Starting phenix.real_space_refine (version: dev) on Mon Jun 6 19:47:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgu_14713/06_2022/7zgu_14713_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgu_14713/06_2022/7zgu_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_14713/06_2022/7zgu_14713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgu_14713/06_2022/7zgu_14713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgu_14713/06_2022/7zgu_14713_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgu_14713/06_2022/7zgu_14713_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4617/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: 20.24, per 1000 atoms: 0.52 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: 15.48 Conformation dependent library (CDL) restraints added in 5.6 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: 5.52 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: 15.30 Time building geometry restraints manager: 16.45 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 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. 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: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 23.200 Check model and map are aligned: 0.580 Convert atoms to be neutral: 0.310 Process input model: 94.220 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.030 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: 128.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 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 : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 *********************** 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 : 4.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 1121 average time/residue: 0.5060 time to fit residues: 910.9782 Evaluate side-chains 888 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 877 time to evaluate : 4.404 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3949 time to fit residues: 14.4248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 201 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 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: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 479 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN ** B 480 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** B 912 GLN ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 ASN C 674 HIS C 824 HIS C 845 GLN ** 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 644 GLN D 771 ASN D 824 HIS D 893 ASN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 HIS ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 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 ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 741 GLN F 845 GLN ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 39690 Z= 0.239 Angle : 0.686 11.911 53544 Z= 0.339 Chirality : 0.043 0.172 6078 Planarity : 0.006 0.095 6714 Dihedral : 7.427 154.349 5256 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 2.43 % 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: -1.37 (0.12), residues: 4782 helix: -0.27 (0.10), residues: 2154 sheet: -0.88 (0.23), residues: 498 loop : -1.52 (0.14), residues: 2130 *********************** 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 1027 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 920 time to evaluate : 4.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 73 residues processed: 959 average time/residue: 0.5398 time to fit residues: 846.9177 Evaluate side-chains 922 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 849 time to evaluate : 4.383 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.3673 time to fit residues: 56.0415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 362 optimal weight: 0.7980 chunk 296 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 436 optimal weight: 0.9990 chunk 471 optimal weight: 2.9990 chunk 388 optimal weight: 0.9980 chunk 433 optimal weight: 0.0870 chunk 148 optimal weight: 7.9990 chunk 350 optimal weight: 6.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** 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 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 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** B 952 ASN ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 893 ASN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 938 HIS ** 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 893 ASN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 952 ASN ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 GLN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 GLN ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6933 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 39690 Z= 0.203 Angle : 0.645 12.181 53544 Z= 0.315 Chirality : 0.041 0.316 6078 Planarity : 0.006 0.101 6714 Dihedral : 7.324 152.177 5256 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.12), residues: 4782 helix: -0.29 (0.11), residues: 2178 sheet: -1.47 (0.21), residues: 600 loop : -1.28 (0.15), residues: 2004 *********************** 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 936 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 864 time to evaluate : 4.206 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 outliers start: 72 outliers final: 45 residues processed: 890 average time/residue: 0.5089 time to fit residues: 733.3519 Evaluate side-chains 841 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 796 time to evaluate : 4.828 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3610 time to fit residues: 37.1505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 2.9990 chunk 328 optimal weight: 2.9990 chunk 226 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 208 optimal weight: 0.0770 chunk 293 optimal weight: 0.9990 chunk 438 optimal weight: 0.6980 chunk 463 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 415 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 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 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 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 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 ASN C 627 GLN C 893 ASN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 938 HIS ** 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 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 952 ASN F 269 GLN ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 845 GLN ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 952 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.113 39690 Z= 0.181 Angle : 0.620 12.187 53544 Z= 0.303 Chirality : 0.040 0.192 6078 Planarity : 0.005 0.111 6714 Dihedral : 7.154 143.538 5256 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 1.93 % 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: -1.29 (0.12), residues: 4782 helix: -0.20 (0.11), residues: 2172 sheet: -1.43 (0.21), residues: 600 loop : -1.28 (0.15), residues: 2010 *********************** 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 937 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 852 time to evaluate : 5.