 0.7798 (mttt) cc_final: 0.7591 (mttt) REVERT: F 853 THR cc_start: 0.8248 (t) cc_final: 0.7844 (p) REVERT: F 876 CYS cc_start: 0.7651 (m) cc_final: 0.7142 (m) REVERT: F 929 ILE cc_start: 0.8564 (mt) cc_final: 0.8102 (mp) REVERT: F 1006 SER cc_start: 0.8170 (m) cc_final: 0.7764 (t) REVERT: F 1019 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7575 (mm-30) REVERT: F 1022 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7187 (tm-30) REVERT: F 1029 THR cc_start: 0.8285 (m) cc_final: 0.7748 (p) outliers start: 121 outliers final: 84 residues processed: 958 average time/residue: 0.5206 time to fit residues: 801.2647 Evaluate side-chains 950 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 863 time to evaluate : 4.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 828 ASN Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 812 ASP Chi-restraints excluded: chain B residue 828 ASN Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 897 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 783 SER Chi-restraints excluded: chain C residue 812 ASP Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 792 LEU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain E residue 828 ASN Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 970 SER Chi-restraints excluded: chain E residue 1028 LEU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 417 ILE Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 812 ASP Chi-restraints excluded: chain F residue 828 ASN Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 910 THR Chi-restraints excluded: chain F residue 948 LEU Chi-restraints excluded: chain F residue 1028 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 1.9990 chunk 328 optimal weight: 0.7980 chunk 226 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 438 optimal weight: 0.9990 chunk 463 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 chunk 415 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 HIS ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 ASN C 627 GLN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 GLN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 GLN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 808 ASN E 885 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 938 HIS ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39690 Z= 0.201 Angle : 0.615 9.971 53544 Z= 0.303 Chirality : 0.041 0.182 6078 Planarity : 0.005 0.065 6714 Dihedral : 7.296 150.071 5256 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.43 % Allowed : 17.69 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.12), residues: 4782 helix: -0.16 (0.11), residues: 2184 sheet: -1.42 (0.21), residues: 594 loop : -1.25 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 243 HIS 0.007 0.001 HIS D 360 PHE 0.032 0.002 PHE F 508 TYR 0.026 0.002 TYR E 143 ARG 0.007 0.000 ARG F 859 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 888 time to evaluate : 4.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.7321 (t80) cc_final: 0.6994 (t80) REVERT: A 239 MET cc_start: 0.6593 (ttp) cc_final: 0.6333 (ttp) REVERT: A 301 MET cc_start: 0.6716 (ttm) cc_final: 0.6370 (ttp) REVERT: A 326 GLU cc_start: 0.7349 (tp30) cc_final: 0.7021 (tp30) REVERT: A 329 ASP cc_start: 0.7944 (m-30) cc_final: 0.7725 (m-30) REVERT: A 351 ARG cc_start: 0.7445 (mtm180) cc_final: 0.7190 (mtm180) REVERT: A 369 GLU cc_start: 0.7066 (tt0) cc_final: 0.6830 (tt0) REVERT: A 419 CYS cc_start: 0.7739 (m) cc_final: 0.7419 (m) REVERT: A 467 TRP cc_start: 0.6272 (t60) cc_final: 0.5791 (t-100) REVERT: A 563 GLU cc_start: 0.7023 (pp20) cc_final: 0.6461 (tm-30) REVERT: A 569 GLU cc_start: 0.7001 (tp30) cc_final: 0.6657 (tp30) REVERT: A 607 GLU cc_start: 0.7631 (tp30) cc_final: 0.7394 (tp30) REVERT: A 613 GLU cc_start: 0.7452 (tt0) cc_final: 0.7180 (tt0) REVERT: A 631 PHE cc_start: 0.7568 (m-10) cc_final: 0.7340 (m-80) REVERT: A 645 ARG cc_start: 0.7796 (mmm160) cc_final: 0.7199 (mmm160) REVERT: A 647 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7861 (ttp) REVERT: A 649 TYR cc_start: 0.7200 (m-80) cc_final: 0.6534 (m-80) REVERT: A 652 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7816 (ttmm) REVERT: A 660 ARG cc_start: 0.6876 (tpp80) cc_final: 0.6454 (ttm-80) REVERT: A 669 CYS cc_start: 0.7113 (m) cc_final: 0.6394 (m) REVERT: A 847 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8135 (mt) REVERT: A 864 GLU cc_start: 0.7199 (tp30) cc_final: 0.6994 (tp30) REVERT: A 930 LYS cc_start: 0.7995 (mttt) cc_final: 0.7558 (mttt) REVERT: A 973 LYS cc_start: 0.8203 (ptmt) cc_final: 0.7653 (ptpp) REVERT: A 974 LEU cc_start: 0.7857 (tt) cc_final: 0.7635 (tt) REVERT: A 991 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6503 (pm20) REVERT: A 1006 SER cc_start: 0.8423 (m) cc_final: 0.7885 (t) REVERT: A 1009 TYR cc_start: 0.6451 (m-80) cc_final: 0.6142 (m-80) REVERT: B 168 TYR cc_start: 0.7587 (t80) cc_final: 0.7335 (t80) REVERT: B 238 LYS cc_start: 0.7277 (tptt) cc_final: 0.6959 (tptp) REVERT: B 250 GLN cc_start: 0.6870 (tp40) cc_final: 0.6545 (mp10) REVERT: B 259 ILE cc_start: 0.7682 (mp) cc_final: 0.7183 (pt) REVERT: B 306 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6539 (mm-30) REVERT: B 337 ARG cc_start: 0.7227 (mtt180) cc_final: 0.6999 (mpp80) REVERT: B 367 HIS cc_start: 0.7068 (m-70) cc_final: 0.6780 (m-70) REVERT: B 409 CYS cc_start: 0.7633 (m) cc_final: 0.6710 (p) REVERT: B 523 MET cc_start: 0.7555 (tpt) cc_final: 0.6942 (tpt) REVERT: B 563 GLU cc_start: 0.7140 (pp20) cc_final: 0.6912 (tm-30) REVERT: B 603 GLN cc_start: 0.7551 (tp40) cc_final: 0.6874 (tm-30) REVERT: B 607 GLU cc_start: 0.7276 (tp30) cc_final: 0.7033 (tp30) REVERT: B 613 GLU cc_start: 0.7555 (tt0) cc_final: 0.7180 (tt0) REVERT: B 632 TYR cc_start: 0.7394 (m-80) cc_final: 0.6712 (m-80) REVERT: B 637 MET cc_start: 0.7212 (tpt) cc_final: 0.6971 (tpt) REVERT: B 785 GLU cc_start: 0.7705 (pt0) cc_final: 0.7217 (pt0) REVERT: B 826 LEU cc_start: 0.7735 (tp) cc_final: 0.7419 (tp) REVERT: B 934 GLU cc_start: 0.6620 (tm-30) cc_final: 0.6016 (tm-30) REVERT: B 988 MET cc_start: 0.7412 (mmm) cc_final: 0.6782 (tmm) REVERT: B 991 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: B 1008 MET cc_start: 0.6470 (mmm) cc_final: 0.5911 (ttt) REVERT: B 1013 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7313 (tm-30) REVERT: C 239 MET cc_start: 0.6452 (ttp) cc_final: 0.6210 (ttp) REVERT: C 282 ASP cc_start: 0.6127 (p0) cc_final: 0.5916 (p0) REVERT: C 337 ARG cc_start: 0.7408 (mtt180) cc_final: 0.7201 (mtm180) REVERT: C 367 HIS cc_start: 0.7154 (m-70) cc_final: 0.6599 (m-70) REVERT: C 409 CYS cc_start: 0.7626 (m) cc_final: 0.7244 (t) REVERT: C 419 CYS cc_start: 0.7980 (m) cc_final: 0.7452 (m) REVERT: C 537 GLU cc_start: 0.5437 (pm20) cc_final: 0.5167 (pm20) REVERT: C 599 LYS cc_start: 0.7696 (tptt) cc_final: 0.7045 (tptt) REVERT: C 603 GLN cc_start: 0.7694 (tp40) cc_final: 0.7075 (tm-30) REVERT: C 607 GLU cc_start: 0.7465 (tp30) cc_final: 0.7255 (tp30) REVERT: C 613 GLU cc_start: 0.7481 (tt0) cc_final: 0.7033 (mt-10) REVERT: C 640 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6563 (mt-10) REVERT: C 641 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6793 (t0) REVERT: C 649 TYR cc_start: 0.7208 (m-80) cc_final: 0.6717 (m-80) REVERT: C 774 ARG cc_start: 0.7389 (mtm110) cc_final: 0.7092 (mtm-85) REVERT: C 853 THR cc_start: 0.8349 (t) cc_final: 0.7985 (p) REVERT: C 933 CYS cc_start: 0.7563 (p) cc_final: 0.7182 (p) REVERT: C 991 GLU cc_start: 0.7062 (pm20) cc_final: 0.6696 (pm20) REVERT: C 1006 SER cc_start: 0.8269 (m) cc_final: 0.7758 (t) REVERT: C 1007 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6777 (mm-30) REVERT: C 1009 TYR cc_start: 0.6738 (m-80) cc_final: 0.6268 (m-80) REVERT: D 142 LYS cc_start: 0.7137 (tttm) cc_final: 0.6744 (tmtt) REVERT: D 238 LYS cc_start: 0.7434 (tptt) cc_final: 0.7056 (tptp) REVERT: D 250 GLN cc_start: 0.7215 (tp40) cc_final: 0.6950 (tp40) REVERT: D 301 MET cc_start: 0.7131 (ttp) cc_final: 0.6754 (ttp) REVERT: D 329 ASP cc_start: 0.7328 (m-30) cc_final: 0.6914 (t70) REVERT: D 367 HIS cc_start: 0.7110 (m-70) cc_final: 0.6741 (m-70) REVERT: D 369 GLU cc_start: 0.6876 (tt0) cc_final: 0.6647 (tt0) REVERT: D 384 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7814 (mtpp) REVERT: D 415 CYS cc_start: 0.6301 (m) cc_final: 0.6003 (m) REVERT: D 585 ASN cc_start: 0.7903 (t0) cc_final: 0.7673 (t0) REVERT: D 614 VAL cc_start: 0.8386 (t) cc_final: 0.8139 (p) REVERT: D 640 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6596 (mm-30) REVERT: D 644 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7796 (mm-40) REVERT: D 741 GLN cc_start: 0.7093 (mm110) cc_final: 0.6814 (mm110) REVERT: D 853 THR cc_start: 0.8494 (t) cc_final: 0.8086 (p) REVERT: D 880 LYS cc_start: 0.7865 (pttt) cc_final: 0.7380 (ptmt) REVERT: D 883 GLN cc_start: 0.6125 (pm20) cc_final: 0.5836 (pm20) REVERT: D 899 VAL cc_start: 0.6443 (m) cc_final: 0.6056 (p) REVERT: D 929 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7826 (mp) REVERT: D 933 CYS cc_start: 0.7363 (m) cc_final: 0.7134 (p) REVERT: D 973 LYS cc_start: 0.8296 (ptmt) cc_final: 0.7870 (ptpp) REVERT: D 990 CYS cc_start: 0.7445 (m) cc_final: 0.6737 (m) REVERT: D 991 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6388 (pm20) REVERT: D 1006 SER cc_start: 0.8249 (m) cc_final: 0.7731 (t) REVERT: D 1009 TYR cc_start: 0.6449 (m-80) cc_final: 0.6200 (m-80) REVERT: D 1019 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7626 (tp30) REVERT: D 1022 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7672 (tm-30) REVERT: D 1023 GLU cc_start: 0.6174 (mp0) cc_final: 0.5612 (mp0) REVERT: E 143 TYR cc_start: 0.6860 (t80) cc_final: 0.6617 (t80) REVERT: E 172 ARG cc_start: 0.6671 (mtt90) cc_final: 0.6314 (mtt90) REVERT: E 175 LYS cc_start: 0.8023 (tttt) cc_final: 0.7732 (tttt) REVERT: E 277 MET cc_start: 0.6588 (ptm) cc_final: 0.6326 (ptm) REVERT: E 289 LYS cc_start: 0.7635 (pttt) cc_final: 0.7393 (pttp) REVERT: E 326 GLU cc_start: 0.7122 (tp30) cc_final: 0.6815 (mp0) REVERT: E 351 ARG cc_start: 0.7383 (mtp180) cc_final: 0.7148 (mtm180) REVERT: E 375 GLU cc_start: 0.7220 (tt0) cc_final: 0.6891 (tt0) REVERT: E 404 VAL cc_start: 0.7879 (t) cc_final: 0.7396 (p) REVERT: E 409 CYS cc_start: 0.7779 (m) cc_final: 0.6996 (t) REVERT: E 415 CYS cc_start: 0.6477 (m) cc_final: 0.4651 (m) REVERT: E 419 CYS cc_start: 0.7642 (m) cc_final: 0.7245 (m) REVERT: E 610 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8103 (ttmm) REVERT: E 611 TRP cc_start: 0.7507 (t60) cc_final: 0.6911 (t60) REVERT: E 613 GLU cc_start: 0.7341 (tt0) cc_final: 0.6960 (tt0) REVERT: E 637 MET cc_start: 0.7033 (tpp) cc_final: 0.6783 (tpp) REVERT: E 645 ARG cc_start: 0.7713 (mmm160) cc_final: 0.7292 (mmm160) REVERT: E 648 ASP cc_start: 0.7749 (m-30) cc_final: 0.7424 (t0) REVERT: E 649 TYR cc_start: 0.7194 (m-80) cc_final: 0.6375 (m-80) REVERT: E 731 ARG cc_start: 0.6792 (ttm170) cc_final: 0.6532 (ttm110) REVERT: E 779 ARG cc_start: 0.6577 (tpp-160) cc_final: 0.6361 (tpp-160) REVERT: E 785 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7329 (pt0) REVERT: E 831 LYS cc_start: 0.8368 (mttt) cc_final: 0.8035 (mttm) REVERT: E 864 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7067 (tp30) REVERT: E 878 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8139 (tppt) REVERT: E 933 CYS cc_start: 0.7644 (m) cc_final: 0.7320 (p) REVERT: E 973 LYS cc_start: 0.8370 (ptmt) cc_final: 0.7793 (ptpp) REVERT: E 987 MET cc_start: 0.6007 (mmt) cc_final: 0.5485 (mmm) REVERT: E 991 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6635 (pm20) REVERT: E 1006 SER cc_start: 0.8161 (m) cc_final: 0.7656 (t) REVERT: E 1009 TYR cc_start: 0.6501 (m-80) cc_final: 0.6186 (m-80) REVERT: E 1019 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7360 (tp30) REVERT: E 1022 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7433 (tm-30) REVERT: F 143 TYR cc_start: 0.6671 (t80) cc_final: 0.6361 (t80) REVERT: F 238 LYS cc_start: 0.7430 (tptt) cc_final: 0.7193 (tptp) REVERT: F 301 MET cc_start: 0.6828 (ttm) cc_final: 0.6314 (ttp) REVERT: F 312 ASP cc_start: 0.7116 (t70) cc_final: 0.6583 (t0) REVERT: F 338 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7250 (mtmm) REVERT: F 369 GLU cc_start: 0.6846 (tt0) cc_final: 0.6428 (tt0) REVERT: F 415 CYS cc_start: 0.6372 (m) cc_final: 0.6102 (m) REVERT: F 426 MET cc_start: 0.7248 (tpt) cc_final: 0.6874 (tpt) REVERT: F 569 GLU cc_start: 0.6834 (tp30) cc_final: 0.6401 (tp30) REVERT: F 603 GLN cc_start: 0.6963 (tp40) cc_final: 0.6754 (tp40) REVERT: F 607 GLU cc_start: 0.7154 (tp30) cc_final: 0.6797 (tp30) REVERT: F 613 GLU cc_start: 0.7347 (tt0) cc_final: 0.7029 (tt0) REVERT: F 637 MET cc_start: 0.7352 (tpt) cc_final: 0.6907 (tpt) REVERT: F 644 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7466 (mm-40) REVERT: F 647 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7811 (mtm) REVERT: F 649 TYR cc_start: 0.7160 (m-80) cc_final: 0.6725 (m-80) REVERT: F 652 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7855 (ttmt) REVERT: F 785 GLU cc_start: 0.7680 (pt0) cc_final: 0.6969 (mt-10) REVERT: F 853 THR cc_start: 0.8283 (t) cc_final: 0.7922 (p) REVERT: F 864 GLU cc_start: 0.7288 (tp30) cc_final: 0.6970 (tp30) REVERT: F 876 CYS cc_start: 0.7700 (m) cc_final: 0.7156 (m) REVERT: F 929 ILE cc_start: 0.8572 (mt) cc_final: 0.8103 (mp) REVERT: F 991 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6680 (pm20) REVERT: F 1006 SER cc_start: 0.8179 (m) cc_final: 0.7794 (t) REVERT: F 1019 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7646 (mm-30) REVERT: F 1029 THR cc_start: 0.8273 (m) cc_final: 0.7753 (p) outliers start: 151 outliers final: 98 residues processed: 950 average time/residue: 0.5034 time to fit residues: 773.3954 Evaluate side-chains 973 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 863 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 828 ASN Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 812 ASP Chi-restraints excluded: chain B residue 828 ASN Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 897 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 970 SER Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 783 SER Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain C residue 812 ASP Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 792 LEU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain E residue 828 ASN Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 864 GLU Chi-restraints excluded: chain E residue 908 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 970 SER Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain E residue 1028 LEU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 812 ASP Chi-restraints excluded: chain F residue 828 ASN Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 910 THR Chi-restraints excluded: chain F residue 991 GLU Chi-restraints excluded: chain F residue 1028 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 345 optimal weight: 0.0010 chunk 191 optimal weight: 9.9990 chunk 395 optimal weight: 5.9990 chunk 320 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 416 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN B 522 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 916 HIS ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 GLN E 638 GLN ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 916 HIS F 509 GLN ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 39690 Z= 0.266 Angle : 0.666 11.014 53544 Z= 0.329 Chirality : 0.043 0.208 6078 Planarity : 0.005 0.068 6714 Dihedral : 7.452 150.608 5256 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.73 % Favored : 93.25 % Rotamer: Outliers : 3.93 % Allowed : 18.89 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.12), residues: 4782 helix: -0.25 (0.10), residues: 2190 sheet: -1.51 (0.20), residues: 588 loop : -1.28 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 776 HIS 0.005 0.001 HIS A 916 PHE 0.054 0.002 PHE A 508 TYR 0.022 0.002 TYR D 649 ARG 0.006 0.000 ARG B 645 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 912 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.7385 (t80) cc_final: 0.7082 (t80) REVERT: A 239 MET cc_start: 0.6510 (ttp) cc_final: 0.6254 (ttp) REVERT: A 269 GLN cc_start: 0.6036 (mp10) cc_final: 0.5798 (mp10) REVERT: A 329 ASP cc_start: 0.8036 (m-30) cc_final: 0.7822 (m-30) REVERT: A 351 ARG cc_start: 0.7452 (mtm180) cc_final: 0.7097 (mtm180) REVERT: A 409 CYS cc_start: 0.7471 (m) cc_final: 0.7077 (m) REVERT: A 413 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7845 (tt) REVERT: A 419 CYS cc_start: 0.7778 (m) cc_final: 0.7502 (m) REVERT: A 523 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6688 (tpp) REVERT: A 563 GLU cc_start: 0.7187 (pp20) cc_final: 0.6715 (tm-30) REVERT: A 569 GLU cc_start: 0.7133 (tp30) cc_final: 0.6770 (tp30) REVERT: A 607 GLU cc_start: 0.7671 (tp30) cc_final: 0.7418 (tp30) REVERT: A 613 GLU cc_start: 0.7460 (tt0) cc_final: 0.7139 (tt0) REVERT: A 631 PHE cc_start: 0.7608 (m-10) cc_final: 0.7388 (m-80) REVERT: A 645 ARG cc_start: 0.7867 (mmm160) cc_final: 0.7301 (mmm160) REVERT: A 647 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7780 (ttp) REVERT: A 649 TYR cc_start: 0.7263 (m-80) cc_final: 0.6557 (m-80) REVERT: A 652 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7874 (ttmm) REVERT: A 660 ARG cc_start: 0.7028 (tpp80) cc_final: 0.6567 (ttm-80) REVERT: A 669 CYS cc_start: 0.7061 (m) cc_final: 0.6356 (m) REVERT: A 672 ASN cc_start: 0.7491 (p0) cc_final: 0.7205 (m-40) REVERT: A 930 LYS cc_start: 0.7991 (mttt) cc_final: 0.7526 (mttt) REVERT: A 973 LYS cc_start: 0.8200 (ptmt) cc_final: 0.7629 (ptpp) REVERT: A 991 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6571 (pm20) REVERT: A 1006 SER cc_start: 0.8341 (m) cc_final: 0.7848 (t) REVERT: B 238 LYS cc_start: 0.7349 (tptt) cc_final: 0.7066 (tptp) REVERT: B 259 ILE cc_start: 0.7740 (mp) cc_final: 0.7248 (pt) REVERT: B 306 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6075 (mm-30) REVERT: B 367 HIS cc_start: 0.7093 (m-70) cc_final: 0.6833 (m-70) REVERT: B 409 CYS cc_start: 0.7587 (m) cc_final: 0.6752 (p) REVERT: B 523 MET cc_start: 0.7521 (tpt) cc_final: 0.6784 (tpt) REVERT: B 613 GLU cc_start: 0.7581 (tt0) cc_final: 0.7211 (tt0) REVERT: B 637 MET cc_start: 0.7221 (tpt) cc_final: 0.6983 (tpt) REVERT: B 758 MET cc_start: 0.6775 (tpt) cc_final: 0.6448 (tpt) REVERT: B 883 GLN cc_start: 0.7374 (mp10) cc_final: 0.7071 (mp10) REVERT: B 988 MET cc_start: 0.7421 (mmm) cc_final: 0.7164 (tmm) REVERT: B 1008 MET cc_start: 0.6371 (mmm) cc_final: 0.5897 (ttt) REVERT: B 1013 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7296 (tm-30) REVERT: C 172 ARG cc_start: 0.6790 (mtt90) cc_final: 0.6561 (mtp85) REVERT: C 239 MET cc_start: 0.6484 (ttp) cc_final: 0.6244 (ttp) REVERT: C 301 MET cc_start: 0.6761 (ttm) cc_final: 0.6262 (ttp) REVERT: C 337 ARG cc_start: 0.7440 (mtt180) cc_final: 0.7216 (mtm180) REVERT: C 367 HIS cc_start: 0.7189 (m-70) cc_final: 0.6597 (m-70) REVERT: C 409 CYS cc_start: 0.7602 (m) cc_final: 0.7233 (t) REVERT: C 419 CYS cc_start: 0.7952 (m) cc_final: 0.7453 (m) REVERT: C 442 VAL cc_start: 0.7495 (p) cc_final: 0.7265 (m) REVERT: C 488 ASP cc_start: 0.7615 (m-30) cc_final: 0.7267 (m-30) REVERT: C 523 MET cc_start: 0.7429 (mmm) cc_final: 0.7176 (tpt) REVERT: C 537 GLU cc_start: 0.5586 (pm20) cc_final: 0.5204 (pm20) REVERT: C 599 LYS cc_start: 0.7672 (tptt) cc_final: 0.7003 (tptt) REVERT: C 603 GLN cc_start: 0.7700 (tp40) cc_final: 0.7497 (tp40) REVERT: C 607 GLU cc_start: 0.7474 (tp30) cc_final: 0.7249 (tp30) REVERT: C 613 GLU cc_start: 0.7547 (tt0) cc_final: 0.7176 (mt-10) REVERT: C 640 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6685 (mt-10) REVERT: C 641 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6853 (t0) REVERT: C 649 TYR cc_start: 0.7219 (m-80) cc_final: 0.6870 (m-80) REVERT: C 758 MET cc_start: 0.7132 (tpt) cc_final: 0.6788 (tpp) REVERT: C 774 ARG cc_start: 0.7341 (mtm110) cc_final: 0.7096 (mtm110) REVERT: C 853 THR cc_start: 0.8415 (t) cc_final: 0.8124 (p) REVERT: C 864 GLU cc_start: 0.7212 (tp30) cc_final: 0.6982 (tp30) REVERT: C 867 LEU cc_start: 0.8231 (pt) cc_final: 0.7969 (pp) REVERT: C 933 CYS cc_start: 0.7685 (p) cc_final: 0.7263 (p) REVERT: C 991 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6722 (pm20) REVERT: C 1006 SER cc_start: 0.8162 (m) cc_final: 0.7704 (t) REVERT: C 1009 TYR cc_start: 0.6727 (m-80) cc_final: 0.6485 (m-80) REVERT: D 142 LYS cc_start: 0.7208 (tttm) cc_final: 0.6862 (tmtt) REVERT: D 238 LYS cc_start: 0.7471 (tptt) cc_final: 0.7118 (tptp) REVERT: D 275 LEU cc_start: 0.7532 (mt) cc_final: 0.7283 (mt) REVERT: D 301 MET cc_start: 0.7114 (ttp) cc_final: 0.6621 (ttp) REVERT: D 367 HIS cc_start: 0.7135 (m-70) cc_final: 0.6792 (m-70) REVERT: D 400 GLN cc_start: 0.7718 (tt0) cc_final: 0.7355 (tt0) REVERT: D 415 CYS cc_start: 0.6328 (m) cc_final: 0.6043 (m) REVERT: D 585 ASN cc_start: 0.7858 (t0) cc_final: 0.7604 (t0) REVERT: D 614 VAL cc_start: 0.8471 (t) cc_final: 0.8253 (p) REVERT: D 640 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6625 (mm-30) REVERT: D 644 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7817 (mm-40) REVERT: D 741 GLN cc_start: 0.7000 (mm110) cc_final: 0.6753 (mm110) REVERT: D 853 THR cc_start: 0.8607 (t) cc_final: 0.8357 (p) REVERT: D 880 LYS cc_start: 0.7879 (pttt) cc_final: 0.7375 (ptmt) REVERT: D 883 GLN cc_start: 0.6171 (pm20) cc_final: 0.5922 (pm20) REVERT: D 929 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.7936 (mp) REVERT: D 933 CYS cc_start: 0.7443 (m) cc_final: 0.7121 (m) REVERT: D 973 LYS cc_start: 0.8304 (ptmt) cc_final: 0.7875 (ptpp) REVERT: D 987 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.5637 (mmm) REVERT: D 990 CYS cc_start: 0.7454 (m) cc_final: 0.6879 (m) REVERT: D 991 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6395 (pm20) REVERT: D 1005 LEU cc_start: 0.7152 (mp) cc_final: 0.6952 (mp) REVERT: D 1006 SER cc_start: 0.8211 (m) cc_final: 0.7712 (t) REVERT: D 1019 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7518 (tp30) REVERT: D 1022 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7660 (tm-30) REVERT: D 1023 GLU cc_start: 0.6187 (mp0) cc_final: 0.5436 (mp0) REVERT: E 143 TYR cc_start: 0.7048 (t80) cc_final: 0.6756 (t80) REVERT: E 145 ARG cc_start: 0.7676 (ttm110) cc_final: 0.7415 (ttm110) REVERT: E 172 ARG cc_start: 0.6721 (mtt90) cc_final: 0.6398 (mtt90) REVERT: E 175 LYS cc_start: 0.8041 (tttt) cc_final: 0.7745 (tttt) REVERT: E 210 ASP cc_start: 0.8107 (p0) cc_final: 0.7800 (p0) REVERT: E 277 MET cc_start: 0.6636 (ptm) cc_final: 0.6341 (ptm) REVERT: E 289 LYS cc_start: 0.7635 (pttt) cc_final: 0.7410 (pttp) REVERT: E 375 GLU cc_start: 0.7358 (tt0) cc_final: 0.7063 (tt0) REVERT: E 409 CYS cc_start: 0.7829 (m) cc_final: 0.7027 (t) REVERT: E 415 CYS cc_start: 0.6459 (m) cc_final: 0.4610 (m) REVERT: E 419 CYS cc_start: 0.7657 (m) cc_final: 0.7278 (m) REVERT: E 523 MET cc_start: 0.6805 (mmm) cc_final: 0.6576 (mtm) REVERT: E 585 ASN cc_start: 0.7701 (t0) cc_final: 0.7480 (t0) REVERT: E 607 GLU cc_start: 0.7242 (tp30) cc_final: 0.6963 (tp30) REVERT: E 610 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8133 (ttmm) REVERT: E 613 GLU cc_start: 0.7308 (tt0) cc_final: 0.6791 (tt0) REVERT: E 638 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6952 (tp40) REVERT: E 648 ASP cc_start: 0.7727 (m-30) cc_final: 0.7480 (t0) REVERT: E 731 ARG cc_start: 0.6809 (ttm170) cc_final: 0.6516 (ttm110) REVERT: E 785 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7232 (pt0) REVERT: E 831 LYS cc_start: 0.8367 (mttt) cc_final: 0.8049 (mttm) REVERT: E 864 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6915 (tp30) REVERT: E 867 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8233 (pp) REVERT: E 878 LYS cc_start: 0.8352 (mmtt) cc_final: 0.8117 (tppt) REVERT: E 933 CYS cc_start: 0.7642 (m) cc_final: 0.7334 (p) REVERT: E 973 LYS cc_start: 0.8320 (ptmt) cc_final: 0.7765 (ptpp) REVERT: E 987 MET cc_start: 0.6037 (mmt) cc_final: 0.5737 (mmt) REVERT: E 991 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6650 (pm20) REVERT: E 1006 SER cc_start: 0.8161 (m) cc_final: 0.7669 (t) REVERT: E 1009 TYR cc_start: 0.6541 (m-80) cc_final: 0.6250 (m-80) REVERT: E 1013 GLU cc_start: 0.7434 (tm-30) cc_final: 0.6995 (tm-30) REVERT: E 1019 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7365 (tp30) REVERT: E 1022 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7433 (tm-30) REVERT: F 143 TYR cc_start: 0.6690 (t80) cc_final: 0.6438 (t80) REVERT: F 238 LYS cc_start: 0.7478 (tptt) cc_final: 0.7250 (tptp) REVERT: F 269 GLN cc_start: 0.4676 (mp10) cc_final: 0.4386 (mp10) REVERT: F 312 ASP cc_start: 0.7227 (t70) cc_final: 0.6697 (t0) REVERT: F 369 GLU cc_start: 0.6899 (tt0) cc_final: 0.6484 (tt0) REVERT: F 384 LYS cc_start: 0.7740 (mtmm) cc_final: 0.7448 (mtmm) REVERT: F 415 CYS cc_start: 0.6434 (m) cc_final: 0.6167 (m) REVERT: F 523 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6688 (mtm) REVERT: F 569 GLU cc_start: 0.6861 (tp30) cc_final: 0.6451 (tp30) REVERT: F 607 GLU cc_start: 0.7176 (tp30) cc_final: 0.6862 (tp30) REVERT: F 613 GLU cc_start: 0.7308 (tt0) cc_final: 0.7002 (tt0) REVERT: F 637 MET cc_start: 0.7379 (tpt) cc_final: 0.7043 (tpt) REVERT: F 644 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7475 (mm-40) REVERT: F 647 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7581 (mtm) REVERT: F 649 TYR cc_start: 0.7142 (m-80) cc_final: 0.6766 (m-80) REVERT: F 669 CYS cc_start: 0.7493 (m) cc_final: 0.7242 (m) REVERT: F 785 GLU cc_start: 0.7639 (pt0) cc_final: 0.7357 (mp0) REVERT: F 806 SER cc_start: 0.7952 (m) cc_final: 0.7705 (m) REVERT: F 853 THR cc_start: 0.8306 (t) cc_final: 0.7977 (p) REVERT: F 864 GLU cc_start: 0.7282 (tp30) cc_final: 0.6987 (tp30) REVERT: F 876 CYS cc_start: 0.7746 (m) cc_final: 0.7207 (m) REVERT: F 912 GLN cc_start: 0.7314 (tp-100) cc_final: 0.7066 (tp-100) REVERT: F 929 ILE cc_start: 0.8549 (mt) cc_final: 0.8287 (mp) REVERT: F 991 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6721 (pm20) REVERT: F 1006 SER cc_start: 0.8119 (m) cc_final: 0.7815 (t) REVERT: F 1019 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7663 (mm-30) REVERT: F 1029 THR cc_start: 0.8231 (m) cc_final: 0.7687 (p) outliers start: 173 outliers final: 110 residues processed: 988 average time/residue: 0.5102 time to fit residues: 814.8042 Evaluate side-chains 991 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 864 time to evaluate : 4.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 828 ASN Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 812 ASP Chi-restraints excluded: chain B residue 828 ASN Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 897 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 970 SER Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 783 SER Chi-restraints excluded: chain C residue 812 ASP Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain C residue 912 GLN Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 791 SER Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 806 SER Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 638 GLN Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 792 LEU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain E residue 828 ASN Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 849 SER Chi-restraints excluded: chain E residue 864 GLU Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 970 SER Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain E residue 1028 LEU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 523 MET Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 812 ASP Chi-restraints excluded: chain F residue 828 ASN Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 910 THR Chi-restraints excluded: chain F residue 948 LEU Chi-restraints excluded: chain F residue 991 GLU Chi-restraints excluded: chain F residue 1028 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 0.0270 chunk 417 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 272 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 464 optimal weight: 1.9990 chunk 385 optimal weight: 0.4980 chunk 215 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 243 optimal weight: 10.0000 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 260 HIS A 360 HIS ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS B 627 GLN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 GLN ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1002 ASN F 149 GLN ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 766 GLN ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 39690 Z= 0.157 Angle : 0.619 13.711 53544 Z= 0.302 Chirality : 0.040 0.174 6078 Planarity : 0.005 0.070 6714 Dihedral : 7.175 142.719 5256 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.57 % Allowed : 20.03 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.12), residues: 4782 helix: 0.03 (0.11), residues: 2190 sheet: -1.90 (0.19), residues: 654 loop : -1.12 (0.15), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 243 HIS 0.005 0.001 HIS A 916 PHE 0.032 0.001 PHE F 304 TYR 0.021 0.001 TYR E 168 ARG 0.008 0.000 ARG C 660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 890 time to evaluate : 4.440 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: A 143 TYR cc_start: 0.7303 (t80) cc_final: 0.6993 (t80) REVERT: A 172 ARG cc_start: 0.6529 (mtt90) cc_final: 0.6156 (mtt90) REVERT: A 239 MET cc_start: 0.6536 (ttp) cc_final: 0.6267 (ttp) REVERT: A 259 ILE cc_start: 0.7589 (mp) cc_final: 0.6989 (pt) REVERT: A 267 VAL cc_start: 0.3987 (OUTLIER) cc_final: 0.3297 (p) REVERT: A 269 GLN cc_start: 0.5585 (mp10) cc_final: 0.5012 (mp10) REVERT: A 298 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6468 (pt) REVERT: A 326 GLU cc_start: 0.7121 (tp30) cc_final: 0.6854 (pp20) REVERT: A 351 ARG cc_start: 0.7394 (mtm180) cc_final: 0.7064 (mtm180) REVERT: A 419 CYS cc_start: 0.7654 (m) cc_final: 0.7415 (m) REVERT: A 523 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6589 (tpp) REVERT: A 563 GLU cc_start: 0.7078 (pp20) cc_final: 0.6766 (tp30) REVERT: A 569 GLU cc_start: 0.7004 (tp30) cc_final: 0.6677 (tp30) REVERT: A 607 GLU cc_start: 0.7628 (tp30) cc_final: 0.7313 (tp30) REVERT: A 613 GLU cc_start: 0.7416 (tt0) cc_final: 0.7073 (tt0) REVERT: A 645 ARG cc_start: 0.7840 (mmm160) cc_final: 0.7218 (mmm160) REVERT: A 647 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7769 (mtm) REVERT: A 649 TYR cc_start: 0.7258 (m-80) cc_final: 0.6561 (m-80) REVERT: A 660 ARG cc_start: 0.6799 (tpp80) cc_final: 0.6424 (ttm-80) REVERT: A 669 CYS cc_start: 0.7013 (m) cc_final: 0.6415 (m) REVERT: A 672 ASN cc_start: 0.7443 (p0) cc_final: 0.7154 (m110) REVERT: A 930 LYS cc_start: 0.7982 (mttt) cc_final: 0.7519 (mttt) REVERT: A 973 LYS cc_start: 0.8223 (ptmt) cc_final: 0.7624 (ptpp) REVERT: A 991 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6490 (pm20) REVERT: A 1006 SER cc_start: 0.8365 (m) cc_final: 0.7868 (t) REVERT: A 1013 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7130 (tm-30) REVERT: B 367 HIS cc_start: 0.7106 (m-70) cc_final: 0.6759 (m-70) REVERT: B 409 CYS cc_start: 0.7583 (m) cc_final: 0.6721 (p) REVERT: B 417 ILE cc_start: 0.7750 (mt) cc_final: 0.7157 (tt) REVERT: B 613 GLU cc_start: 0.7545 (tt0) cc_final: 0.7225 (tt0) REVERT: B 652 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7950 (ttmm) REVERT: B 758 MET cc_start: 0.6675 (tpt) cc_final: 0.6372 (tpt) REVERT: B 831 LYS cc_start: 0.7893 (mttt) cc_final: 0.7620 (mttm) REVERT: B 845 GLN cc_start: 0.7640 (tp40) cc_final: 0.7367 (tp-100) REVERT: B 883 GLN cc_start: 0.7361 (mp10) cc_final: 0.7068 (mp10) REVERT: B 988 MET cc_start: 0.7582 (mmm) cc_final: 0.7065 (tmm) REVERT: B 1008 MET cc_start: 0.6355 (mmm) cc_final: 0.5826 (ttt) REVERT: B 1013 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7311 (tm-30) REVERT: C 145 ARG cc_start: 0.7563 (ttp-110) cc_final: 0.7144 (ttm110) REVERT: C 239 MET cc_start: 0.6428 (ttp) cc_final: 0.6190 (ttp) REVERT: C 259 ILE cc_start: 0.7534 (mp) cc_final: 0.6996 (pt) REVERT: C 301 MET cc_start: 0.6774 (ttm) cc_final: 0.6258 (ttp) REVERT: C 337 ARG cc_start: 0.7435 (mtt180) cc_final: 0.7225 (mtm180) REVERT: C 338 LYS cc_start: 0.7704 (mtpp) cc_final: 0.7443 (mtpp) REVERT: C 367 HIS cc_start: 0.7102 (m-70) cc_final: 0.6519 (m-70) REVERT: C 409 CYS cc_start: 0.7611 (m) cc_final: 0.7218 (t) REVERT: C 419 CYS cc_start: 0.7928 (m) cc_final: 0.7416 (m) REVERT: C 442 VAL cc_start: 0.7482 (p) cc_final: 0.7241 (m) REVERT: C 488 ASP cc_start: 0.7571 (m-30) cc_final: 0.7213 (m-30) REVERT: C 523 MET cc_start: 0.7318 (mmm) cc_final: 0.6970 (tpp) REVERT: C 603 GLN cc_start: 0.7640 (tp40) cc_final: 0.7428 (tp40) REVERT: C 607 GLU cc_start: 0.7443 (tp30) cc_final: 0.7204 (tp30) REVERT: C 613 GLU cc_start: 0.7461 (tt0) cc_final: 0.7110 (mt-10) REVERT: C 640 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6619 (mt-10) REVERT: C 641 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6693 (t0) REVERT: C 645 ARG cc_start: 0.7310 (mtm110) cc_final: 0.6035 (mtm110) REVERT: C 649 TYR cc_start: 0.7206 (m-80) cc_final: 0.6816 (m-80) REVERT: C 741 GLN cc_start: 0.7159 (mm110) cc_final: 0.6945 (mm110) REVERT: C 853 THR cc_start: 0.8417 (t) cc_final: 0.8097 (p) REVERT: C 864 GLU cc_start: 0.7150 (tp30) cc_final: 0.6862 (tp30) REVERT: C 867 LEU cc_start: 0.8231 (pt) cc_final: 0.7960 (pp) REVERT: C 933 CYS cc_start: 0.7685 (p) cc_final: 0.7296 (p) REVERT: C 991 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6648 (pm20) REVERT: C 1006 SER cc_start: 0.8213 (m) cc_final: 0.7735 (t) REVERT: C 1009 TYR cc_start: 0.6675 (m-80) cc_final: 0.6431 (m-80) REVERT: D 142 LYS cc_start: 0.7148 (tttm) cc_final: 0.6850 (tmtt) REVERT: D 238 LYS cc_start: 0.7433 (tptt) cc_final: 0.7083 (tptp) REVERT: D 250 GLN cc_start: 0.7187 (tp40) cc_final: 0.6903 (tp40) REVERT: D 275 LEU cc_start: 0.7532 (mt) cc_final: 0.7266 (mt) REVERT: D 301 MET cc_start: 0.7048 (ttp) cc_final: 0.6648 (ttp) REVERT: D 351 ARG cc_start: 0.7658 (mtm180) cc_final: 0.7247 (mtm180) REVERT: D 367 HIS cc_start: 0.7152 (m-70) cc_final: 0.6763 (m-70) REVERT: D 369 GLU cc_start: 0.6993 (tt0) cc_final: 0.6718 (tt0) REVERT: D 400 GLN cc_start: 0.7686 (tt0) cc_final: 0.7359 (tt0) REVERT: D 409 CYS cc_start: 0.7610 (m) cc_final: 0.6919 (t) REVERT: D 415 CYS cc_start: 0.6217 (m) cc_final: 0.4488 (m) REVERT: D 585 ASN cc_start: 0.7776 (t0) cc_final: 0.7551 (t0) REVERT: D 611 TRP cc_start: 0.7333 (t60) cc_final: 0.6807 (t60) REVERT: D 614 VAL cc_start: 0.8457 (t) cc_final: 0.8240 (p) REVERT: D 640 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6672 (mm-30) REVERT: D 660 ARG cc_start: 0.6974 (mtp85) cc_final: 0.6705 (mtp85) REVERT: D 853 THR cc_start: 0.8566 (t) cc_final: 0.8176 (p) REVERT: D 880 LYS cc_start: 0.7909 (pttt) cc_final: 0.7380 (ptmt) REVERT: D 883 GLN cc_start: 0.6141 (pm20) cc_final: 0.5917 (pm20) REVERT: D 942 LYS cc_start: 0.8407 (mmtp) cc_final: 0.8164 (mmtm) REVERT: D 973 LYS cc_start: 0.8308 (ptmt) cc_final: 0.7867 (ptpp) REVERT: D 990 CYS cc_start: 0.7417 (m) cc_final: 0.6734 (m) REVERT: D 991 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6303 (pm20) REVERT: D 1005 LEU cc_start: 0.7173 (mp) cc_final: 0.6960 (mp) REVERT: D 1006 SER cc_start: 0.8198 (m) cc_final: 0.7697 (t) REVERT: D 1019 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7035 (tp30) REVERT: D 1022 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7606 (tm-30) REVERT: D 1023 GLU cc_start: 0.6220 (mp0) cc_final: 0.4216 (mp0) REVERT: E 145 ARG cc_start: 0.7642 (ttm110) cc_final: 0.7336 (ttm110) REVERT: E 172 ARG cc_start: 0.6723 (mtt90) cc_final: 0.6341 (mtt90) REVERT: E 175 LYS cc_start: 0.8033 (tttt) cc_final: 0.7732 (tttt) REVERT: E 210 ASP cc_start: 0.8105 (p0) cc_final: 0.7789 (p0) REVERT: E 275 LEU cc_start: 0.7715 (mp) cc_final: 0.7489 (mp) REVERT: E 277 MET cc_start: 0.6552 (ptm) cc_final: 0.6269 (ptm) REVERT: E 367 HIS cc_start: 0.7022 (m-70) cc_final: 0.6593 (m-70) REVERT: E 375 GLU cc_start: 0.7320 (tt0) cc_final: 0.7011 (tt0) REVERT: E 404 VAL cc_start: 0.7845 (t) cc_final: 0.7431 (p) REVERT: E 409 CYS cc_start: 0.7796 (m) cc_final: 0.6973 (t) REVERT: E 415 CYS cc_start: 0.6330 (m) cc_final: 0.4298 (m) REVERT: E 419 CYS cc_start: 0.7648 (m) cc_final: 0.7217 (m) REVERT: E 585 ASN cc_start: 0.7583 (t0) cc_final: 0.7360 (t0) REVERT: E 610 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8243 (mtmm) REVERT: E 611 TRP cc_start: 0.7609 (t60) cc_final: 0.6974 (t60) REVERT: E 613 GLU cc_start: 0.7252 (tt0) cc_final: 0.6861 (tt0) REVERT: E 648 ASP cc_start: 0.7678 (m-30) cc_final: 0.7458 (t0) REVERT: E 649 TYR cc_start: 0.7227 (m-80) cc_final: 0.6352 (m-80) REVERT: E 731 ARG cc_start: 0.6790 (ttm170) cc_final: 0.6480 (ttm110) REVERT: E 785 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7297 (pt0) REVERT: E 831 LYS cc_start: 0.8289 (mttt) cc_final: 0.8081 (mttm) REVERT: E 867 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8247 (pp) REVERT: E 878 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8101 (tppt) REVERT: E 933 CYS cc_start: 0.7617 (m) cc_final: 0.7314 (p) REVERT: E 973 LYS cc_start: 0.8297 (ptmt) cc_final: 0.7714 (ptpp) REVERT: E 987 MET cc_start: 0.6079 (mmt) cc_final: 0.5689 (mmm) REVERT: E 991 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6579 (pm20) REVERT: E 1006 SER cc_start: 0.8132 (m) cc_final: 0.7670 (t) REVERT: E 1009 TYR cc_start: 0.6422 (m-80) cc_final: 0.6180 (m-80) REVERT: E 1013 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6942 (tm-30) REVERT: E 1019 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7373 (tp30) REVERT: E 1022 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7464 (tm-30) REVERT: F 143 TYR cc_start: 0.6626 (t80) cc_final: 0.6407 (t80) REVERT: F 272 LEU cc_start: 0.7839 (mt) cc_final: 0.7460 (tt) REVERT: F 312 ASP cc_start: 0.7249 (t70) cc_final: 0.6705 (t0) REVERT: F 369 GLU cc_start: 0.6896 (tt0) cc_final: 0.6453 (tt0) REVERT: F 384 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7393 (mtmm) REVERT: F 415 CYS cc_start: 0.6351 (m) cc_final: 0.5754 (m) REVERT: F 426 MET cc_start: 0.7274 (tpt) cc_final: 0.6913 (tpt) REVERT: F 563 GLU cc_start: 0.6848 (tm-30) cc_final: 0.6415 (tm-30) REVERT: F 607 GLU cc_start: 0.7159 (tp30) cc_final: 0.6785 (tp30) REVERT: F 611 TRP cc_start: 0.7393 (t60) cc_final: 0.6641 (t60) REVERT: F 613 GLU cc_start: 0.7256 (tt0) cc_final: 0.6947 (tt0) REVERT: F 637 MET cc_start: 0.7384 (tpt) cc_final: 0.7027 (tpt) REVERT: F 644 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7420 (mm-40) REVERT: F 645 ARG cc_start: 0.7021 (mtm110) cc_final: 0.6803 (mtm110) REVERT: F 647 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7533 (mtm) REVERT: F 649 TYR cc_start: 0.7164 (m-80) cc_final: 0.6747 (m-80) REVERT: F 876 CYS cc_start: 0.7666 (m) cc_final: 0.7130 (m) REVERT: F 929 ILE cc_start: 0.8579 (mt) cc_final: 0.8270 (mp) REVERT: F 987 MET cc_start: 0.6052 (mmt) cc_final: 0.5727 (mmm) REVERT: F 991 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6587 (pm20) REVERT: F 1006 SER cc_start: 0.8123 (m) cc_final: 0.7838 (t) REVERT: F 1019 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7534 (mm-30) REVERT: F 1029 THR cc_start: 0.8240 (m) cc_final: 0.7708 (p) outliers start: 157 outliers final: 97 residues processed: 966 average time/residue: 0.5049 time to fit residues: 785.7692 Evaluate side-chains 972 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 862 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 828 ASN Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 812 ASP Chi-restraints excluded: chain B residue 828 ASN Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 783 SER Chi-restraints excluded: chain C residue 812 ASP Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 912 GLN Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 632 TYR Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 786 CYS Chi-restraints excluded: chain E residue 792 LEU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain E residue 828 ASN Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 970 SER Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain E residue 1028 LEU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 796 SER Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 812 ASP Chi-restraints excluded: chain F residue 828 ASN Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 264 optimal weight: 1.9990 chunk 339 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 390 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 462 optimal weight: 0.9990 chunk 289 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 213 optimal weight: 0.0770 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 GLN ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 ASN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 771 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39690 Z= 0.180 Angle : 0.632 11.496 53544 Z= 0.306 Chirality : 0.041 0.178 6078 Planarity : 0.004 0.067 6714 Dihedral : 7.064 142.205 5256 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.82 % Allowed : 20.74 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.12), residues: 4782 helix: 0.08 (0.11), residues: 2196 sheet: -1.48 (0.20), residues: 588 loop : -1.26 (0.15), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 478 HIS 0.005 0.001 HIS A 938 PHE 0.034 0.001 PHE E 642 TYR 0.027 0.001 TYR E 143 ARG 0.006 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 865 time to evaluate : 4.391 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: A 143 TYR cc_start: 0.7279 (t80) cc_final: 0.6964 (t80) REVERT: A 172 ARG cc_start: 0.6580 (mtt90) cc_final: 0.6206 (mtt90) REVERT: A 239 MET cc_start: 0.6507 (ttp) cc_final: 0.6251 (ttp) REVERT: A 259 ILE cc_start: 0.7584 (mp) cc_final: 0.6987 (pt) REVERT: A 267 VAL cc_start: 0.4062 (OUTLIER) cc_final: 0.3805 (m) REVERT: A 269 GLN cc_start: 0.5750 (mp10) cc_final: 0.5380 (mp10) REVERT: A 298 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6542 (pt) REVERT: A 326 GLU cc_start: 0.7184 (tp30) cc_final: 0.6825 (tm-30) REVERT: A 329 ASP cc_start: 0.7926 (m-30) cc_final: 0.7420 (p0) REVERT: A 351 ARG cc_start: 0.7384 (mtm180) cc_final: 0.7018 (mtm180) REVERT: A 419 CYS cc_start: 0.7673 (m) cc_final: 0.7432 (m) REVERT: A 523 MET cc_start: 0.6947 (mmm) cc_final: 0.6611 (tpp) REVERT: A 563 GLU cc_start: 0.7167 (pp20) cc_final: 0.6867 (tp30) REVERT: A 569 GLU cc_start: 0.7025 (tp30) cc_final: 0.6716 (tp30) REVERT: A 607 GLU cc_start: 0.7664 (tp30) cc_final: 0.7362 (tp30) REVERT: A 613 GLU cc_start: 0.7424 (tt0) cc_final: 0.7112 (tt0) REVERT: A 645 ARG cc_start: 0.7885 (mmm160) cc_final: 0.7236 (mmm160) REVERT: A 649 TYR cc_start: 0.7236 (m-80) cc_final: 0.6569 (m-80) REVERT: A 660 ARG cc_start: 0.6918 (tpp80) cc_final: 0.6535 (ttm-80) REVERT: A 930 LYS cc_start: 0.7961 (mttt) cc_final: 0.7502 (mttt) REVERT: A 974 LEU cc_start: 0.7855 (tt) cc_final: 0.7624 (tt) REVERT: A 991 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6527 (pm20) REVERT: A 1006 SER cc_start: 0.8365 (m) cc_final: 0.7876 (t) REVERT: A 1013 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7169 (tm-30) REVERT: B 240 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5540 (mtm) REVERT: B 259 ILE cc_start: 0.7654 (mp) cc_final: 0.7151 (pt) REVERT: B 323 GLN cc_start: 0.8374 (mm110) cc_final: 0.8155 (mm110) REVERT: B 367 HIS cc_start: 0.7111 (m-70) cc_final: 0.6759 (m-70) REVERT: B 599 LYS cc_start: 0.7552 (tptt) cc_final: 0.6928 (tptt) REVERT: B 613 GLU cc_start: 0.7539 (tt0) cc_final: 0.7251 (tt0) REVERT: B 638 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7451 (mm-40) REVERT: B 652 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7932 (ttmm) REVERT: B 845 GLN cc_start: 0.7665 (tp40) cc_final: 0.7399 (tp-100) REVERT: B 883 GLN cc_start: 0.7392 (mp10) cc_final: 0.7088 (mp10) REVERT: B 929 ILE cc_start: 0.8244 (mt) cc_final: 0.8007 (mp) REVERT: B 930 LYS cc_start: 0.8113 (mttt) cc_final: 0.7800 (mttt) REVERT: B 988 MET cc_start: 0.7569 (mmm) cc_final: 0.7051 (tmm) REVERT: B 1008 MET cc_start: 0.6362 (mmm) cc_final: 0.5886 (ttt) REVERT: B 1013 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7326 (tm-30) REVERT: C 142 LYS cc_start: 0.7243 (tttm) cc_final: 0.7005 (tttm) REVERT: C 145 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.7142 (ttm110) REVERT: C 172 ARG cc_start: 0.6774 (mtt90) cc_final: 0.6488 (mtp85) REVERT: C 239 MET cc_start: 0.6450 (ttp) cc_final: 0.6230 (ttp) REVERT: C 259 ILE cc_start: 0.7548 (mp) cc_final: 0.7032 (pt) REVERT: C 298 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6483 (pt) REVERT: C 301 MET cc_start: 0.6756 (ttm) cc_final: 0.6241 (ttp) REVERT: C 337 ARG cc_start: 0.7438 (mtt180) cc_final: 0.7223 (mtm180) REVERT: C 338 LYS cc_start: 0.7736 (mtpp) cc_final: 0.7490 (mtpp) REVERT: C 367 HIS cc_start: 0.7132 (m-70) cc_final: 0.6584 (m-70) REVERT: C 409 CYS cc_start: 0.7633 (m) cc_final: 0.7247 (t) REVERT: C 417 ILE cc_start: 0.8019 (mt) cc_final: 0.7588 (tt) REVERT: C 419 CYS cc_start: 0.7901 (m) cc_final: 0.7406 (m) REVERT: C 442 VAL cc_start: 0.7509 (p) cc_final: 0.7257 (m) REVERT: C 488 ASP cc_start: 0.7527 (m-30) cc_final: 0.7164 (m-30) REVERT: C 523 MET cc_start: 0.7295 (mmm) cc_final: 0.6856 (tpp) REVERT: C 603 GLN cc_start: 0.7634 (tp40) cc_final: 0.7430 (tp40) REVERT: C 607 GLU cc_start: 0.7451 (tp30) cc_final: 0.7199 (tp30) REVERT: C 613 GLU cc_start: 0.7474 (tt0) cc_final: 0.7130 (mt-10) REVERT: C 640 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6610 (mt-10) REVERT: C 641 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6822 (t0) REVERT: C 649 TYR cc_start: 0.7174 (m-80) cc_final: 0.6833 (m-80) REVERT: C 741 GLN cc_start: 0.7139 (mm110) cc_final: 0.6936 (mm110) REVERT: C 839 LEU cc_start: 0.8246 (mp) cc_final: 0.7952 (mm) REVERT: C 853 THR cc_start: 0.8423 (t) cc_final: 0.8112 (p) REVERT: C 864 GLU cc_start: 0.7176 (tp30) cc_final: 0.6895 (tp30) REVERT: C 867 LEU cc_start: 0.8254 (pt) cc_final: 0.7992 (pp) REVERT: C 937 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7197 (mm) REVERT: C 991 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6642 (pm20) REVERT: C 1006 SER cc_start: 0.8203 (m) cc_final: 0.7768 (t) REVERT: C 1009 TYR cc_start: 0.6655 (m-80) cc_final: 0.6414 (m-80) REVERT: D 142 LYS cc_start: 0.7141 (tttm) cc_final: 0.6851 (tmtt) REVERT: D 164 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7262 (tt) REVERT: D 238 LYS cc_start: 0.7432 (tptt) cc_final: 0.7146 (tptp) REVERT: D 275 LEU cc_start: 0.7540 (mt) cc_final: 0.7264 (mt) REVERT: D 367 HIS cc_start: 0.7162 (m-70) cc_final: 0.6790 (m-70) REVERT: D 369 GLU cc_start: 0.7030 (tt0) cc_final: 0.6731 (tt0) REVERT: D 400 GLN cc_start: 0.7687 (tt0) cc_final: 0.7348 (tt0) REVERT: D 409 CYS cc_start: 0.7618 (m) cc_final: 0.6919 (t) REVERT: D 415 CYS cc_start: 0.6248 (m) cc_final: 0.4488 (m) REVERT: D 585 ASN cc_start: 0.7797 (t0) cc_final: 0.7419 (t0) REVERT: D 607 GLU cc_start: 0.7300 (tp30) cc_final: 0.7050 (tp30) REVERT: D 611 TRP cc_start: 0.7424 (t60) cc_final: 0.6824 (t60) REVERT: D 614 VAL cc_start: 0.8473 (t) cc_final: 0.8265 (p) REVERT: D 640 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6615 (mm-30) REVERT: D 660 ARG cc_start: 0.7017 (mtp85) cc_final: 0.6750 (mtp85) REVERT: D 853 THR cc_start: 0.8546 (t) cc_final: 