Starting phenix.real_space_refine on Thu Mar 21 22:47:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wka_32564/03_2024/7wka_32564.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wka_32564/03_2024/7wka_32564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wka_32564/03_2024/7wka_32564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wka_32564/03_2024/7wka_32564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wka_32564/03_2024/7wka_32564.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wka_32564/03_2024/7wka_32564.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 139 5.16 5 C 20002 2.51 5 N 5231 2.21 5 O 5981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31353 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 996} Chain breaks: 7 Chain: "C" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 7 Chain: "c" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "d" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Chain: "B" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 7 Chain: "a" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 16.46, per 1000 atoms: 0.52 Number of scatterers: 31353 At special positions: 0 Unit cell: (218.6, 137.718, 178.159, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 139 16.00 O 5981 8.00 N 5231 7.00 C 20002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS c 147 " - pdb=" SG CYS c 202 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 92 " distance=2.04 Simple disulfide: pdb=" SG CYS d 138 " - pdb=" SG CYS d 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 147 " - pdb=" SG CYS a 202 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 92 " distance=2.03 Simple disulfide: pdb=" SG CYS b 138 " - pdb=" SG CYS b 198 " distance=2.03 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: 11.00 Conformation dependent library (CDL) restraints added in 5.7 seconds 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7540 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 68 sheets defined 18.4% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.516A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.779A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.640A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.819A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.667A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.831A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.691A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.539A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.643A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.704A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 931 removed outlier: 3.594A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 939 removed outlier: 3.525A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.866A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.752A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.981A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.872A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.538A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.815A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.731A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 4.079A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.686A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.659A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 752' Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.646A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.953A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 4.076A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.636A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.648A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.711A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.815A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 963 removed outlier: 3.888A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.642A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.012A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.798A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 87 removed outlier: 4.124A pdb=" N ALA d 87 " --> pdb=" O GLU d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 125 through 132 removed outlier: 3.668A pdb=" N LEU d 129 " --> pdb=" O SER d 125 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER d 131 " --> pdb=" O GLU d 127 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 3.590A pdb=" N ARG d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.668A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.323A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.861A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.737A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.691A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.883A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.709A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.869A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 removed outlier: 3.882A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.603A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.628A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.689A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.749A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.802A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.607A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.892A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.914A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 32 removed outlier: 3.574A pdb=" N ARG a 31 " --> pdb=" O SER a 28 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE a 32 " --> pdb=" O PHE a 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 28 through 32' Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.896A pdb=" N SER a 91 " --> pdb=" O SER a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 198 removed outlier: 4.010A pdb=" N SER a 197 " --> pdb=" O SER a 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 87 removed outlier: 4.223A pdb=" N ALA b 87 " --> pdb=" O GLU b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 132 removed outlier: 3.612A pdb=" N LEU b 129 " --> pdb=" O SER b 125 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER b 131 " --> pdb=" O GLU b 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 192 removed outlier: 3.894A pdb=" N ARG b 192 " --> pdb=" O ASP b 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.920A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.968A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.664A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.937A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.422A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.602A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 357 removed outlier: 4.380A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.670A pdb=" N TYR A 453 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.503A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.294A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.720A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.044A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.553A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.522A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.743A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC3, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.030A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.563A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 