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 36 residues processed: 890 average time/residue: 0.5372 time to fit residues: 786.3391 Evaluate side-chains 835 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 799 time to evaluate : 4.711 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3783 time to fit residues: 31.8582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 345 optimal weight: 0.0270 chunk 191 optimal weight: 0.3980 chunk 395 optimal weight: 6.9990 chunk 320 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 416 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** 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 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 HIS ** 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 893 ASN ** 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 644 GLN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 GLN ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 GLN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 938 HIS ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6969 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.115 39690 Z= 0.221 Angle : 0.643 10.330 53544 Z= 0.315 Chirality : 0.041 0.362 6078 Planarity : 0.006 0.139 6714 Dihedral : 7.195 140.251 5256 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 1.84 % 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: -1.27 (0.12), residues: 4782 helix: -0.18 (0.11), residues: 2172 sheet: -1.43 (0.20), residues: 600 loop : -1.27 (0.15), residues: 2010 *********************** 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 932 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 851 time to evaluate : 4.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 44 residues processed: 876 average time/residue: 0.5218 time to fit residues: 739.8782 Evaluate side-chains 848 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 804 time to evaluate : 4.463 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.3590 time to fit residues: 36.4329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 0.7980 chunk 417 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 114 optimal weight: 0.3980 chunk 464 optimal weight: 2.9990 chunk 385 optimal weight: 1.9990 chunk 215 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 893 ASN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 771 ASN E 808 ASN E 885 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6982 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 39690 Z= 0.218 Angle : 0.664 10.839 53544 Z= 0.324 Chirality : 0.042 0.263 6078 Planarity : 0.006 0.120 6714 Dihedral : 7.191 140.528 5256 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.25 (0.12), residues: 4782 helix: -0.08 (0.11), residues: 2142 sheet: -1.45 (0.20), residues: 594 loop : -1.35 (0.14), residues: 2046 *********************** 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 916 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 844 time to evaluate : 4.614 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 outliers start: 72 outliers final: 28 residues processed: 881 average time/residue: 0.5087 time to fit residues: 726.9717 Evaluate side-chains 829 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 801 time to evaluate : 4.309 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3913 time to fit residues: 25.9381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 264 optimal weight: 0.0070 chunk 339 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 390 optimal weight: 0.3980 chunk 259 optimal weight: 4.9990 chunk 462 optimal weight: 2.9990 chunk 289 optimal weight: 0.4980 chunk 282 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 overall best weight: 0.5802 ------------------------------------------------------------------------------- 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 865 ASN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 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 741 GLN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 GLN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 HIS ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 GLN E 644 GLN E 771 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN ** F 644 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: 0.6966 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 39690 Z= 0.193 Angle : 0.656 11.140 53544 Z= 0.322 Chirality : 0.040 0.248 6078 Planarity : 0.006 0.128 6714 Dihedral : 7.060 141.258 5256 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 1.59 % 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: -1.18 (0.12), residues: 4782 helix: 0.01 (0.11), residues: 2154 sheet: -1.49 (0.20), residues: 594 loop : -1.33 (0.14), residues: 2034 *********************** 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 891 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 821 time to evaluate : 4.637 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 outliers start: 70 outliers final: 32 residues processed: 858 average time/residue: 0.5201 time to fit residues: 727.0439 Evaluate side-chains 829 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 797 time to evaluate : 4.290 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3968 time to fit residues: 29.3955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 0.7980 chunk 184 optimal weight: 0.9980 chunk 276 optimal weight: 0.0050 chunk 139 optimal weight: 0.0670 chunk 90 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 294 optimal weight: 1.9990 chunk 315 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 43 optimal weight: 0.0370 chunk 363 optimal weight: 2.9990 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** 