0.8163 (p) REVERT: D 880 LYS cc_start: 0.7899 (pttt) cc_final: 0.7436 (ptmt) REVERT: D 942 LYS cc_start: 0.8411 (mmtp) cc_final: 0.8170 (mmtm) REVERT: D 973 LYS cc_start: 0.8292 (ptmt) cc_final: 0.7863 (ptpp) REVERT: D 987 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.5600 (mmm) REVERT: D 990 CYS cc_start: 0.7477 (m) cc_final: 0.6844 (m) REVERT: D 991 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6306 (pm20) REVERT: D 1005 LEU cc_start: 0.7200 (mp) cc_final: 0.6985 (mp) REVERT: D 1006 SER cc_start: 0.8198 (m) cc_final: 0.7728 (t) REVERT: D 1019 GLU cc_start: 0.7893 (mm-30) cc_final: 0.6953 (tp30) REVERT: D 1022 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7580 (tm-30) REVERT: D 1023 GLU cc_start: 0.6210 (mp0) cc_final: 0.4155 (mp0) REVERT: E 145 ARG cc_start: 0.7643 (ttm110) cc_final: 0.7297 (ttm110) REVERT: E 172 ARG cc_start: 0.6670 (mtt90) cc_final: 0.6324 (mtt90) REVERT: E 175 LYS cc_start: 0.8073 (tttt) cc_final: 0.7770 (tttt) REVERT: E 210 ASP cc_start: 0.8090 (p0) cc_final: 0.7788 (p0) REVERT: E 277 MET cc_start: 0.6561 (ptm) cc_final: 0.6275 (ptm) REVERT: E 285 PRO cc_start: 0.6311 (Cg_exo) cc_final: 0.6074 (Cg_endo) REVERT: E 367 HIS cc_start: 0.7023 (m-70) cc_final: 0.6612 (m-70) REVERT: E 375 GLU cc_start: 0.7362 (tt0) cc_final: 0.7035 (tt0) REVERT: E 404 VAL cc_start: 0.7865 (t) cc_final: 0.7481 (p) REVERT: E 409 CYS cc_start: 0.7835 (m) cc_final: 0.7010 (t) REVERT: E 415 CYS cc_start: 0.6326 (m) cc_final: 0.4438 (m) REVERT: E 419 CYS cc_start: 0.7676 (m) cc_final: 0.7289 (m) REVERT: E 502 PHE cc_start: 0.7059 (m-10) cc_final: 0.6679 (m-10) REVERT: E 585 ASN cc_start: 0.7572 (t0) cc_final: 0.7331 (t0) REVERT: E 611 TRP cc_start: 0.7647 (t60) cc_final: 0.7006 (t60) REVERT: E 613 GLU cc_start: 0.7254 (tt0) cc_final: 0.6890 (tt0) REVERT: E 649 TYR cc_start: 0.7224 (m-80) cc_final: 0.6402 (m-80) REVERT: E 663 HIS cc_start: 0.7696 (m90) cc_final: 0.7493 (m-70) REVERT: E 731 ARG cc_start: 0.6819 (ttm170) cc_final: 0.6513 (ttm110) REVERT: E 777 LEU cc_start: 0.8308 (mp) cc_final: 0.7862 (mm) REVERT: E 785 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7211 (pt0) REVERT: E 831 LYS cc_start: 0.8319 (mttt) cc_final: 0.7839 (mttm) REVERT: E 867 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8302 (pp) REVERT: E 878 LYS cc_start: 0.8293 (mmtt) cc_final: 0.8048 (tppt) REVERT: E 933 CYS cc_start: 0.7629 (m) cc_final: 0.7314 (p) REVERT: E 971 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.7016 (tt) REVERT: E 973 LYS cc_start: 0.8287 (ptmt) cc_final: 0.7768 (ptpp) REVERT: E 991 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6565 (pm20) REVERT: E 1006 SER cc_start: 0.8150 (m) cc_final: 0.7682 (t) REVERT: E 1009 TYR cc_start: 0.6418 (m-80) cc_final: 0.6201 (m-80) REVERT: E 1013 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6991 (tm-30) REVERT: E 1019 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7356 (tp30) REVERT: E 1022 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7478 (tm-30) REVERT: F 143 TYR cc_start: 0.6660 (t80) cc_final: 0.6402 (t80) REVERT: F 172 ARG cc_start: 0.6467 (mtt90) cc_final: 0.6215 (mtt90) REVERT: F 272 LEU cc_start: 0.7829 (mt) cc_final: 0.7364 (tt) REVERT: F 312 ASP cc_start: 0.7310 (t70) cc_final: 0.6783 (t0) REVERT: F 369 GLU cc_start: 0.6940 (tt0) cc_final: 0.6509 (tt0) REVERT: F 409 CYS cc_start: 0.7967 (m) cc_final: 0.7658 (m) REVERT: F 415 CYS cc_start: 0.6382 (m) cc_final: 0.6164 (m) REVERT: F 426 MET cc_start: 0.7306 (tpt) cc_final: 0.6947 (tpt) REVERT: F 563 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6555 (tm-30) REVERT: F 607 GLU cc_start: 0.7180 (tp30) cc_final: 0.6802 (tp30) REVERT: F 611 TRP cc_start: 0.7442 (t60) cc_final: 0.6693 (t60) REVERT: F 613 GLU cc_start: 0.7273 (tt0) cc_final: 0.6971 (tt0) REVERT: F 637 MET cc_start: 0.7400 (tpt) cc_final: 0.7045 (tpt) REVERT: F 644 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7467 (mm-40) REVERT: F 645 ARG cc_start: 0.7068 (mtm110) cc_final: 0.6841 (mtm110) REVERT: F 647 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7549 (mtm) REVERT: F 649 TYR cc_start: 0.7165 (m-80) cc_final: 0.6722 (m-80) REVERT: F 785 GLU cc_start: 0.7642 (pt0) cc_final: 0.7032 (mt-10) REVERT: F 800 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8145 (mt) REVERT: F 876 CYS cc_start: 0.7680 (m) cc_final: 0.7167 (m) REVERT: F 929 ILE cc_start: 0.8598 (mt) cc_final: 0.8310 (mp) REVERT: F 987 MET cc_start: 0.6283 (mmt) cc_final: 0.5840 (mmm) REVERT: F 991 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6597 (pm20) REVERT: F 1006 SER cc_start: 0.8124 (m) cc_final: 0.7824 (t) REVERT: F 1029 THR cc_start: 0.8225 (m) cc_final: 0.7695 (p) outliers start: 168 outliers final: 105 residues processed: 950 average time/residue: 0.5094 time to fit residues: 777.8706 Evaluate side-chains 973 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 850 time to evaluate : 4.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 828 ASN Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 812 ASP Chi-restraints excluded: chain B residue 828 ASN Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 970 SER Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 783 SER Chi-restraints excluded: chain C residue 812 ASP Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 912 GLN Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 632 TYR Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 791 SER Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 522 HIS Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 775 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 786 CYS Chi-restraints excluded: chain E residue 792 LEU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 828 ASN Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 849 SER Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 971 LEU Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain E residue 1028 LEU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 812 ASP Chi-restraints excluded: chain F residue 828 ASN Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 276 optimal weight: 0.0870 chunk 139 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 294 optimal weight: 0.3980 chunk 315 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 363 optimal weight: 0.0040 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN ** C 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 771 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39690 Z= 0.155 Angle : 0.626 11.537 53544 Z= 0.301 Chirality : 0.040 0.180 6078 Planarity : 0.005 0.076 6714 Dihedral : 6.902 141.808 5256 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.46 % Allowed : 21.33 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.12), residues: 4782 helix: 0.32 (0.11), residues: 2142 sheet: -1.85 (0.19), residues: 654 loop : -1.10 (0.15), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 478 HIS 0.005 0.001 HIS B 938 PHE 0.024 0.001 PHE A 528 TYR 0.029 0.001 TYR E 143 ARG 0.006 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 866 time to evaluate : 4.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.7228 (t80) cc_final: 0.6904 (t80) REVERT: A 172 ARG cc_start: 0.6596 (mtt90) cc_final: 0.6235 (mtt90) REVERT: A 239 MET cc_start: 0.6499 (ttp) cc_final: 0.6232 (ttp) REVERT: A 259 ILE cc_start: 0.7572 (mp) cc_final: 0.6996 (pt) REVERT: A 267 VAL cc_start: 0.4080 (OUTLIER) cc_final: 0.3437 (m) REVERT: A 272 LEU cc_start: 0.7890 (tp) cc_final: 0.7617 (tt) REVERT: A 298 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6451 (pt) REVERT: A 329 ASP cc_start: 0.7904 (m-30) cc_final: 0.7402 (p0) REVERT: A 351 ARG cc_start: 0.7388 (mtm180) cc_final: 0.7074 (mtm180) REVERT: A 419 CYS cc_start: 0.7712 (m) cc_final: 0.7468 (m) REVERT: A 505 MET cc_start: 0.4410 (ppp) cc_final: 0.3796 (ppp) REVERT: A 523 MET cc_start: 0.6904 (mmm) cc_final: 0.6572 (tpp) REVERT: A 532 MET cc_start: 0.7843 (tpp) cc_final: 0.7520 (tpt) REVERT: A 563 GLU cc_start: 0.7133 (pp20) cc_final: 0.6838 (tp30) REVERT: A 569 GLU cc_start: 0.6947 (tp30) cc_final: 0.6656 (tp30) REVERT: A 607 GLU cc_start: 0.7651 (tp30) cc_final: 0.7292 (tp30) REVERT: A 613 GLU cc_start: 0.7404 (tt0) cc_final: 0.7118 (tt0) REVERT: A 647 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7907 (mtm) REVERT: A 649 TYR cc_start: 0.7248 (m-80) cc_final: 0.6504 (m-80) REVERT: A 660 ARG cc_start: 0.6802 (tpp80) cc_final: 0.6441 (ttm-80) REVERT: A 669 CYS cc_start: 0.7061 (m) cc_final: 0.6690 (m) REVERT: A 672 ASN cc_start: 0.7258 (m110) cc_final: 0.7002 (m110) REVERT: A 859 ARG cc_start: 0.7415 (mtt-85) cc_final: 0.7215 (mtt-85) REVERT: A 930 LYS cc_start: 0.7945 (mttt) cc_final: 0.7493 (mttt) REVERT: A 973 LYS cc_start: 0.8221 (ptmt) cc_final: 0.7686 (ptpp) REVERT: A 974 LEU cc_start: 0.7820 (tt) cc_final: 0.7605 (tt) REVERT: A 988 MET cc_start: 0.7069 (mmm) cc_final: 0.6032 (tmm) REVERT: A 991 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6341 (pm20) REVERT: A 1006 SER cc_start: 0.8334 (m) cc_final: 0.7877 (t) REVERT: A 1013 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7189 (tm-30) REVERT: B 145 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7266 (ttm-80) REVERT: B 240 MET cc_start: 0.5825 (OUTLIER) cc_final: 0.5307 (mtm) REVERT: B 259 ILE cc_start: 0.7655 (mp) cc_final: 0.7133 (pt) REVERT: B 260 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.6139 (t-90) REVERT: B 262 ARG cc_start: 0.7571 (ttm-80) cc_final: 0.7300 (ttm-80) REVERT: B 267 VAL cc_start: 0.4107 (OUTLIER) cc_final: 0.3786 (p) REVERT: B 300 LEU cc_start: 0.7364 (mt) cc_final: 0.6907 (mp) REVERT: B 323 GLN cc_start: 0.8383 (mm110) cc_final: 0.8162 (mm110) REVERT: B 367 HIS cc_start: 0.7097 (m-70) cc_final: 0.6704 (m-70) REVERT: B 610 LYS cc_start: 0.8485 (mppt) cc_final: 0.8268 (mppt) REVERT: B 613 GLU cc_start: 0.7528 (tt0) cc_final: 0.7231 (tt0) REVERT: B 652 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7945 (ttmm) REVERT: B 676 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7646 (m) REVERT: B 845 GLN cc_start: 0.7613 (tp40) cc_final: 0.7366 (tp-100) REVERT: B 883 GLN cc_start: 0.7409 (mp10) cc_final: 0.7103 (mp10) REVERT: B 929 ILE cc_start: 0.8203 (mt) cc_final: 0.7982 (mp) REVERT: B 988 MET cc_start: 0.7544 (mmm) cc_final: 0.7015 (tmm) REVERT: B 1008 MET cc_start: 0.6357 (mmm) cc_final: 0.5876 (ttt) REVERT: B 1013 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7312 (tm-30) REVERT: B 1029 THR cc_start: 0.8212 (m) cc_final: 0.7734 (p) REVERT: C 142 LYS cc_start: 0.7207 (tttm) cc_final: 0.6972 (tttm) REVERT: C 145 ARG cc_start: 0.7516 (ttp-110) cc_final: 0.7114 (ttm110) REVERT: C 239 MET cc_start: 0.6426 (ttp) cc_final: 0.6207 (ttp) REVERT: C 259 ILE cc_start: 0.7532 (mp) cc_final: 0.7019 (pt) REVERT: C 298 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6478 (pt) REVERT: C 337 ARG cc_start: 0.7454 (mtt180) cc_final: 0.7236 (mtm180) REVERT: C 338 LYS cc_start: 0.7724 (mtpp) cc_final: 0.7482 (mtpp) REVERT: C 367 HIS cc_start: 0.7114 (m-70) cc_final: 0.6554 (m-70) REVERT: C 400 GLN cc_start: 0.7480 (tt0) cc_final: 0.7221 (tt0) REVERT: C 409 CYS cc_start: 0.7635 (m) cc_final: 0.7295 (t) REVERT: C 417 ILE cc_start: 0.7953 (mt) cc_final: 0.7538 (tt) REVERT: C 419 CYS cc_start: 0.7895 (m) cc_final: 0.7410 (m) REVERT: C 442 VAL cc_start: 0.7500 (p) cc_final: 0.7251 (m) REVERT: C 477 ILE cc_start: 0.7306 (pt) cc_final: 0.6965 (tp) REVERT: C 488 ASP cc_start: 0.7503 (m-30) cc_final: 0.7146 (m-30) REVERT: C 523 MET cc_start: 0.7289 (mmm) cc_final: 0.6910 (tpp) REVERT: C 603 GLN cc_start: 0.7600 (tp40) cc_final: 0.7394 (tp40) REVERT: C 613 GLU cc_start: 0.7435 (tt0) cc_final: 0.7130 (mt-10) REVERT: C 640 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6615 (mt-10) REVERT: C 641 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.6835 (t0) REVERT: C 645 ARG