566 " --> pdb=" O ALA C 575 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.888A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.835A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.591A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.817A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.567A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C1061 " --> pdb=" O GLN C1054 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.347A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.975A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'c' and resid 9 through 12 removed outlier: 6.565A pdb=" N GLU c 10 " --> pdb=" O THR c 117 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR c 95 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL c 37 " --> pdb=" O TYR c 95 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN c 35 " --> pdb=" O ALA c 97 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N MET c 34 " --> pdb=" O MET c 50 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N MET c 50 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP c 36 " --> pdb=" O ILE c 48 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG c 40 " --> pdb=" O GLY c 44 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU c 57 " --> pdb=" O HIS c 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 9 through 12 removed outlier: 6.565A pdb=" N GLU c 10 " --> pdb=" O THR c 117 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS c 96 " --> pdb=" O TRP c 110 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TRP c 110 " --> pdb=" O CYS c 96 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG c 98 " --> pdb=" O ALA c 108 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'c' and resid 17 through 23 removed outlier: 3.620A pdb=" N LEU c 20 " --> pdb=" O MET c 81 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET c 81 " --> pdb=" O LEU c 20 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR c 71 " --> pdb=" O TYR c 80 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'c' and resid 127 through 131 removed outlier: 3.576A pdb=" N GLY c 146 " --> pdb=" O LEU c 131 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER c 187 " --> pdb=" O HIS c 171 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 127 through 131 removed outlier: 3.576A pdb=" N GLY c 146 " --> pdb=" O LEU c 131 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR c 152 " --> pdb=" O TYR c 182 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'c' and resid 158 through 161 removed outlier: 3.789A pdb=" N THR c 158 " --> pdb=" O ALA c 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.893A pdb=" N SER d 7 " --> pdb=" O SER d 22 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER d 22 " --> pdb=" O SER d 7 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS d 23 " --> pdb=" O PHE d 75 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE d 75 " --> pdb=" O CYS d 23 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP d 74 " --> pdb=" O SER d 71 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 10 through 14 removed outlier: 6.594A pdb=" N LEU d 11 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS d 111 " --> pdb=" O LEU d 11 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL d 13 " --> pdb=" O LYS d 111 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP d 39 " --> pdb=" O LEU d 51 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AE6, first strand: chain 'd' and resid 118 through 122 removed outlier: 3.672A pdb=" N VAL d 137 " --> pdb=" O PHE d 122 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR d 177 " --> pdb=" O ASN d 142 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'd' and resid 157 through 158 removed outlier: 3.941A pdb=" N TYR d 196 " --> pdb=" O PHE d 213 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE d 213 " --> pdb=" O TYR d 196 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.102A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.644A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.816A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.403A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.524A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.771A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.857A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.752A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.519A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.689A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AG2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.876A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AG4, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.657A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS a 99 " --> pdb=" O TRP a 33 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP a 33 " --> pdb=" O LYS a 99 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET a 34 " --> pdb=" O MET a 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG a 40 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.657A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG a 98 " --> pdb=" O TYR a 109 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR a 109 " --> pdb=" O ARG a 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 17 through 23 removed outlier: 3.752A pdb=" N THR a 71 " --> pdb=" O TYR a 80 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 127 through 131 removed outlier: 3.548A pdb=" N SER a 186 " --> pdb=" O CYS a 147 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER a 187 " --> pdb=" O HIS a 171 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 127 through 131 removed outlier: 3.548A pdb=" N SER a 186 " --> pdb=" O CYS a 147 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR a 183 " --> pdb=" O VAL a 176 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'a' and resid 158 through 161 removed outlier: 3.508A pdb=" N THR a 211 " --> pdb=" O HIS a 206 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 5 through 7 removed outlier: 3.795A pdb=" N SER b 7 " --> pdb=" O SER b 22 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE b 21 " --> pdb=" O LEU b 77 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS b 23 " --> pdb=" O PHE b 75 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE b 75 " --> pdb=" O CYS b 23 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP b 74 " --> pdb=" O SER b 71 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 10 through 14 removed outlier: 6.296A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS b 111 " --> pdb=" O LEU b 11 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL b 13 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP b 39 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN b 41 " --> pdb=" O LYS b 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 10 through 14 removed outlier: 6.296A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS b 111 " --> pdb=" O LEU b 11 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL b 13 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS b 94 " --> pdb=" O ALA b 101 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA b 101 " --> pdb=" O HIS b 94 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 118 through 122 removed outlier: 3.551A pdb=" N VAL b 137 " --> pdb=" O PHE b 122 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR b 177 " --> pdb=" O ASN b 142 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 157 through 158 removed outlier: 3.758A pdb=" N TYR b 196 " --> pdb=" O PHE b 213 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE b 213 " --> pdb=" O TYR b 196 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA b 200 " --> pdb=" O ILE b 209 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE b 209 " --> pdb=" O ALA b 200 " (cutoff:3.500A) 929 hydrogen bonds defined for protein. 