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 663 HIS C 865 ASN C 893 ASN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 GLN E 771 ASN E 893 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6948 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 39690 Z= 0.177 Angle : 0.656 11.980 53544 Z= 0.319 Chirality : 0.040 0.181 6078 Planarity : 0.006 0.145 6714 Dihedral : 6.904 143.039 5256 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.14 (0.12), residues: 4782 helix: 0.09 (0.11), residues: 2160 sheet: -1.40 (0.20), residues: 588 loop : -1.39 (0.14), residues: 2034 *********************** 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 878 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 833 time to evaluate : 4.586 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 outliers start: 45 outliers final: 23 residues processed: 854 average time/residue: 0.5185 time to fit residues: 722.4711 Evaluate side-chains 829 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 806 time to evaluate : 4.516 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3658 time to fit residues: 22.3616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 0.8980 chunk 443 optimal weight: 0.2980 chunk 404 optimal weight: 0.0570 chunk 431 optimal weight: 10.0000 chunk 259 optimal weight: 0.0470 chunk 187 optimal weight: 0.7980 chunk 338 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 389 optimal weight: 0.9980 chunk 407 optimal weight: 5.9990 chunk 429 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN C 585 ASN C 893 ASN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 ASN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 GLN E 644 GLN E 771 ASN E 893 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 938 HIS ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 39690 Z= 0.180 Angle : 0.662 11.982 53544 Z= 0.323 Chirality : 0.040 0.220 6078 Planarity : 0.007 0.145 6714 Dihedral : 6.804 144.594 5256 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 0.82 % 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: 0.07 (0.11), residues: 2166 sheet: -1.36 (0.20), residues: 588 loop : -1.30 (0.15), residues: 2028 *********************** 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 868 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 832 time to evaluate : 4.265 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 outliers start: 36 outliers final: 20 residues processed: 851 average time/residue: 0.5134 time to fit residues: 710.3528 Evaluate side-chains 826 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 806 time to evaluate : 4.299 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4234 time to fit residues: 21.1876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 0.8980 chunk 455 optimal weight: 0.8980 chunk 278 optimal weight: 0.9990 chunk 216 optimal weight: 0.5980 chunk 316 optimal weight: 9.9990 chunk 478 optimal weight: 4.9990 chunk 440 optimal weight: 9.9990 chunk 380 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 294 optimal weight: 0.6980 chunk 233 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 ASN C 893 ASN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 ASN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 GLN E 771 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 638 GLN ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6962 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.143 39690 Z= 0.225 Angle : 0.709 12.959 53544 Z= 0.352 Chirality : 0.042 0.316 6078 Planarity : 0.007 0.154 6714 Dihedral : 6.868 150.020 5256 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 0.43 % 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: -1.10 (0.12), residues: 4782 helix: 0.06 (0.11), residues: 2166 sheet: -1.39 (0.20), residues: 588 loop : -1.28 (0.15), residues: 2028 ********************** 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 835 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 816 time to evaluate : 4.981 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 outliers start: 19 outliers final: 8 residues processed: 823 average time/residue: 0.5572 time to fit residues: 750.5205 Evaluate side-chains 813 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 805 time to evaluate : 4.275 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4098 time to fit residues: 12.1039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 3.9990 chunk 405 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 351 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 381 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 391 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** 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 956 HIS B1001 GLN ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 893 ASN C 911 ASN C 912 GLN D 644 GLN D 771 ASN ** D 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 916 HIS ** D 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 GLN E 771 ASN ** E 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.177864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.144784 restraints weight = 61581.136| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.25 r_work: 0.3806 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work: 0.3777 rms_B_bonded: 3.02 restraints_weight: 0.1250 r_work: 0.3762 rms_B_bonded: 3.11 restraints_weight: 0.0625 r_work: 0.3745 rms_B_bonded: 3.24 restraints_weight: 0.0312 r_work: 0.3727 rms_B_bonded: 3.41 restraints_weight: 0.0156 r_work: 0.3707 rms_B_bonded: 3.62 restraints_weight: 0.0078 r_work: 0.3686 rms_B_bonded: 3.87 restraints_weight: 0.0039 r_work: 0.3663 rms_B_bonded: 4.17 restraints_weight: 0.0020 r_work: 0.3638 rms_B_bonded: 4.52 restraints_weight: 0.0010 r_work: 0.3610 rms_B_bonded: 4.93 restraints_weight: 0.0005 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.116 39690 Z= 0.274 Angle : 0.753 13.939 53544 Z= 0.371 Chirality : 0.044 0.273 6078 Planarity : 0.007 0.154 6714 Dihedral : 7.218 164.436 5256 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer Outliers : 0.73 % 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: 2130 sheet: -1.57 (0.19), residues: 606 loop : -1.17 (0.15), residues: 2046 =============================================================================== Job complete usr+sys time: 11579.94 seconds wall clock time: 209 minutes 4.42 seconds (12544.42 seconds total)