cc_start: 0.7293 (mtm110) cc_final: 0.6297 (mtm110) REVERT: C 839 LEU cc_start: 0.8255 (mp) cc_final: 0.7965 (mm) REVERT: C 853 THR cc_start: 0.8404 (t) cc_final: 0.8083 (p) REVERT: C 864 GLU cc_start: 0.7130 (tp30) cc_final: 0.6840 (tp30) REVERT: C 867 LEU cc_start: 0.8235 (pt) cc_final: 0.7970 (pp) REVERT: C 937 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7166 (mm) REVERT: C 991 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6623 (pm20) REVERT: C 1009 TYR cc_start: 0.6633 (m-80) cc_final: 0.6402 (m-80) REVERT: D 142 LYS cc_start: 0.7077 (tttm) cc_final: 0.6795 (tmtt) REVERT: D 164 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7233 (tt) REVERT: D 238 LYS cc_start: 0.7422 (tptt) cc_final: 0.7145 (tptp) REVERT: D 275 LEU cc_start: 0.7557 (mt) cc_final: 0.7280 (mt) REVERT: D 277 MET cc_start: 0.6589 (ptm) cc_final: 0.6348 (ptm) REVERT: D 298 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.5706 (pt) REVERT: D 301 MET cc_start: 0.7109 (ttp) cc_final: 0.6726 (ttp) REVERT: D 367 HIS cc_start: 0.7143 (m-70) cc_final: 0.6777 (m-70) REVERT: D 369 GLU cc_start: 0.7039 (tt0) cc_final: 0.6745 (tt0) REVERT: D 409 CYS cc_start: 0.7594 (m) cc_final: 0.6902 (t) REVERT: D 415 CYS cc_start: 0.6142 (m) cc_final: 0.4345 (m) REVERT: D 585 ASN cc_start: 0.7758 (t0) cc_final: 0.7371 (t0) REVERT: D 611 TRP cc_start: 0.7413 (t60) cc_final: 0.6868 (t60) REVERT: D 614 VAL cc_start: 0.8450 (t) cc_final: 0.8245 (p) REVERT: D 640 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6597 (mm-30) REVERT: D 660 ARG cc_start: 0.6919 (mtp85) cc_final: 0.6673 (mtp85) REVERT: D 853 THR cc_start: 0.8530 (t) cc_final: 0.8155 (p) REVERT: D 880 LYS cc_start: 0.7894 (pttt) cc_final: 0.7425 (ptmt) REVERT: D 934 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6148 (tm-30) REVERT: D 973 LYS cc_start: 0.8287 (ptmt) cc_final: 0.7860 (ptpp) REVERT: D 987 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.5891 (mmm) REVERT: D 991 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6261 (pm20) REVERT: D 1005 LEU cc_start: 0.7214 (mp) cc_final: 0.6995 (mp) REVERT: D 1006 SER cc_start: 0.8202 (m) cc_final: 0.7743 (t) REVERT: D 1019 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7166 (tp30) REVERT: D 1022 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7534 (tm-30) REVERT: E 142 LYS cc_start: 0.7107 (tttm) cc_final: 0.6885 (tptm) REVERT: E 145 ARG cc_start: 0.7629 (ttm110) cc_final: 0.7270 (ttm110) REVERT: E 172 ARG cc_start: 0.6591 (mtt90) cc_final: 0.6251 (mtt90) REVERT: E 175 LYS cc_start: 0.8066 (tttt) cc_final: 0.7761 (tttt) REVERT: E 210 ASP cc_start: 0.8096 (p0) cc_final: 0.7822 (p0) REVERT: E 277 MET cc_start: 0.6540 (ptm) cc_final: 0.6249 (ptm) REVERT: E 367 HIS cc_start: 0.7010 (m-70) cc_final: 0.6678 (m90) REVERT: E 375 GLU cc_start: 0.7338 (tt0) cc_final: 0.7005 (tt0) REVERT: E 404 VAL cc_start: 0.7877 (t) cc_final: 0.7502 (p) REVERT: E 409 CYS cc_start: 0.7838 (m) cc_final: 0.7064 (t) REVERT: E 415 CYS cc_start: 0.6310 (m) cc_final: 0.4305 (m) REVERT: E 419 CYS cc_start: 0.7677 (m) cc_final: 0.7245 (m) REVERT: E 502 PHE cc_start: 0.7010 (m-10) cc_final: 0.6628 (m-10) REVERT: E 585 ASN cc_start: 0.7547 (t0) cc_final: 0.7322 (t0) REVERT: E 611 TRP cc_start: 0.7622 (t60) cc_final: 0.7010 (t60) REVERT: E 649 TYR cc_start: 0.7270 (m-80) cc_final: 0.6969 (m-80) REVERT: E 663 HIS cc_start: 0.7686 (m90) cc_final: 0.7459 (m-70) REVERT: E 731 ARG cc_start: 0.6809 (ttm170) cc_final: 0.6512 (ttm110) REVERT: E 777 LEU cc_start: 0.8272 (mp) cc_final: 0.7833 (mt) REVERT: E 785 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: E 831 LYS cc_start: 0.8333 (mttt) cc_final: 0.8018 (mttm) REVERT: E 877 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7194 (mt-10) REVERT: E 878 LYS cc_start: 0.8305 (mmtt) cc_final: 0.8075 (tppt) REVERT: E 933 CYS cc_start: 0.7628 (m) cc_final: 0.7326 (p) REVERT: E 973 LYS cc_start: 0.8273 (ptmt) cc_final: 0.7766 (ptpp) REVERT: E 991 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6544 (pm20) REVERT: E 1006 SER cc_start: 0.8156 (m) cc_final: 0.7680 (t) REVERT: E 1009 TYR cc_start: 0.6374 (m-80) cc_final: 0.6126 (m-80) REVERT: E 1019 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7327 (tp30) REVERT: E 1022 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7430 (tm-30) REVERT: F 143 TYR cc_start: 0.6649 (t80) cc_final: 0.6415 (t80) REVERT: F 172 ARG cc_start: 0.6440 (mtt90) cc_final: 0.6186 (mtt90) REVERT: F 272 LEU cc_start: 0.7759 (mt) cc_final: 0.7379 (tt) REVERT: F 312 ASP cc_start: 0.7343 (t70) cc_final: 0.6839 (t0) REVERT: F 369 GLU cc_start: 0.6944 (tt0) cc_final: 0.6515 (tt0) REVERT: F 415 CYS cc_start: 0.6294 (m) cc_final: 0.5881 (m) REVERT: F 426 MET cc_start: 0.7309 (tpt) cc_final: 0.6951 (tpt) REVERT: F 607 GLU cc_start: 0.7180 (tp30) cc_final: 0.6827 (tp30) REVERT: F 611 TRP cc_start: 0.7437 (t60) cc_final: 0.6667 (t60) REVERT: F 613 GLU cc_start: 0.7251 (tt0) cc_final: 0.6955 (tt0) REVERT: F 637 MET cc_start: 0.7409 (tpt) cc_final: 0.7034 (tpt) REVERT: F 644 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7442 (mm-40) REVERT: F 645 ARG cc_start: 0.7059 (mtm110) cc_final: 0.6859 (mtm110) REVERT: F 647 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7566 (mtm) REVERT: F 649 TYR cc_start: 0.7155 (m-80) cc_final: 0.6733 (m-80) REVERT: F 785 GLU cc_start: 0.7615 (pt0) cc_final: 0.7078 (mt-10) REVERT: F 876 CYS cc_start: 0.7662 (m) cc_final: 0.7143 (m) REVERT: F 929 ILE cc_start: 0.8575 (mt) cc_final: 0.8298 (mp) REVERT: F 987 MET cc_start: 0.6539 (mmt) cc_final: 0.6180 (mmt) REVERT: F 991 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: F 1006 SER cc_start: 0.8132 (m) cc_final: 0.7833 (t) REVERT: F 1029 THR cc_start: 0.8216 (m) cc_final: 0.7848 (p) outliers start: 152 outliers final: 103 residues processed: 945 average time/residue: 0.5051 time to fit residues: 771.5672 Evaluate side-chains 970 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 847 time to evaluate : 4.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 828 ASN Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 812 ASP Chi-restraints excluded: chain B residue 828 ASN Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 522 HIS Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 812 ASP Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 522 HIS Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 644 GLN Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 765 LEU Chi-restraints excluded: chain E residue 775 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 786 CYS Chi-restraints excluded: chain E residue 792 LEU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 828 ASN Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 908 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain E residue 1028 LEU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 600 ILE Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 796 SER Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 812 ASP Chi-restraints excluded: chain F residue 828 ASN Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 973 LYS Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 0.7980 chunk 443 optimal weight: 0.3980 chunk 404 optimal weight: 0.9990 chunk 431 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 187 optimal weight: 0.6980 chunk 338 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 389 optimal weight: 0.8980 chunk 407 optimal weight: 0.5980 chunk 429 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS ** A 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 ASN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 771 ASN E 893 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39690 Z= 0.176 Angle : 0.647 12.331 53544 Z= 0.311 Chirality : 0.040 0.260 6078 Planarity : 0.004 0.077 6714 Dihedral : 6.889 146.107 5256 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.21 % Allowed : 21.96 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4782 helix: 0.28 (0.11), residues: 2166 sheet: -1.47 (0.20), residues: 588 loop : -1.29 (0.15), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 243 HIS 0.005 0.001 HIS D 938 PHE 0.032 0.001 PHE B 581 TYR 0.025 0.001 TYR E 168 ARG 0.009 0.000 ARG E 645 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 855 time to evaluate : 4.604 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: A 143 TYR cc_start: 0.7249 (t80) cc_final: 0.6922 (t80) REVERT: A 172 ARG cc_start: 0.6615 (mtt90) cc_final: 0.6248 (mtt90) REVERT: A 239 MET cc_start: 0.6476 (ttp) cc_final: 0.6219 (ttp) REVERT: A 259 ILE cc_start: 0.7587 (mp) cc_final: 0.7028 (pt) REVERT: A 298 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6435 (pt) REVERT: A 329 ASP cc_start: 0.7909 (m-30) cc_final: 0.7395 (p0) REVERT: A 351 ARG cc_start: 0.7371 (mtm180) cc_final: 0.7020 (mtm180) REVERT: A 419 CYS cc_start: 0.7663 (m) cc_final: 0.7420 (m) REVERT: A 523 MET cc_start: 0.6908 (mmm) cc_final: 0.6577 (tpp) REVERT: A 532 MET cc_start: 0.7861 (tpp) cc_final: 0.7534 (tpt) REVERT: A 563 GLU cc_start: 0.7201 (pp20) cc_final: 0.6967 (tp30) REVERT: A 569 GLU cc_start: 0.6970 (tp30) cc_final: 0.6685 (tp30) REVERT: A 607 GLU cc_start: 0.7659 (tp30) cc_final: 0.7357 (tp30) REVERT: A 613 GLU cc_start: 0.7420 (tt0) cc_final: 0.7129 (tt0) REVERT: A 649 TYR cc_start: 0.7232 (m-80) cc_final: 0.6494 (m-80) REVERT: A 660 ARG cc_start: 0.6880 (tpp80) cc_final: 0.6514 (ttm-80) REVERT: A 864 GLU cc_start: 0.7177 (tp30) cc_final: 0.6967 (tp30) REVERT: A 973 LYS cc_start: 0.8228 (ptmt) cc_final: 0.7650 (ptpp) REVERT: A 974 LEU cc_start: 0.7809 (tt) cc_final: 0.7609 (tt) REVERT: A 988 MET cc_start: 0.7077 (mmm) cc_final: 0.6034 (tmm) REVERT: A 991 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6325 (pm20) REVERT: A 1006 SER cc_start: 0.8338 (m) cc_final: 0.7894 (t) REVERT: A 1013 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7358 (tm-30) REVERT: B 145 ARG cc_start: 0.7556 (ttm110) cc_final: 0.7240 (ttm-80) REVERT: B 240 MET cc_start: 0.5906 (OUTLIER) cc_final: 0.5428 (mtm) REVERT: B 259 ILE cc_start: 0.7696 (mp) cc_final: 0.7171 (pt) REVERT: B 260 HIS cc_start: 0.6690 (OUTLIER) cc_final: 0.6226 (t-90) REVERT: B 267 VAL cc_start: 0.4196 (OUTLIER) cc_final: 0.3893 (p) REVERT: B 367 HIS cc_start: 0.7125 (m-70) cc_final: 0.6732 (m-70) REVERT: B 523 MET cc_start: 0.7135 (mtp) cc_final: 0.6891 (mtp) REVERT: B 613 GLU cc_start: 0.7528 (tt0) cc_final: 0.7222 (tt0) REVERT: B 638 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7314 (tp40) REVERT: B 652 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7954 (ttmm) REVERT: B 845 GLN cc_start: 0.7644 (tp40) cc_final: 0.7391 (tp-100) REVERT: B 883 GLN cc_start: 0.7425 (mp10) cc_final: 0.7107 (mp10) REVERT: B 929 ILE cc_start: 0.8202 (mt) cc_final: 0.7978 (mp) REVERT: B 988 MET cc_start: 0.7553 (mmm) cc_final: 0.7021 (tmm) REVERT: B 1008 MET cc_start: 0.6382 (mmm) cc_final: 0.5928 (ttt) REVERT: B 1013 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7330 (tm-30) REVERT: B 1029 THR cc_start: 0.8218 (m) cc_final: 0.7761 (p) REVERT: C 145 ARG cc_start: 0.7519 (ttp-110) cc_final: 0.7241 (ttm110) REVERT: C 172 ARG cc_start: 0.6739 (mtt90) cc_final: 0.6468 (mtp85) REVERT: C 239 MET cc_start: 0.6431 (ttp) cc_final: 0.6217 (ttp) REVERT: C 259 ILE cc_start: 0.7558 (mp) cc_final: 0.7040 (pt) REVERT: C 298 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6479 (pt) REVERT: C 301 MET cc_start: 0.6744 (ttm) cc_final: 0.6230 (ttp) REVERT: C 337 ARG cc_start: 0.7458 (mtt180) cc_final: 0.7242 (mtm180) REVERT: C 338 LYS cc_start: 0.7731 (mtpp) cc_final: 0.7498 (mtpp) REVERT: C 367 HIS cc_start: 0.7120 (m-70) cc_final: 0.6582 (m-70) REVERT: C 400 GLN cc_start: 0.7478 (tt0) cc_final: 0.7220 (tt0) REVERT: C 409 CYS cc_start: 0.7640 (m) cc_final: 0.7294 (t) REVERT: C 417 ILE cc_start: 0.7989 (mt) cc_final: 0.7561 (tt) REVERT: C 