2469 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: 14.24 Time building geometry restraints manager: 12.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6953 1.33 - 1.45: 7717 1.45 - 1.58: 17260 1.58 - 1.70: 0 1.70 - 1.83: 178 Bond restraints: 32108 Sorted by residual: bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.436 -0.102 2.34e-02 1.83e+03 1.91e+01 bond pdb=" N GLN C 271 " pdb=" CA GLN C 271 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.65e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.416 -0.082 2.34e-02 1.83e+03 1.23e+01 bond pdb=" N VAL A 367 " pdb=" CA VAL A 367 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N VAL d 33 " pdb=" CA VAL d 33 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.89e+00 ... (remaining 32103 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.83: 1440 107.83 - 115.38: 18942 115.38 - 122.94: 19647 122.94 - 130.50: 3540 130.50 - 138.06: 127 Bond angle restraints: 43696 Sorted by residual: angle pdb=" C VAL C 524 " pdb=" N CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sigma weight residual 121.54 133.08 -11.54 1.91e+00 2.74e-01 3.65e+01 angle pdb=" C ASN B 122 " pdb=" N ALA B 123 " pdb=" CA ALA B 123 " ideal model delta sigma weight residual 121.54 132.68 -11.14 1.91e+00 2.74e-01 3.40e+01 angle pdb=" C GLY B 639 " pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 121.54 131.99 -10.45 1.91e+00 2.74e-01 3.00e+01 angle pdb=" N SER B 161 " pdb=" CA SER B 161 " pdb=" C SER B 161 " ideal model delta sigma weight residual 111.04 102.66 8.38 1.55e+00 4.16e-01 2.92e+01 angle pdb=" C GLY C 639 " pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 ... (remaining 43691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.49: 18535 14.49 - 28.98: 489 28.98 - 43.47: 119 43.47 - 57.97: 18 57.97 - 72.46: 15 Dihedral angle restraints: 19176 sinusoidal: 7466 harmonic: 11710 Sorted by residual: dihedral pdb=" CA LYS C 795 " pdb=" C LYS C 795 " pdb=" N TYR C 796 " pdb=" CA TYR C 796 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA CYS C 525 " pdb=" C CYS C 525 " pdb=" N GLY C 526 " pdb=" CA GLY C 526 " ideal model delta harmonic sigma weight residual 180.00 156.20 23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ARG C 634 " pdb=" C ARG C 634 " pdb=" N VAL C 635 " pdb=" CA VAL C 635 " ideal model delta harmonic sigma weight residual 180.00 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 19173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4292 0.082 - 0.163: 593 0.163 - 0.245: 44 0.245 - 0.327: 5 0.327 - 0.408: 1 Chirality restraints: 4935 Sorted by residual: chirality pdb=" CA VAL B 159 " pdb=" N VAL B 159 " pdb=" C VAL B 159 " pdb=" CB VAL B 159 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB ILE A 312 " pdb=" CA ILE A 312 " pdb=" CG1 ILE A 312 " pdb=" CG2 ILE A 312 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE C 312 " pdb=" CA ILE C 312 " pdb=" CG1 ILE C 312 " pdb=" CG2 ILE C 312 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 4932 not shown) Planarity restraints: 5629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 266 " -0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR A 266 " 0.061 2.00e-02 2.50e+03 pdb=" O TYR A 266 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 267 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 22 " -0.016 2.00e-02 2.50e+03 3.11e-02 9.68e+00 pdb=" C THR B 22 " 0.054 2.00e-02 2.50e+03 pdb=" O THR B 22 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN B 23 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 23 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C GLN C 23 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN C 23 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 24 " 0.017 2.00e-02 2.50e+03 ... (remaining 5626 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9878 2.86 - 3.37: 23783 3.37 - 3.88: 50617 3.88 - 4.39: 52037 4.39 - 4.90: 94601 Nonbonded interactions: 230916 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.353 2.440 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.354 2.440 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.356 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.356 2.440 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.360 2.440 ... (remaining 230911 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' } ncs_group { reference = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'b' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.020 Extract box with map and model: 10.970 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 81.170 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 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 : 0.005 0.102 32108 Z= 0.305 Angle : 0.794 11.544 43696 Z= 0.464 Chirality : 0.054 0.408 4935 Planarity : 0.006 0.072 5629 Dihedral : 8.145 66.816 11498 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.14 % Rotamer: Outliers : 0.23 % Allowed : 0.71 % Favored : 99.06 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.05 % 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: -2.58 (0.11), residues: 3961 helix: -4.92 (0.06), residues: 522 sheet: -0.32 (0.14), residues: 963 loop : -1.59 (0.10), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 33 HIS 0.015 0.002 HIS B 954 PHE 0.027 0.003 PHE B 490 TYR 0.019 0.002 TYR a 103 ARG 0.007 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 950 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.8321 (t80) cc_final: 0.8094 (t80) REVERT: A 206 LYS cc_start: 0.7858 (tptt) cc_final: 0.7628 (tppt) REVERT: A 275 PHE cc_start: 0.8231 (m-10) cc_final: 0.7888 (m-80) REVERT: A 277 LEU cc_start: 0.8671 (mt) cc_final: 0.8411 (mp) REVERT: A 339 ASP cc_start: 0.8599 (m-30) cc_final: 0.8115 (t70) REVERT: A 385 THR cc_start: 0.8976 (p) cc_final: 0.8740 (p) REVERT: A 386 LYS cc_start: 0.7920 (mttt) cc_final: 0.7635 (mttt) REVERT: A 546 LEU cc_start: 0.8168 (tt) cc_final: 0.7887 (tt) REVERT: A 654 GLU cc_start: 0.7923 (tt0) cc_final: 0.7555 (tt0) REVERT: A 663 ASP cc_start: 0.7020 (m-30) cc_final: 0.6811 (m-30) REVERT: A 743 CYS cc_start: 0.6662 (m) cc_final: 0.6108 (m) REVERT: A 814 LYS cc_start: 0.8694 (mttt) cc_final: 0.8425 (mmmt) REVERT: A 964 LYS cc_start: 0.8639 (mttt) cc_final: 0.8372 (tppt) REVERT: A 1033 VAL cc_start: 0.7823 (t) cc_final: 0.7600 (t) REVERT: A 1109 PHE cc_start: 0.5439 (p90) cc_final: 0.5152 (p90) REVERT: C 49 HIS cc_start: 0.7202 (t70) cc_final: 0.6792 (t70) REVERT: C 106 PHE cc_start: 0.7284 (m-10) cc_final: 0.6744 (m-10) REVERT: C 115 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7081 (mt0) REVERT: C 206 LYS cc_start: 0.7726 (tptt) cc_final: 0.7255 (tppt) REVERT: C 226 LEU cc_start: 0.7433 (tp) cc_final: 0.7214 (mt) REVERT: C 270 LEU cc_start: 0.8053 (mt) cc_final: 0.7733 (mt) REVERT: C 305 SER cc_start: 0.8796 (p) cc_final: 0.8462 (t) REVERT: C 338 PHE cc_start: 0.6882 (m-10) cc_final: 0.6099 (m-10) REVERT: C 339 ASP cc_start: 0.7535 (m-30) cc_final: 0.7298 (m-30) REVERT: C 540 ASN cc_start: 0.6191 (m-40) cc_final: 0.5989 (t0) REVERT: C 552 LEU cc_start: 0.7639 (mt) cc_final: 0.7258 (mt) REVERT: C 585 LEU cc_start: 0.6596 (mt) cc_final: 0.6392 (mt) REVERT: C 654 GLU cc_start: 0.7724 (tt0) cc_final: 0.7454 (tt0) REVERT: C 719 THR cc_start: 0.8078 (t) cc_final: 0.7767 (p) REVERT: C 725 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6290 (mt-10) REVERT: C 747 THR cc_start: 0.8021 (p) cc_final: 0.7717 (p) REVERT: C 751 ASN cc_start: 0.8597 (m-40) cc_final: 0.8343 (m-40) REVERT: C 775 ASP cc_start: 0.8080 (m-30) cc_final: 0.7801 (m-30) REVERT: C 780 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7280 (mt-10) REVERT: C 867 ASP cc_start: 0.8135 (m-30) cc_final: 0.7890 (m-30) REVERT: C 884 SER cc_start: 0.8491 (m) cc_final: 0.8228 (p) REVERT: C 894 LEU cc_start: 0.7091 (mp) cc_final: 0.6638 (mp) REVERT: C 953 ASN cc_start: 0.8447 (m-40) cc_final: 0.8036 (m-40) REVERT: C 969 LYS cc_start: 0.8471 (mttt) cc_final: 0.8153 (mmtm) REVERT: C 990 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7369 (mt-10) REVERT: C 1051 SER cc_start: 0.8598 (m) cc_final: 0.8218 (p) REVERT: C 1061 VAL cc_start: 0.8763 (t) cc_final: 0.8508 (p) REVERT: C 1073 LYS cc_start: 0.8215 (tttt) cc_final: 0.8006 (tttp) REVERT: C 1084 ASP cc_start: 0.7502 (p0) cc_final: 0.6936 (p0) REVERT: C 1125 ASN cc_start: 0.8152 (p0) cc_final: 0.7944 (p0) REVERT: c 102 ASP cc_start: 0.3369 (OUTLIER) cc_final: 0.3061 (t0) REVERT: B 33 THR cc_start: 0.8330 (p) cc_final: 0.8076 (t) REVERT: B 36 VAL cc_start: 0.8765 (t) cc_final: 0.8454 (p) REVERT: B 55 PHE cc_start: 0.7334 (m-10) cc_final: 0.6592 (m-10) REVERT: B 106 PHE cc_start: 0.6238 (m-10) cc_final: 0.5979 (m-80) REVERT: B 119 ILE cc_start: 0.8889 (mt) cc_final: 0.8329 (mm) REVERT: B 127 VAL cc_start: 0.8617 (t) cc_final: 0.8310 (m) REVERT: B 189 LEU cc_start: 0.8591 (tp) cc_final: 0.8290 (tp) REVERT: B 204 TYR cc_start: 0.5870 (m-80) cc_final: 0.5617 (m-80) REVERT: B 221 SER cc_start: 0.8752 (t) cc_final: 0.8368 (m) REVERT: B 296 LEU cc_start: 0.8734 (tp) cc_final: 0.8482 (tp) REVERT: B 309 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7259 (mt-10) REVERT: B 492 LEU cc_start: 0.8337 (tp) cc_final: 0.8038 (pt) REVERT: B 534 VAL cc_start: 0.7721 (t) cc_final: 0.7293 (m) REVERT: B 535 LYS cc_start: 0.7992 (mtpt) cc_final: 0.7637 (tmtt) REVERT: B 654 GLU cc_start: 0.7420 (tt0) cc_final: 0.7167 (tt0) REVERT: B 658 ASN cc_start: 0.8919 (m-40) cc_final: 0.8023 (m-40) REVERT: B 721 SER cc_start: 0.7856 (t) cc_final: 0.7322 (p) REVERT: B 740 MET cc_start: 0.7478 (mtp) cc_final: 0.7257 (mtt) REVERT: B 969 LYS cc_start: 0.8549 (mttt) cc_final: 0.8073 (mttm) REVERT: B 979 ASP cc_start: 0.8231 (m-30) cc_final: 0.7372 (m-30) REVERT: B 990 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7924 (mt-10) REVERT: B 1000 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7344 (mtm-85) REVERT: B 1073 LYS cc_start: 0.8083 (tttt) cc_final: 0.7819 (mtpp) REVERT: B 1106 GLN cc_start: 0.6251 (mm-40) cc_final: 0.6043 (mm-40) REVERT: B 1116 THR cc_start: 0.7278 (p) cc_final: 0.7015 (p) REVERT: B 1119 ASN cc_start: 0.7925 (m-40) cc_final: 0.7545 (m110) REVERT: a 33 TRP cc_start: 0.4327 (m-10) cc_final: 0.3414 (m-10) REVERT: a 61 ASN cc_start: 0.8206 (t0) cc_final: 0.7436 (t0) REVERT: a 69 THR cc_start: 0.7032 (m) cc_final: 0.6609 (p) REVERT: a 81 MET cc_start: 0.4890 (ttp) cc_final: 0.3028 (ttp) REVERT: b 43 LYS cc_start: 0.8017 (mttt) cc_final: 0.7816 (mmtt) REVERT: b 53 TYR cc_start: 0.6516 (p90) cc_final: 0.6289 (p90) REVERT: b 140 LEU cc_start: 0.5156 (mp) cc_final: 0.4613 (mp) outliers start: 8 outliers final: 4 residues processed: 958 average time/residue: 0.4522 time to fit residues: 674.2187 Evaluate side-chains 682 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 677 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain d residue 34 TYR Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain B residue 161 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 161 optimal weight: 0.0030 chunk 312 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 232 optimal weight: 20.0000 chunk 362 optimal weight: 0.4980 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 505 HIS A 519 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 895 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1048 HIS A1054 GLN A1083 HIS C 317 ASN C 343 ASN C 394 ASN C 474 GLN C 519 HIS C 564 GLN C 717 ASN C1054 GLN C1088 HIS C1106 GLN C1113 GLN c 52 HIS ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 343 ASN B 505 HIS B 544 ASN B 717 ASN B 895 GLN B1005 GLN B1054 GLN B1113 GLN a 171 HIS b 93 HIS ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32108 Z= 0.249 Angle : 0.650 10.231 43696 Z= 0.343 Chirality : 0.046 0.284 4935 Planarity : 0.006 0.198 5629 Dihedral : 4.852 46.460 4319 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.69 % Favored : 98.21 % Rotamer: Outliers : 2.17 % Allowed : 8.32 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % 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: -1.63 (0.11), residues: 3961 helix: -2.61 (0.15), residues: 589 sheet: 0.26 (0.15), residues: 985 loop : -1.28 (0.11), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP a 36 HIS 0.005 0.001 HIS A1064 PHE 0.040 0.002 PHE C 400 TYR 0.029 0.002 TYR B1110 ARG 0.026 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 711 time to evaluate : 3.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6521 (mp) REVERT: A 33 THR cc_start: 0.7645 (p) cc_final: 0.7430 (p) REVERT: A 133 PHE cc_start: 0.6580 (m-10) cc_final: 0.6345 (m-10) REVERT: A 135 PHE cc_start: 0.7222 (t80) cc_final: 0.6760 (t80) REVERT: A 195 LYS cc_start: 0.2830 (mmmt) cc_final: 0.1783 (mmmt) REVERT: A 226 LEU cc_start: 0.7927 (tp) cc_final: 0.7494 (mm) REVERT: A 275 PHE cc_start: 0.8298 (m-10) cc_final: 0.8071 (m-80) REVERT: A 339 ASP cc_start: 0.8552 (m-30) cc_final: 0.8142 (t0) REVERT: A 386 LYS cc_start: 0.8160 (mttt) cc_final: 0.7822 (mttm) REVERT: A 546 LEU cc_start: 0.8361 (tt) cc_final: 0.8044 (tt) REVERT: A 654 GLU cc_start: 0.7681 (tt0) cc_final: 0.7289 (tt0) REVERT: A 721 SER cc_start: 0.8234 (t) cc_final: 0.7741 (p) REVERT: A 740 MET cc_start: 0.8054 (mmm) cc_final: 0.7780 (mmm) REVERT: A 743 CYS cc_start: 0.6314 (m) cc_final: 0.6096 (m) REVERT: A 764 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8276 (ttmt) REVERT: A 814 LYS cc_start: 0.8803 (mttt) cc_final: 0.8539 (mmmt) REVERT: A 823 PHE cc_start: 0.8255 (t80) cc_final: 0.7923 (t80) REVERT: A 884 SER cc_start: 0.8195 (m) cc_final: 0.7824 (t) REVERT: A 935 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7937 (mm-40) REVERT: A 955 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8731 (t0) REVERT: A 964 LYS cc_start: 0.8511 (mttt) cc_final: 0.8150 (tppt) REVERT: A 969 LYS cc_start: 0.8486 (mttt) cc_final: 0.7923 (mmtm) REVERT: A 1010 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8107 (mp10) REVERT: A 1031 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7260 (mm-30) REVERT: A 1072 GLU cc_start: 0.8962 (pm20) cc_final: 0.8577 (pm20) REVERT: A 1075 PHE cc_start: 0.8525 (m-10) cc_final: 0.8255 (m-80) REVERT: A 1119 ASN cc_start: 0.7972 (m-40) cc_final: 0.7710 (m-40) REVERT: A 1122 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8379 (p) REVERT: C 98 SER cc_start: 0.8594 (p) cc_final: 0.8384 (p) REVERT: C 195 LYS cc_start: 0.5940 (mmmt) cc_final: 0.5645 (mmmt) REVERT: C 224 GLU cc_start: 0.8114 (mp0) cc_final: 0.7903 (mp0) REVERT: C 226 LEU cc_start: 0.7778 (tp) cc_final: 0.7402 (mm) REVERT: C 269 TYR cc_start: 0.5744 (m-80) cc_final: 0.5376 (m-80) REVERT: C 271 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7884 (mm-40) REVERT: C 304 LYS cc_start: 0.8815 (mttt) cc_final: 0.8574 (ttmm) REVERT: C 328 ARG cc_start: 0.4940 (mmt180) cc_final: 0.4411 (mmp-170) REVERT: C 396 TYR cc_start: 0.8142 (m-80) cc_final: 0.7684 (m-10) REVERT: C 509 ARG cc_start: 0.5147 (tmt170) cc_final: 0.4516 (mmt180) REVERT: C 528 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7916 (mmtt) REVERT: C 533 LEU cc_start: 0.8930 (mt) cc_final: 0.8680 (mp) REVERT: C 654 GLU cc_start: 0.7604 (tt0) cc_final: 0.7301 (tt0) REVERT: C 725 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6490 (mt-10) REVERT: C 747 THR cc_start: 0.8379 (p) cc_final: 0.8099 (p) REVERT: C 884 SER cc_start: 0.8539 (m) cc_final: 0.8154 (p) REVERT: C 933 LYS cc_start: 0.8422 (mttt) cc_final: 0.8064 (mtpp) REVERT: C 969 LYS cc_start: 0.8762 (mttt) cc_final: 0.8382 (mmtm) REVERT: C 976 VAL cc_start: 0.8430 (t) cc_final: 0.8130 (t) REVERT: C 990 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7200 (mt-10) REVERT: C 1031 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7579 (mm-30) REVERT: C 1045 LYS cc_start: 0.7973 (tttt) cc_final: 0.7696 (ttmm) REVERT: C 1051 SER cc_start: 0.8703 (m) cc_final: 0.8261 (p) REVERT: C 1102 TRP cc_start: 0.8362 (m100) cc_final: 0.8062 (m100) REVERT: c 81 MET cc_start: 0.4877 (ttp) cc_final: 0.4668 (ttp) REVERT: c 106 TRP cc_start: 0.6172 (p90) cc_final: 0.5828 (p90) REVERT: B 33 THR cc_start: 0.8358 (p) cc_final: 0.8148 (t) REVERT: B 36 VAL cc_start: 0.8973 (t) cc_final: 0.8602 (p) REVERT: B 55 PHE cc_start: 0.7588 (m-10) cc_final: 0.7038 (m-10) REVERT: B 106 PHE cc_start: 0.6701 (m-10) cc_final: 0.6186 (m-80) REVERT: B 133 PHE cc_start: 0.7540 (m-10) cc_final: 0.7134 (m-10) REVERT: B 206 LYS cc_start: 0.8127 (tptp) cc_final: 0.7848 (tptt) REVERT: B 221 SER cc_start: 0.8893 (t) cc_final: 0.8539 (m) REVERT: B 270 LEU cc_start: 0.7804 (mm) cc_final: 0.7580 (mm) REVERT: B 289 VAL cc_start: 0.8705 (t) cc_final: 0.8464 (m) REVERT: B 309 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7291 (mt-10) REVERT: B 342 PHE cc_start: 0.7404 (t80) cc_final: 0.7097 (t80) REVERT: B 365 TYR cc_start: 0.7621 (m-80) cc_final: 0.7111 (m-80) REVERT: B 386 LYS cc_start: 0.8430 (mtmt) cc_final: 0.7973 (mtmt) REVERT: B 675 GLN cc_start: 0.7334 (pp30) cc_final: 0.7127 (pp30) REVERT: B 721 SER cc_start: 0.8186 (t) cc_final: 0.7941 (t) REVERT: B 773 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: B 776 LYS cc_start: 0.8611 (mttt) cc_final: 0.8407 (tttt) REVERT: B 914 ASN cc_start: 0.8167 (m-40) cc_final: 0.7943 (m-40) REVERT: B 978 ASN cc_start: 0.8232 (p0) cc_final: 0.7760 (p0) REVERT: B 979 ASP cc_start: 0.8290 (m-30) cc_final: 0.7739 (m-30) REVERT: B 990 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8065 (pt0) REVERT: B 1005 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7751 (tp40) REVERT: B 1017 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7773 (tm-30) REVERT: B 1073 LYS cc_start: 0.8400 (tttt) cc_final: 0.8097 (mtpp) REVERT: B 1084 ASP cc_start: 0.7299 (p0) cc_final: 0.7066 (p0) REVERT: B 1106 GLN cc_start: 0.6837 (mm-40) cc_final: 0.6523 (mm-40) REVERT: B 1111 GLU cc_start: 0.7762 (mp0) cc_final: 0.7526 (mp0) REVERT: B 1116 THR cc_start: 0.7706 (p) cc_final: 0.7451 (p) REVERT: B 1119 ASN cc_start: 0.8320 (m-40) cc_final: 0.7905 (m110) REVERT: a 33 TRP cc_start: 0.4085 (m-10) cc_final: 0.3813 (m-10) REVERT: a 61 ASN cc_start: 0.8487 (t0) cc_final: 0.8059 (t0) REVERT: a 161 TRP cc_start: 0.5403 (m-90) cc_final: 0.5085 (m-90) REVERT: b 44 PRO cc_start: 0.7893 (Cg_endo) cc_final: 0.7655 (Cg_exo) outliers start: 76 outliers final: 45 residues processed: 755 average time/residue: 0.4353 time to fit residues: 518.5376 Evaluate side-chains 673 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 623 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 151 LYS Chi-restraints excluded: chain b residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 201 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 301 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 99 optimal weight: 0.1980 chunk 362 optimal weight: 0.7980 chunk 392 optimal weight: 5.9990 chunk 323 optimal weight: 0.5980 chunk 359 optimal weight: 6.9990 chunk 123 optimal weight: 0.5980 chunk 291 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1058 HIS A1071 GLN A1113 GLN C 394 ASN C 474 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 170 GLN ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 901 GLN B 907 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 32108 Z= 0.181 Angle : 0.567 10.184 43696 Z= 0.294 Chirality : 0.044 0.302 4935 Planarity : 0.004 0.167 5629 Dihedral : 4.430 38.560 4313 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.94 % Favored : 97.96 % Rotamer: Outliers : 2.22 % Allowed : 11.55 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % 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: -0.99 (0.12), residues: 3961 helix: -0.98 (0.19), residues: 613 sheet: 0.39 (0.15), residues: 1058 loop : -1.08 (0.11), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP a 36 HIS 0.013 0.001 HIS A 66 PHE 0.028 0.002 PHE A 497 TYR 0.020 0.001 TYR B1138 ARG 0.015 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 657 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6809 (m-90) cc_final: 0.6605 (m-10) REVERT: A 133 PHE cc_start: 0.6978 (m-10) cc_final: 0.6684 (m-10) REVERT: A 135 PHE cc_start: 0.7265 (t80) cc_final: 0.6788 (t80) REVERT: A 195 LYS cc_start: 0.3023 (mmmt) cc_final: 0.1744 (mmmt) REVERT: A 206 LYS cc_start: 0.8281 (tppt) cc_final: 0.7762 (tptt) REVERT: A 226 LEU cc_start: 0.7869 (tp) cc_final: 0.7472 (mm) REVERT: A 258 TRP cc_start: 0.5519 (m100) cc_final: 0.4297 (m-10) REVERT: A 290 ASP cc_start: 0.7605 (t0) cc_final: 0.7331 (t0) REVERT: A 339 ASP cc_start: 0.8557 (m-30) cc_final: 0.8142 (t70) REVERT: A 543 PHE cc_start: 0.8043 (m-80) cc_final: 0.7736 (m-80) REVERT: A 546 LEU cc_start: 0.8307 (tt) cc_final: 0.7941 (tt) REVERT: A 654 GLU cc_start: 0.7793 (tt0) cc_final: 0.7417 (tt0) REVERT: A 696 THR cc_start: 0.8702 (m) cc_final: 0.8347 (p) REVERT: A 721 SER cc_start: 0.8313 (t) cc_final: 0.7811 (p) REVERT: A 740 MET cc_start: 0.8183 (mmm) cc_final: 0.7863 (mmm) REVERT: A 764 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8158 (ttpp) REVERT: A 780 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7396 (mt-10) REVERT: A 814 LYS cc_start: 0.8853 (mttt) cc_final: 0.8442 (mmmt) REVERT: A 823 PHE cc_start: 0.8311 (t80) cc_final: 0.7921 (t80) REVERT: A 868 