419 CYS cc_start: 0.7917 (m) cc_final: 0.7414 (m) REVERT: C 442 VAL cc_start: 0.7499 (p) cc_final: 0.7254 (m) REVERT: C 467 TRP cc_start: 0.6037 (t60) cc_final: 0.5754 (t-100) REVERT: C 488 ASP cc_start: 0.7501 (m-30) cc_final: 0.7160 (m-30) REVERT: C 523 MET cc_start: 0.7290 (mmm) cc_final: 0.6985 (tpp) REVERT: C 603 GLN cc_start: 0.7612 (tp40) cc_final: 0.7401 (tp40) REVERT: C 613 GLU cc_start: 0.7443 (tt0) cc_final: 0.7096 (mt-10) REVERT: C 640 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6616 (mt-10) REVERT: C 641 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6840 (t0) REVERT: C 645 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6246 (mtm110) REVERT: C 649 TYR cc_start: 0.7172 (m-80) cc_final: 0.6849 (m-80) REVERT: C 839 LEU cc_start: 0.8266 (mp) cc_final: 0.7976 (mm) REVERT: C 853 THR cc_start: 0.8404 (t) cc_final: 0.8095 (p) REVERT: C 864 GLU cc_start: 0.7155 (tp30) cc_final: 0.6851 (tp30) REVERT: C 867 LEU cc_start: 0.8244 (pt) cc_final: 0.7982 (pp) REVERT: C 937 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7175 (mm) REVERT: C 991 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: C 1009 TYR cc_start: 0.6648 (m-80) cc_final: 0.6406 (m-80) REVERT: D 164 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7247 (tt) REVERT: D 238 LYS cc_start: 0.7424 (tptt) cc_final: 0.7161 (tptp) REVERT: D 275 LEU cc_start: 0.7585 (mt) cc_final: 0.7312 (mt) REVERT: D 277 MET cc_start: 0.6596 (ptm) cc_final: 0.6345 (ptm) REVERT: D 298 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.5713 (pt) REVERT: D 301 MET cc_start: 0.7114 (ttp) cc_final: 0.6734 (ttp) REVERT: D 312 ASP cc_start: 0.7314 (t70) cc_final: 0.7038 (t0) REVERT: D 323 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7906 (mm-40) REVERT: D 367 HIS cc_start: 0.7166 (m-70) cc_final: 0.6804 (m-70) REVERT: D 369 GLU cc_start: 0.7035 (tt0) cc_final: 0.6754 (tt0) REVERT: D 406 PHE cc_start: 0.8120 (t80) cc_final: 0.7792 (t80) REVERT: D 409 CYS cc_start: 0.7616 (m) cc_final: 0.6930 (t) REVERT: D 415 CYS cc_start: 0.6189 (m) cc_final: 0.4366 (m) REVERT: D 585 ASN cc_start: 0.7778 (t0) cc_final: 0.7372 (t0) REVERT: D 611 TRP cc_start: 0.7454 (t60) cc_final: 0.6885 (t60) REVERT: D 640 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6518 (mm-30) REVERT: D 644 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7482 (mm110) REVERT: D 660 ARG cc_start: 0.6975 (mtp85) cc_final: 0.6673 (mtp85) REVERT: D 771 ASN cc_start: 0.7209 (t0) cc_final: 0.6915 (t0) REVERT: D 853 THR cc_start: 0.8519 (t) cc_final: 0.8165 (p) REVERT: D 880 LYS cc_start: 0.7896 (pttt) cc_final: 0.7423 (ptmt) REVERT: D 899 VAL cc_start: 0.6434 (m) cc_final: 0.6210 (p) REVERT: D 934 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6165 (tm-30) REVERT: D 973 LYS cc_start: 0.8296 (ptmt) cc_final: 0.7887 (ptpp) REVERT: D 987 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.5886 (mmm) REVERT: D 991 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6276 (pm20) REVERT: D 1005 LEU cc_start: 0.7219 (mp) cc_final: 0.7003 (mp) REVERT: D 1006 SER cc_start: 0.8199 (m) cc_final: 0.7733 (t) REVERT: D 1019 GLU cc_start: 0.7888 (mm-30) cc_final: 0.6962 (tp30) REVERT: D 1022 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7552 (tm-30) REVERT: D 1023 GLU cc_start: 0.6246 (mp0) cc_final: 0.4396 (mp0) REVERT: E 142 LYS cc_start: 0.7084 (tttm) cc_final: 0.6861 (tptm) REVERT: E 145 ARG cc_start: 0.7636 (ttm110) cc_final: 0.7269 (ttm110) REVERT: E 172 ARG cc_start: 0.6588 (mtt90) cc_final: 0.6250 (mtt90) REVERT: E 175 LYS cc_start: 0.8083 (tttt) cc_final: 0.7785 (tttt) REVERT: E 210 ASP cc_start: 0.8089 (p0) cc_final: 0.7814 (p0) REVERT: E 277 MET cc_start: 0.6508 (ptm) cc_final: 0.6221 (ptm) REVERT: E 367 HIS cc_start: 0.7014 (m-70) cc_final: 0.6674 (m90) REVERT: E 375 GLU cc_start: 0.7355 (tt0) cc_final: 0.7015 (tt0) REVERT: E 404 VAL cc_start: 0.7875 (t) cc_final: 0.7484 (p) REVERT: E 409 CYS cc_start: 0.7842 (m) cc_final: 0.7013 (t) REVERT: E 415 CYS cc_start: 0.6303 (m) cc_final: 0.4303 (m) REVERT: E 419 CYS cc_start: 0.7661 (m) cc_final: 0.7244 (m) REVERT: E 502 PHE cc_start: 0.6981 (m-10) cc_final: 0.6631 (m-10) REVERT: E 585 ASN cc_start: 0.7547 (t0) cc_final: 0.7316 (t0) REVERT: E 611 TRP cc_start: 0.7613 (t60) cc_final: 0.6975 (t60) REVERT: E 629 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6646 (mm-30) REVERT: E 645 ARG cc_start: 0.7755 (mmm160) cc_final: 0.7288 (mmm160) REVERT: E 663 HIS cc_start: 0.7695 (m90) cc_final: 0.7480 (m-70) REVERT: E 731 ARG cc_start: 0.6821 (ttm170) cc_final: 0.6518 (ttm110) REVERT: E 777 LEU cc_start: 0.8271 (mp) cc_final: 0.7769 (mm) REVERT: E 785 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7194 (pt0) REVERT: E 831 LYS cc_start: 0.8297 (mttt) cc_final: 0.8029 (mttm) REVERT: E 853 THR cc_start: 0.8434 (t) cc_final: 0.8027 (p) REVERT: E 878 LYS cc_start: 0.8291 (mmtt) cc_final: 0.8049 (tppt) REVERT: E 933 CYS cc_start: 0.7619 (m) cc_final: 0.7323 (p) REVERT: E 973 LYS cc_start: 0.8325 (ptmt) cc_final: 0.7775 (ptpp) REVERT: E 991 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6538 (pm20) REVERT: E 1006 SER cc_start: 0.8161 (m) cc_final: 0.7706 (t) REVERT: E 1009 TYR cc_start: 0.6392 (m-80) cc_final: 0.6142 (m-80) REVERT: E 1019 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7310 (tp30) REVERT: E 1022 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7431 (tm-30) REVERT: F 172 ARG cc_start: 0.6446 (mtt90) cc_final: 0.6181 (mtt90) REVERT: F 272 LEU cc_start: 0.7771 (mt) cc_final: 0.7357 (tt) REVERT: F 312 ASP cc_start: 0.7353 (t70) cc_final: 0.6861 (t0) REVERT: F 322 TRP cc_start: 0.7481 (t60) cc_final: 0.7083 (t60) REVERT: F 323 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7226 (mm110) REVERT: F 369 GLU cc_start: 0.6948 (tt0) cc_final: 0.6511 (tt0) REVERT: F 415 CYS cc_start: 0.6351 (m) cc_final: 0.5942 (m) REVERT: F 426 MET cc_start: 0.7318 (tpt) cc_final: 0.6963 (tpt) REVERT: F 489 LEU cc_start: 0.8263 (tt) cc_final: 0.7699 (pp) REVERT: F 552 LYS cc_start: 0.6218 (mmtt) cc_final: 0.6003 (mmtm) REVERT: F 607 GLU cc_start: 0.7188 (tp30) cc_final: 0.6837 (tp30) REVERT: F 611 TRP cc_start: 0.7462 (t60) cc_final: 0.7006 (t60) REVERT: F 613 GLU cc_start: 0.7250 (tt0) cc_final: 0.6961 (tt0) REVERT: F 637 MET cc_start: 0.7393 (tpt) cc_final: 0.7033 (tpt) REVERT: F 641 ASP cc_start: 0.6988 (t0) cc_final: 0.6755 (t70) REVERT: F 644 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7441 (mm-40) REVERT: F 645 ARG cc_start: 0.7106 (mtm110) cc_final: 0.6813 (mtm110) REVERT: F 647 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7559 (mtm) REVERT: F 649 TYR cc_start: 0.7153 (m-80) cc_final: 0.6750 (m-80) REVERT: F 785 GLU cc_start: 0.7627 (pt0) cc_final: 0.7061 (mt-10) REVERT: F 800 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8150 (mt) REVERT: F 876 CYS cc_start: 0.7679 (m) cc_final: 0.7169 (m) REVERT: F 929 ILE cc_start: 0.8584 (mt) cc_final: 0.8311 (mp) REVERT: F 987 MET cc_start: 0.6524 (mmt) cc_final: 0.6192 (mmt) REVERT: F 991 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6562 (pm20) REVERT: F 1006 SER cc_start: 0.8141 (m) cc_final: 0.7841 (t) REVERT: F 1029 THR cc_start: 0.8240 (m) cc_final: 0.7832 (p) outliers start: 141 outliers final: 105 residues processed: 924 average time/residue: 0.5019 time to fit residues: 750.8527 Evaluate side-chains 972 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 847 time to evaluate : 4.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 828 ASN Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 812 ASP Chi-restraints excluded: chain B residue 828 ASN Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 522 HIS Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 812 ASP Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 912 GLN Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 632 TYR Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 791 SER Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 379 LYS Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 765 LEU Chi-restraints excluded: chain E residue 775 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 786 CYS Chi-restraints excluded: chain E residue 792 LEU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 828 ASN Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 908 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain E residue 1028 LEU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 323 GLN Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 600 ILE Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 812 ASP Chi-restraints excluded: chain F residue 828 ASN Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 973 LYS Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 0.4980 chunk 455 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 316 optimal weight: 10.0000 chunk 478 optimal weight: 4.9990 chunk 440 optimal weight: 5.9990 chunk 380 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 294 optimal weight: 0.9980 chunk 233 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 771 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39690 Z= 0.181 Angle : 0.653 13.156 53544 Z= 0.313 Chirality : 0.041 0.272 6078 Planarity : 0.005 0.085 6714 Dihedral : 6.889 149.917 5256 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.02 % Allowed : 22.44 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4782 helix: 0.27 (0.11), residues: 2154 sheet: -1.89 (0.19), residues: 654 loop : -1.07 (0.15), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 243 HIS 0.006 0.001 HIS D 674 PHE 0.027 0.001 PHE B 581 TYR 0.028 0.001 TYR E 649 ARG 0.008 0.000 ARG D 645 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 870 time to evaluate : 5.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.7236 (t80) cc_final: 0.6902 (t80) REVERT: A 172 ARG cc_start: 0.6612 (mtt90) cc_final: 0.6237 (mtt90) REVERT: A 239 MET cc_start: 0.6461 (ttp) cc_final: 0.6204 (ttp) REVERT: A 259 ILE cc_start: 0.7595 (mp) cc_final: 0.7050 (pt) REVERT: A 272 LEU cc_start: 0.8030 (tp) cc_final: 0.7753 (tt) REVERT: A 298 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6429 (pt) REVERT: A 351 ARG cc_start: 0.7350 (mtm180) cc_final: 0.6990 (mtm180) REVERT: A 370 ILE cc_start: 0.7499 (mm) cc_final: 0.7250 (tp) REVERT: A 419 CYS cc_start: 0.7689 (m) cc_final: 0.7439 (m) REVERT: A 523 MET cc_start: 0.6889 (mmm) cc_final: 0.6566 (tpp) REVERT: A 563 GLU cc_start: 0.7230 (pp20) cc_final: 0.7012 (tp30) REVERT: A 569 GLU cc_start: 0.6972 (tp30) cc_final: 0.6688 (tp30) REVERT: A 607 GLU cc_start: 0.7671 (tp30) cc_final: 0.7379 (tp30) REVERT: A 649 TYR cc_start: 0.7217 (m-80) cc_final: 0.6645 (m-80) REVERT: A 660 ARG cc_start: 0.6889 (tpp80) cc_final: 0.6525 (ttm-80) REVERT: A 864 GLU cc_start: 0.7123 (tp30) cc_final: 0.6820 (tp30) REVERT: A 897 THR cc_start: 0.8039 (m) cc_final: 0.7838 (m) REVERT: A 973 LYS cc_start: 0.8228 (ptmt) cc_final: 0.7648 (ptpp) REVERT: A 988 MET cc_start: 0.7066 (mmm) cc_final: 0.6023 (tmm) REVERT: A 991 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6334 (pm20) REVERT: A 1006 SER cc_start: 0.8322 (m) cc_final: 0.7906 (t) REVERT: A 1013 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7364 (tm-30) REVERT: B 240 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5362 (mtm) REVERT: B 259 ILE cc_start: 0.7682 (mp) cc_final: 0.7143 (pt) REVERT: B 260 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.6223 (t-90) REVERT: B 262 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.7321 (ttm-80) REVERT: B 267 VAL cc_start: 0.4256 (OUTLIER) cc_final: 0.3926 (p) REVERT: B 300 LEU cc_start: 0.7381 (mt) cc_final: 0.6896 (mp) REVERT: B 323 GLN cc_start: 0.8278 (mm110) cc_final: 0.8051 (mm110) REVERT: B 367 HIS cc_start: 0.7128 (m-70) cc_final: 0.6762 (m90) REVERT: B 523 MET cc_start: 0.7141 (mtp) cc_final: 0.6891 (mtp) REVERT: B 613 GLU cc_start: 0.7534 (tt0) cc_final: 0.7253 (tt0) REVERT: B 638 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7367 (tp40) REVERT: B 652 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7958 (ttmm) REVERT: B 845 GLN cc_start: 0.7651 (tp40) cc_final: 0.7399 (tp-100) REVERT: B 883 GLN cc_start: 0.7439 (mp10) cc_final: 0.7115 (mp10) REVERT: B 929 ILE cc_start: 0.8185 (mt) cc_final: 0.7969 (mp) REVERT: B 988 MET cc_start: 0.7557 (mmm) cc_final: 0.7016 (tmm) REVERT: B 1008 MET cc_start: 0.6336 (mmm) cc_final: 0.5915 (ttt) REVERT: B 1013 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7345 (tm-30) REVERT: B 1029 THR cc_start: 0.8219 (m) cc_final: 0.7768 (p) REVERT: C 145 ARG cc_start: 0.7511 (ttp-110) cc_final: 0.7241 (ttm110) REVERT: C 172 ARG cc_start: 0.6730 (mtt90) cc_final: 0.6460 (mtp85) REVERT: C 239 MET cc_start: 0.6437 (ttp) cc_final: 0.6222 (ttp) REVERT: C 259 ILE cc_start: 0.7590 (mp) cc_final: 0.7072 (pt) REVERT: C 298 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6425 (pt) REVERT: C 301 MET cc_start: 0.6746 (ttm) cc_final: 0.6238 (ttp) REVERT: C 337 ARG cc_start: 0.7442 (mtt180) cc_final: 0.7227 (mtm180) REVERT: C 338 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7512 (mtpp) REVERT: C 367 HIS cc_start: 0.7148 (m-70) cc_final: 0.6618 (m-70) REVERT: C 383 PHE cc_start: 0.7600 (m-10) cc_final: 0.7381 (m-10) REVERT: C 400 GLN cc_start: 0.7462 (tt0) cc_final: 0.7206 (tt0) REVERT: C 409 CYS cc_start: 0.7623 (m) cc_final: 0.7290 (t) REVERT: C 417 ILE cc_start: 0.7999 (mt) cc_final: 0.7559 (tt) REVERT: C 419 CYS cc_start: 0.7918 (m) cc_final: 0.7383 (m) REVERT: C 442 VAL cc_start: 0.7489 (p) cc_final: 0.7246 (m) REVERT: C 488 ASP cc_start: 0.7501 (m-30) cc_final: 0.7160 (m-30) REVERT: C 523 MET cc_start: 0.7288 (mmm) cc_final: 0.6983 (tpp) REVERT: C 603 GLN cc_start: 0.7605 (tp40) cc_final: 0.5908 (tp40) REVERT: C 613 GLU cc_start: 0.7472 (tt0) cc_final: 0.7259 (mt-10) REVERT: C 640 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6643 (mt-10) REVERT: C 641 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6843 (t0) REVERT: C 645 ARG cc_start: 0.7287 (mtm110) cc_final: 0.6264 (mtm110) REVERT: C 649 TYR cc_start: 0.7160 (m-80) cc_final: 0.6927 (m-80) REVERT: C 839 LEU cc_start: 0.8281 (mp) cc_final: 0.7987 (mm) REVERT: C 853 THR cc_start: 0.8405 (t) cc_final: 0.8108 (p) REVERT: C 864 GLU cc_start: 0.7147 (tp30) cc_final: 0.6867 (tp30) REVERT: C 937 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7183 (mm) REVERT: C 991 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6628 (pm20) REVERT: C 1009 TYR cc_start: 0.6629 (m-80) cc_final: 0.6389 (m-80) REVERT: D 164 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7244 (tt) REVERT: D 238 LYS cc_start: 0.7412 (tptt) cc_final: 0.7168 (tptp) REVERT: D 275 LEU cc_start: 0.7580 (mt) cc_final: 0.7295 (mt) REVERT: D 277 MET cc_start: 0.6576 (ptm) cc_final: 0.6339 (ptm) REVERT: D 298 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5684 (pt) REVERT: D 301 MET cc_start: 0.7111 (ttp) cc_final: 0.6682 (ttp) REVERT: D 312 ASP cc_start: 0.7359 (t70) cc_final: 0.6849 (t0) REVERT: D 323 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7916 (mm-40) REVERT: D 367 HIS cc_start: 0.7162 (m-70) cc_final: 0.6815 (m-70) REVERT: D 369 GLU cc_start: 0.7047 (tt0) cc_final: 0.6786 (tt0) REVERT: D 406 PHE cc_start: 0.8119 (t80) cc_final: 0.7785 (t80) REVERT: D 409 CYS cc_start: 0.7591 (m) cc_final: 0.6899 (t) REVERT: D 415 CYS cc_start: 0.6211 (m) cc_final: 0.4407 (m) REVERT: D 585 ASN cc_start: 0.7764 (t0) cc_final: 0.7325 (t0) REVERT: D 611 TRP cc_start: 0.7422 (t60) cc_final: 0.6821 (t60) REVERT: D 640 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6495 (mm-30) REVERT: D 660 ARG cc_start: 0.6983 (mtp85) cc_final: 0.6682 (mtp85) REVERT: D 771 ASN cc_start: 0.7201 (t0) cc_final: 0.6914 (t0) REVERT: D 853 THR cc_start: 0.8492 (t) cc_final: 0.8159 (p) REVERT: D 880 LYS cc_start: 0.7900 (pttt) cc_final: 0.7412 (ptmt) REVERT: D 899 VAL cc_start: 0.6469 (m) cc_final: 0.6259 (p) REVERT: D 934 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6220 (tm-30) REVERT: D 942 LYS cc_start: 0.8370 (mmtp) cc_final: 0.8151 (mmtm) REVERT: D 973 LYS cc_start: 0.8315 (ptmt) cc_final: 0.7885 (ptpp) REVERT: D 987 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6330 (mmt) REVERT: D 991 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6276 (pm20) REVERT: D 1005 LEU cc_start: 0.7232 (mp) cc_final: 0.7018 (mp) REVERT: D 1006 SER cc_start: 0.8181 (m) cc_final: 0.7737 (t) REVERT: D 1019 GLU cc_start: 0.7878 (mm-30) cc_final: 0.6895 (tp30) REVERT: D 1022 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7522 (tm-30) REVERT: D 1023 GLU cc_start: 0.6246 (mp0) cc_final: 0.4329 (mp0) REVERT: E 142 LYS cc_start: 0.7078 (tttm) cc_final: 0.6863 (tttm) REVERT: E 145 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7263 (ttm110) REVERT: E 172 ARG cc_start: 0.6560 (mtt90) cc_final: 0.6228 (mtt90) REVERT: E 175 LYS cc_start: 0.8069 (tttt) cc_final: 0.7771 (tttt) REVERT: E 210 ASP cc_start: 0.8084 (p0) cc_final: 0.7811 (p0) REVERT: E 277 MET cc_start: 0.6474 (ptm) cc_final: 0.6204 (ptm) REVERT: E 367 HIS cc_start: 0.7022 (m-70) cc_final: 0.6708 (m90) REVERT: E 375 GLU cc_start: 0.7358 (tt0) cc_final: 0.7021 (tt0) REVERT: E 404 VAL cc_start: 0.7881 (t) cc_final: 0.7508 (p) REVERT: E 409 CYS cc_start: 0.7841 (m) cc_final: 0.6999 (t) REVERT: E 415 CYS cc_start: 0.6333 (m) cc_final: 0.4391 (m) REVERT: E 419 CYS cc_start: 0.7686 (m) cc_final: 0.7261 (m) REVERT: E 502 PHE cc_start: 0.6972 (m-10) cc_final: 0.6641 (m-10) REVERT: E 585 ASN cc_start: 0.7569 (t0) cc_final: 0.7324 (t0) REVERT: E 611 TRP cc_start: 0.7586 (t60) cc_final: 0.6923 (t60) REVERT: E 613 GLU cc_start: 0.7277 (tt0) cc_final: 0.6874 (tt0) REVERT: E 629 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6616 (mm-30) REVERT: E 663 HIS cc_start: 0.7690 (m90) cc_final: 0.7477 (m-70) REVERT: E 731 ARG cc_start: 0.6829 (ttm170) cc_final: 0.6529 (ttm110) REVERT: E 777 LEU cc_start: 0.8205 (mp) cc_final: 0.7744 (mm) REVERT: E 785 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7193 (pt0) REVERT: E 831 LYS cc_start: 0.8302 (mttt) cc_final: 0.8028 (mttm) REVERT: E 853 THR cc_start: 0.8425 (t) cc_final: 0.8027 (p) REVERT: E 877 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6997 (mp0) REVERT: E 878 LYS cc_start: 0.8289 (mmtt) cc_final: 0.8044 (tppt) REVERT: E 933 CYS cc_start: 0.7620 (m) cc_final: 0.7326 (p) REVERT: E 973 LYS cc_start: 0.8327 (ptmt) cc_final: 0.7780 (ptpp) REVERT: E 991 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: E 1006 SER cc_start: 0.8162 (m) cc_final: 0.7704 (t) REVERT: E 1009 TYR cc_start: 0.6390 (m-80) cc_final: 0.6151 (m-80) REVERT: E 1019 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7340 (tp30) REVERT: E 1022 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7446 (tm-30) REVERT: F 172 ARG cc_start: 0.6452 (mtt90) cc_final: 0.6191 (mtt90) REVERT: F 272 LEU cc_start: 0.7771 (mt) cc_final: 0.7375 (tt) REVERT: F 312 ASP cc_start: 0.7372 (t70) cc_final: 0.7044 (t0) REVERT: F 322 TRP cc_start: 0.7451 (t60) cc_final: 0.7088 (t60) REVERT: F 323 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7261 (mm110) REVERT: F 369 GLU cc_start: 0.6966 (tt0) cc_final: 0.6524 (tt0) REVERT: F 379 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.7004 (mmtt) REVERT: F 415 CYS cc_start: 0.6360 (m) cc_final: 0.5957 (m) REVERT: F 426 MET cc_start: 0.7320 (tpt) cc_final: 0.6963 (tpt) REVERT: F 489 LEU cc_start: 0.8245 (tt) cc_final: 0.7678 (pp) REVERT: F 552 LYS cc_start: 0.6181 (mmtt) cc_final: 0.5976 (mmtm) REVERT: F 607 GLU cc_start: 0.7195 (tp30) cc_final: 0.6845 (tp30) REVERT: F 611 TRP cc_start: 0.7465 (t60) cc_final: 0.6996 (t60) REVERT: F 613 GLU cc_start: 0.7245 (tt0) cc_final: 0.6958 (tt0) REVERT: F 637 MET cc_start: 0.7393 (tpt) cc_final: 0.7050 (tpt) REVERT: F 641 ASP cc_start: 0.6979 (t0) cc_final: 0.6774 (t70) REVERT: F 644 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7453 (mm-40) REVERT: F 645 ARG cc_start: 0.7106 (mtm110) cc_final: 0.6816 (mtm110) REVERT: F 647 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7534 (mtm) REVERT: F 649 TYR cc_start: 0.7146 (m-80) cc_final: 0.6734 (m-80) REVERT: F 785 GLU cc_start: 0.7630 (pt0) cc_final: 0.7052 (mt-10) REVERT: F 800 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8169 (mt) REVERT: F 806 SER cc_start: 0.7930 (m) cc_final: 0.7701 (m) REVERT: F 876 CYS cc_start: 0.7653 (m) cc_final: 0.7146 (m) REVERT: F 929 ILE cc_start: 0.8585 (mt) cc_final: 0.8310 (mp) REVERT: F 987 MET cc_start: 0.6562 (mmt) cc_final: 0.6241 (mmt) REVERT: F 991 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6563 (pm20) REVERT: F 1006 SER cc_start: 0.8131 (m) cc_final: 0.7840 (t) REVERT: F 1029 THR cc_start: 0.8239 (m) cc_final: 0.7835 (p) outliers start: 133 outliers final: 105 residues processed: 935 average time/residue: 0.5024 time to fit residues: 758.7994 Evaluate side-chains 989 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 864 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 828 ASN Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 812 ASP Chi-restraints excluded: chain B residue 828 ASN Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 522 HIS Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 812 ASP Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 912 GLN Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 632 TYR Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 791 SER Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 379 LYS Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 765 LEU Chi-restraints excluded: chain E residue 775 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 786 CYS Chi-restraints excluded: chain E residue 792 LEU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 828 ASN Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 908 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain E residue 1028 LEU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 323 GLN Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 379 LYS Chi-restraints excluded: chain F residue 600 ILE Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 796 SER Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 812 ASP Chi-restraints excluded: chain F residue 828 ASN Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 973 LYS Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 0.8980 chunk 405 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 351 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 381 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 391 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 GLN ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 ASN C 603 GLN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 771 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 GLN ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.178564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.146091 restraints weight = 61775.097| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 3.20 r_work: 0.3692 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39690 Z= 0.178 Angle : 0.651 12.220 53544 Z= 0.312 Chirality : 0.041 0.297 6078 Planarity : 0.005 0.116 6714 Dihedral : 6.864 156.586 5256 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.07 % Allowed : 22.60 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.12), residues: 4782 helix: 0.30 (0.11), residues: 2142 sheet: -1.89 (0.19), residues: 654 loop : -1.07 (0.15), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 243 HIS 0.004 0.001 HIS B 938 PHE 0.035 0.001 PHE B 581 TYR 0.026 0.001 TYR E 168 ARG 0.008 0.000 ARG B 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12698.25 seconds wall clock time: 229 minutes 9.89 seconds (13749.89 seconds total)