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7399 (tp30) REVERT: A 884 SER cc_start: 0.8154 (m) cc_final: 0.7944 (t) REVERT: A 935 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7985 (mm-40) REVERT: A 1031 GLU cc_start: 0.7725 (mm-30) cc_final: 0.6628 (mp0) REVERT: A 1086 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6966 (ptmm) REVERT: A 1119 ASN cc_start: 0.7836 (m-40) cc_final: 0.7613 (m-40) REVERT: C 106 PHE cc_start: 0.7210 (m-10) cc_final: 0.6946 (m-10) REVERT: C 203 ILE cc_start: 0.8413 (mp) cc_final: 0.8175 (pt) REVERT: C 271 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7946 (mm-40) REVERT: C 298 GLU cc_start: 0.9005 (tp30) cc_final: 0.8173 (tm-30) REVERT: C 315 THR cc_start: 0.7607 (p) cc_final: 0.7094 (p) REVERT: C 528 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7915 (mmtm) REVERT: C 613 GLN cc_start: 0.7139 (pt0) cc_final: 0.6897 (pt0) REVERT: C 643 PHE cc_start: 0.8218 (t80) cc_final: 0.7874 (t80) REVERT: C 654 GLU cc_start: 0.7506 (tt0) cc_final: 0.7264 (tt0) REVERT: C 725 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6547 (mt-10) REVERT: C 816 SER cc_start: 0.8051 (p) cc_final: 0.6852 (m) REVERT: C 884 SER cc_start: 0.8457 (m) cc_final: 0.8002 (t) REVERT: C 896 ILE cc_start: 0.8559 (mt) cc_final: 0.8303 (tt) REVERT: C 933 LYS cc_start: 0.8376 (mttt) cc_final: 0.8070 (mtpp) REVERT: C 935 GLN cc_start: 0.8306 (tp40) cc_final: 0.7542 (tm-30) REVERT: C 957 GLN cc_start: 0.8170 (tt0) cc_final: 0.7922 (tt0) REVERT: C 969 LYS cc_start: 0.8798 (mttt) cc_final: 0.8387 (mmtm) REVERT: C 976 VAL cc_start: 0.8760 (t) cc_final: 0.7902 (t) REVERT: C 979 ASP cc_start: 0.8236 (m-30) cc_final: 0.7844 (p0) REVERT: C 983 ARG cc_start: 0.5411 (mmm160) cc_final: 0.5134 (tpt90) REVERT: C 990 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7124 (mt-10) REVERT: C 1019 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7200 (tpp-160) REVERT: C 1045 LYS cc_start: 0.7963 (tttt) cc_final: 0.7676 (ttmm) REVERT: C 1073 LYS cc_start: 0.8292 (tttt) cc_final: 0.8055 (mtpp) REVERT: C 1081 ILE cc_start: 0.8448 (pt) cc_final: 0.8181 (pt) REVERT: c 81 MET cc_start: 0.5126 (ttp) cc_final: 0.4876 (ttp) REVERT: c 106 TRP cc_start: 0.6178 (p90) cc_final: 0.5814 (p90) REVERT: B 33 THR cc_start: 0.8351 (p) cc_final: 0.8090 (t) REVERT: B 36 VAL cc_start: 0.8910 (t) cc_final: 0.8569 (p) REVERT: B 55 PHE cc_start: 0.7654 (m-10) cc_final: 0.7183 (m-10) REVERT: B 119 ILE cc_start: 0.8867 (mm) cc_final: 0.8607 (mm) REVERT: B 133 PHE cc_start: 0.7764 (m-80) cc_final: 0.7069 (m-10) REVERT: B 194 PHE cc_start: 0.6485 (m-80) cc_final: 0.6187 (m-80) REVERT: B 221 SER cc_start: 0.8903 (t) cc_final: 0.8563 (m) REVERT: B 309 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7181 (mt-10) REVERT: B 315 THR cc_start: 0.7373 (m) cc_final: 0.7070 (m) REVERT: B 353 TRP cc_start: 0.6938 (p90) cc_final: 0.6728 (p90) REVERT: B 386 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8158 (mtmt) REVERT: B 675 GLN cc_start: 0.7486 (pp30) cc_final: 0.7126 (pp30) REVERT: B 721 SER cc_start: 0.8403 (t) cc_final: 0.7769 (p) REVERT: B 765 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.8028 (ttp-170) REVERT: B 790 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8292 (tptp) REVERT: B 954 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.8290 (m170) REVERT: B 969 LYS cc_start: 0.8675 (mttt) cc_final: 0.8081 (mtpp) REVERT: B 978 ASN cc_start: 0.8338 (p0) cc_final: 0.7738 (p0) REVERT: B 979 ASP cc_start: 0.8333 (m-30) cc_final: 0.7761 (m-30) REVERT: B 1005 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7773 (tp40) REVERT: B 1017 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7685 (tm-30) REVERT: B 1073 LYS cc_start: 0.8396 (tttt) cc_final: 0.8127 (mtpp) REVERT: B 1111 GLU cc_start: 0.7752 (mp0) cc_final: 0.7495 (mp0) REVERT: B 1119 ASN cc_start: 0.8535 (m-40) cc_final: 0.8071 (m110) REVERT: a 61 ASN cc_start: 0.8425 (t0) cc_final: 0.8027 (t0) REVERT: a 69 THR cc_start: 0.7653 (m) cc_final: 0.6707 (p) REVERT: a 106 TRP cc_start: 0.6324 (p90) cc_final: 0.5788 (p90) REVERT: a 161 TRP cc_start: 0.5453 (m-90) cc_final: 0.5144 (m-90) REVERT: b 49 LYS cc_start: 0.7720 (mttt) cc_final: 0.7417 (mttt) outliers start: 78 outliers final: 49 residues processed: 701 average time/residue: 0.4318 time to fit residues: 470.3616 Evaluate side-chains 658 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 606 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 151 LYS Chi-restraints excluded: chain b residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 358 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 chunk 188 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 364 optimal weight: 7.9990 chunk 385 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 345 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 690 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS C 134 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 644 GLN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 207 HIS B 334 ASN B 439 ASN ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN B1088 HIS B1113 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 32108 Z= 0.371 Angle : 0.703 9.963 43696 Z= 0.369 Chirality : 0.047 0.295 4935 Planarity : 0.005 0.164 5629 Dihedral : 4.834 27.895 4311 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.03 % Favored : 96.87 % Rotamer: Outliers : 3.59 % Allowed : 11.66 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % 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: -0.85 (0.12), residues: 3961 helix: -0.37 (0.20), residues: 634 sheet: 0.48 (0.15), residues: 1045 loop : -1.14 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP a 36 HIS 0.041 0.002 HIS A 66 PHE 0.046 0.003 PHE A 970 TYR 0.029 0.002 TYR C 396 ARG 0.015 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 691 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8889 (m) cc_final: 0.8556 (p) REVERT: A 133 PHE cc_start: 0.7203 (m-80) cc_final: 0.6917 (m-10) REVERT: A 290 ASP cc_start: 0.7853 (t0) cc_final: 0.7619 (t70) REVERT: A 291 CYS cc_start: 0.7286 (t) cc_final: 0.6963 (t) REVERT: A 293 LEU cc_start: 0.8099 (tp) cc_final: 0.7553 (tt) REVERT: A 339 ASP cc_start: 0.8754 (m-30) cc_final: 0.8372 (t0) REVERT: A 386 LYS cc_start: 0.8219 (mttt) cc_final: 0.8003 (mttm) REVERT: A 387 LEU cc_start: 0.9372 (mt) cc_final: 0.9154 (mt) REVERT: A 543 PHE cc_start: 0.8214 (m-80) cc_final: 0.7940 (m-80) REVERT: A 546 LEU cc_start: 0.8480 (tt) cc_final: 0.8127 (tt) REVERT: A 654 GLU cc_start: 0.7901 (tt0) cc_final: 0.7541 (tt0) REVERT: A 725 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: A 739 THR cc_start: 0.8900 (m) cc_final: 0.8674 (p) REVERT: A 740 MET cc_start: 0.8426 (mmm) cc_final: 0.8195 (mmm) REVERT: A 764 LYS cc_start: 0.8645 (ttpp) cc_final: 0.8384 (ttpp) REVERT: A 814 LYS cc_start: 0.8997 (mttt) cc_final: 0.8445 (mmmt) REVERT: A 823 PHE cc_start: 0.8483 (t80) cc_final: 0.8015 (t80) REVERT: A 868 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7852 (mm-30) REVERT: A 884 SER cc_start: 0.8348 (m) cc_final: 0.7849 (t) REVERT: A 900 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8025 (mtm) REVERT: A 935 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8136 (mm-40) REVERT: A 964 LYS cc_start: 0.8650 (tppt) cc_final: 0.8286 (tppt) REVERT: A 969 LYS cc_start: 0.8817 (mttt) cc_final: 0.8283 (mttm) REVERT: A 981 PHE cc_start: 0.7251 (t80) cc_final: 0.6980 (t80) REVERT: A 1031 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7129 (mp0) REVERT: A 1072 GLU cc_start: 0.8935 (pm20) cc_final: 0.8618 (pm20) REVERT: A 1073 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8583 (mtpp) REVERT: A 1097 SER cc_start: 0.8973 (t) cc_final: 0.8760 (p) REVERT: A 1109 PHE cc_start: 0.5096 (p90) cc_final: 0.4847 (p90) REVERT: C 56 LEU cc_start: 0.8582 (tp) cc_final: 0.8305 (tp) REVERT: C 271 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8164 (mm-40) REVERT: C 276 LEU cc_start: 0.8501 (tp) cc_final: 0.8296 (tt) REVERT: C 313 TYR cc_start: 0.7880 (m-80) cc_final: 0.7323 (m-80) REVERT: C 365 TYR cc_start: 0.7481 (m-10) cc_final: 0.7189 (m-10) REVERT: C 528 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7957 (mmtm) REVERT: C 571 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6430 (m-30) REVERT: C 613 GLN cc_start: 0.7665 (pt0) cc_final: 0.7439 (pt0) REVERT: C 643 PHE cc_start: 0.8078 (t80) cc_final: 0.7749 (t80) REVERT: C 654 GLU cc_start: 0.7679 (tt0) cc_final: 0.7439 (tt0) REVERT: C 725 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6758 (mt-10) REVERT: C 739 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7082 (p) REVERT: C 816 SER cc_start: 0.8136 (p) cc_final: 0.7005 (m) REVERT: C 896 ILE cc_start: 0.8678 (mt) cc_final: 0.8457 (tt) REVERT: C 933 LYS cc_start: 0.8380 (mttt) cc_final: 0.8140 (mmmm) REVERT: C 935 GLN cc_start: 0.8486 (tp40) cc_final: 0.7932 (tm-30) REVERT: C 969 LYS cc_start: 0.9068 (mttt) cc_final: 0.8589 (mttm) REVERT: C 990 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7192 (mt-10) REVERT: C 1006 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8239 (m) REVERT: C 1045 LYS cc_start: 0.8160 (tttt) cc_final: 0.7844 (ttmm) REVERT: C 1107 ARG cc_start: 0.8317 (tpp80) cc_final: 0.7580 (tpp80) REVERT: C 1111 GLU cc_start: 0.8614 (tt0) cc_final: 0.8338 (mt-10) REVERT: C 1125 ASN cc_start: 0.8694 (p0) cc_final: 0.8483 (p0) REVERT: C 1129 VAL cc_start: 0.9130 (t) cc_final: 0.8821 (m) REVERT: c 81 MET cc_start: 0.5482 (ttp) cc_final: 0.5209 (ttp) REVERT: c 106 TRP cc_start: 0.6249 (p90) cc_final: 0.5900 (p90) REVERT: B 33 THR cc_start: 0.8454 (p) cc_final: 0.8146 (t) REVERT: B 36 VAL cc_start: 0.9044 (t) cc_final: 0.8718 (m) REVERT: B 55 PHE cc_start: 0.7456 (m-80) cc_final: 0.6504 (m-10) REVERT: B 67 VAL cc_start: 0.7147 (OUTLIER) cc_final: 0.6823 (p) REVERT: B 106 PHE cc_start: 0.6919 (m-10) cc_final: 0.6653 (m-10) REVERT: B 119 ILE cc_start: 0.9125 (mm) cc_final: 0.8866 (mm) REVERT: B 129 LYS cc_start: 0.8801 (mttt) cc_final: 0.8441 (mmmm) REVERT: B 133 PHE cc_start: 0.8257 (m-80) cc_final: 0.7420 (m-80) REVERT: B 221 SER cc_start: 0.9029 (t) cc_final: 0.8665 (m) REVERT: B 309 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7221 (mt-10) REVERT: B 386 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8205 (mtmt) REVERT: B 515 PHE cc_start: 0.7360 (m-10) cc_final: 0.7077 (m-10) REVERT: B 603 ASN cc_start: 0.8657 (p0) cc_final: 0.8199 (p0) REVERT: B 643 PHE cc_start: 0.7863 (t80) cc_final: 0.7614 (t80) REVERT: B 654 GLU cc_start: 0.6708 (mp0) cc_final: 0.6488 (mp0) REVERT: B 773 GLU cc_start: 0.8493 (tt0) cc_final: 0.7770 (tm-30) REVERT: B 795 LYS cc_start: 0.8882 (mtpp) cc_final: 0.8510 (mttm) REVERT: B 884 SER cc_start: 0.8751 (m) cc_final: 0.7903 (p) REVERT: B 921 LYS cc_start: 0.8768 (mttt) cc_final: 0.8356 (mmmm) REVERT: B 969 LYS cc_start: 0.8798 (mttt) cc_final: 0.8258 (mtpp) REVERT: B 974 SER cc_start: 0.8465 (p) cc_final: 0.7699 (t) REVERT: B 978 ASN cc_start: 0.8543 (p0) cc_final: 0.7980 (p0) REVERT: B 979 ASP cc_start: 0.8414 (m-30) cc_final: 0.7836 (m-30) REVERT: B 984 LEU cc_start: 0.7672 (mt) cc_final: 0.7152 (tp) REVERT: B 988 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: B 1017 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 1073 LYS cc_start: 0.8533 (tttt) cc_final: 0.8277 (mtpp) REVERT: B 1106 GLN cc_start: 0.6983 (mm-40) cc_final: 0.6316 (mm-40) REVERT: B 1110 TYR cc_start: 0.8734 (t80) cc_final: 0.8301 (t80) REVERT: B 1111 GLU cc_start: 0.8192 (mp0) cc_final: 0.7672 (mp0) REVERT: B 1112 PRO cc_start: 0.9297 (Cg_endo) cc_final: 0.9025 (Cg_exo) REVERT: a 50 MET cc_start: 0.8066 (ttp) cc_final: 0.7848 (ttp) REVERT: a 61 ASN cc_start: 0.8778 (t0) cc_final: 0.8415 (t0) REVERT: a 161 TRP cc_start: 0.5760 (m-90) cc_final: 0.5431 (m-90) REVERT: b 49 LYS cc_start: 0.7957 (mttt) cc_final: 0.7618 (mttt) REVERT: b 59 GLU cc_start: 0.8190 (tp30) cc_final: 0.7932 (tp30) REVERT: b 75 PHE cc_start: 0.6819 (m-10) cc_final: 0.6618 (m-80) outliers start: 126 outliers final: 79 residues processed: 772 average time/residue: 0.4433 time to fit residues: 535.2790 Evaluate side-chains 709 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 623 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 321 optimal weight: 1.9990 chunk 218 optimal weight: 30.0000 chunk 5 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 329 optimal weight: 0.6980 chunk 266 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 196 optimal weight: 0.5980 chunk 346 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 394 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 926 GLN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 563 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32108 Z= 0.217 Angle : 0.591 10.521 43696 Z= 0.303 Chirality : 0.044 0.294 4935 Planarity : 0.004 0.123 5629 Dihedral : 4.558 27.362 4311 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.45 % Rotamer: Outliers : 3.25 % Allowed : 14.45 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % 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: -0.63 (0.13), residues: 3961 helix: 0.21 (0.21), residues: 630 sheet: 0.52 (0.15), residues: 1037 loop : -1.07 (0.12), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP a 36 HIS 0.005 0.001 HIS B1064 PHE 0.048 0.002 PHE B 855 TYR 0.019 0.001 TYR B1138 ARG 0.014 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 646 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7644 (t80) cc_final: 0.7352 (t80) REVERT: A 50 SER cc_start: 0.8774 (m) cc_final: 0.8449 (p) REVERT: A 133 PHE cc_start: 0.7284 (m-80) cc_final: 0.6965 (m-10) REVERT: A 135 PHE cc_start: 0.7570 (t80) cc_final: 0.7172 (t80) REVERT: A 290 ASP cc_start: 0.7725 (t0) cc_final: 0.7444 (t70) REVERT: A 291 CYS cc_start: 0.7002 (t) cc_final: 0.6712 (t) REVERT: A 304 LYS cc_start: 0.8268 (mttt) cc_final: 0.8040 (mttt) REVERT: A 313 TYR cc_start: 0.8115 (m-80) cc_final: 0.7748 (m-80) REVERT: A 338 PHE cc_start: 0.6290 (m-80) cc_final: 0.5694 (m-80) REVERT: A 339 ASP cc_start: 0.8736 (m-30) cc_final: 0.8319 (t0) REVERT: A 386 LYS cc_start: 0.8092 (mttt) cc_final: 0.7822 (mttm) REVERT: A 516 GLU cc_start: 0.6915 (mp0) cc_final: 0.6136 (mp0) REVERT: A 537 LYS cc_start: 0.8849 (tptp) cc_final: 0.8509 (tmtt) REVERT: A 543 PHE cc_start: 0.8206 (m-80) cc_final: 0.7929 (m-80) REVERT: A 546 LEU cc_start: 0.8492 (tt) cc_final: 0.8156 (tt) REVERT: A 654 GLU cc_start: 0.7842 (tt0) cc_final: 0.7509 (tt0) REVERT: A 739 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8036 (p) REVERT: A 764 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8367 (ttmm) REVERT: A 814 LYS cc_start: 0.8967 (mttt) cc_final: 0.8519 (mmmt) REVERT: A 823 PHE cc_start: 0.8501 (t80) cc_final: 0.8019 (t80) REVERT: A 868 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7904 (tp30) REVERT: A 884 SER cc_start: 0.8298 (m) cc_final: 0.7861 (t) REVERT: A 900 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7903 (mtm) REVERT: A 918 GLU cc_start: 0.8092 (mp0) cc_final: 0.7538 (mp0) REVERT: A 935 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8105 (mm-40) REVERT: A 950 ASP cc_start: 0.8031 (t0) cc_final: 0.7731 (t0) REVERT: A 964 LYS cc_start: 0.8661 (tppt) cc_final: 0.8281 (tppt) REVERT: A 969 LYS cc_start: 0.8776 (mttt) cc_final: 0.8277 (mttm) REVERT: A 1045 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8497 (mmmm) REVERT: A 1073 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8383 (mtpp) REVERT: C 200 TYR cc_start: 0.7334 (m-80) cc_final: 0.7052 (m-80) REVERT: C 313 TYR cc_start: 0.7869 (m-80) cc_final: 0.7322 (m-80) REVERT: C 339 ASP cc_start: 0.8513 (m-30) cc_final: 0.8285 (t0) REVERT: C 365 TYR cc_start: 0.7522 (m-10) cc_final: 0.7111 (m-10) REVERT: C 528 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7963 (mmtm) REVERT: C 643 PHE cc_start: 0.8032 (t80) cc_final: 0.7702 (t80) REVERT: C 654 GLU cc_start: 0.7602 (tt0) cc_final: 0.7375 (tt0) REVERT: C 675 GLN cc_start: 0.8633 (pp30) cc_final: 0.8410 (pp30) REVERT: C 725 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6839 (mt-10) REVERT: C 816 SER cc_start: 0.8100 (p) cc_final: 0.7301 (m) REVERT: C 861 LEU cc_start: 0.8830 (mm) cc_final: 0.8532 (mt) REVERT: C 896 ILE cc_start: 0.8609 (mt) cc_final: 0.8366 (tt) REVERT: C 933 LYS cc_start: 0.8309 (mttt) cc_final: 0.8099 (mmmm) REVERT: C 935 GLN cc_start: 0.8512 (tp40) cc_final: 0.7967 (tm-30) REVERT: C 969 LYS cc_start: 0.9029 (mttt) cc_final: 0.8552 (mttm) REVERT: C 983 ARG cc_start: 0.5824 (mmm160) cc_final: 0.5411 (tmt170) REVERT: C 990 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7083 (mt-10) REVERT: C 1045 LYS cc_start: 0.8136 (tttt) cc_final: 0.7878 (tppp) REVERT: C 1129 VAL cc_start: 0.9063 (t) cc_final: 0.8752 (m) REVERT: C 1139 ASP cc_start: 0.8339 (t0) cc_final: 0.7916 (t0) REVERT: c 81 MET cc_start: 0.5414 (ttp) cc_final: 0.5157 (ttp) REVERT: c 106 TRP cc_start: 0.6224 (p90) cc_final: 0.5887 (p90) REVERT: B 33 THR cc_start: 0.8346 (p) cc_final: 0.8055 (t) REVERT: B 36 VAL cc_start: 0.8990 (t) cc_final: 0.8651 (m) REVERT: B 55 PHE cc_start: 0.7517 (m-80) cc_final: 0.6932 (m-10) REVERT: B 67 VAL cc_start: 0.7060 (OUTLIER) cc_final: 0.6729 (p) REVERT: B 106 PHE cc_start: 0.6901 (m-10) cc_final: 0.6533 (m-10) REVERT: B 119 ILE cc_start: 0.9073 (mm) cc_final: 0.8799 (mm) REVERT: B 125 ASN cc_start: 0.5646 (p0) cc_final: 0.4124 (t0) REVERT: B 129 LYS cc_start: 0.8769 (mttt) cc_final: 0.8442 (mmmm) REVERT: B 195 LYS cc_start: 0.4329 (tptt) cc_final: 0.3610 (tppt) REVERT: B 206 LYS cc_start: 0.7868 (tptp) cc_final: 0.7570 (tptt) REVERT: B 221 SER cc_start: 0.9058 (t) cc_final: 0.8647 (m) REVERT: B 386 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8038 (mtmt) REVERT: B 515 PHE cc_start: 0.7383 (m-10) cc_final: 0.7075 (m-10) REVERT: B 603 ASN cc_start: 0.8612 (p0) cc_final: 0.8050 (p0) REVERT: B 765 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.8054 (ttm-80) REVERT: B 773 GLU cc_start: 0.8462 (tt0) cc_final: 0.7858 (tm-30) REVERT: B 795 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8525 (mttm) REVERT: B 805 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7582 (tt) REVERT: B 884 SER cc_start: 0.8745 (m) cc_final: 0.8129 (t) REVERT: B 921 LYS cc_start: 0.8773 (mttt) cc_final: 0.8412 (mmtp) REVERT: B 978 ASN cc_start: 0.8512 (p0) cc_final: 0.7930 (p0) REVERT: B 979 ASP cc_start: 0.8393 (m-30) cc_final: 0.7780 (m-30) REVERT: B 984 LEU cc_start: 0.7688 (mt) cc_final: 0.7193 (tp) REVERT: B 988 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: B 1017 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 1073 LYS cc_start: 0.8529 (tttt) cc_final: 0.8283 (mtpp) REVERT: B 1082 CYS cc_start: 0.6187 (t) cc_final: 0.5763 (t) REVERT: B 1111 GLU cc_start: 0.8188 (mp0) cc_final: 0.7340 (mp0) REVERT: B 1112 PRO cc_start: 0.9273 (Cg_endo) cc_final: 0.8976 (Cg_exo) REVERT: B 1125 ASN cc_start: 0.8086 (p0) cc_final: 0.7713 (p0) REVERT: a 61 ASN cc_start: 0.8650 (t0) cc_final: 0.8358 (t0) REVERT: b 49 LYS cc_start: 0.7860 (mttt) cc_final: 0.7524 (mttt) REVERT: b 75 PHE cc_start: 0.6838 (m-10) cc_final: 0.6597 (m-10) outliers start: 114 outliers final: 82 residues processed: 714 average time/residue: 0.4512 time to fit residues: 500.8003 Evaluate side-chains 709 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 622 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 153 PHE Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 65 ARG Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 129 optimal weight: 0.5980 chunk 347 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 226 optimal weight: 50.0000 chunk 95 optimal weight: 1.9990 chunk 386 optimal weight: 0.4980 chunk 320 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1054 GLN C 49 HIS C 331 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 926 GLN C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 439 ASN B1083 HIS B1101 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32108 Z= 0.181 Angle : 0.572 10.961 43696 Z= 0.290 Chirality : 0.044 0.276 4935 Planarity : 0.004 0.103 5629 Dihedral : 4.370 26.650 4311 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.68 % Favored : 97.25 % Rotamer: Outliers : 3.14 % Allowed : 15.11 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % 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: -0.44 (0.13), residues: 3961 helix: 0.59 (0.21), residues: 615 sheet: 0.53 (0.16), residues: 1043 loop : -0.95 (0.12), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 436 HIS 0.005 0.001 HIS B1101 PHE 0.031 0.002 PHE A1109 TYR 0.022 0.001 TYR A 741 ARG 0.010 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 641 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7574 (t80) cc_final: 0.7321 (t80) REVERT: A 50 SER cc_start: 0.8751 (m) cc_final: 0.8467 (p) REVERT: A 133 PHE cc_start: 0.7292 (m-80) cc_final: 0.7018 (m-10) REVERT: A 200 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7493 (t80) REVERT: A 290 ASP cc_start: 0.7751 (t0) cc_final: 0.7446 (t70) REVERT: A 293 LEU cc_start: 0.8499 (tt) cc_final: 0.8112 (tp) REVERT: A 304 LYS cc_start: 0.8312 (mttt) cc_final: 0.8074 (mttt) REVERT: A 313 TYR cc_start: 0.8089 (m-80) cc_final: 0.7732 (m-80) REVERT: A 338 PHE cc_start: 0.6370 (m-80) cc_final: 0.5937 (m-80) REVERT: A 339 ASP cc_start: 0.8684 (m-30) cc_final: 0.8276 (t0) REVERT: A 370 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7306 (p0) REVERT: A 386 LYS cc_start: 0.8137 (mttt) cc_final: 0.7714 (mttm) REVERT: A 537 LYS cc_start: 0.8858 (tptp) cc_final: 0.8521 (tmtt) REVERT: A 543 PHE cc_start: 0.8170 (m-80) cc_final: 0.7883 (m-80) REVERT: A 546 LEU cc_start: 0.8515 (tt) cc_final: 0.8170 (tt) REVERT: A 654 GLU cc_start: 0.7807 (tt0) cc_final: 0.7460 (tt0) REVERT: A 764 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8366 (ttmm) REVERT: A 814 LYS cc_start: 0.8974 (mttt) cc_final: 0.8443 (mmmt) REVERT: A 823 PHE cc_start: 0.8504 (t80) cc_final: 0.8020 (t80) REVERT: A 868 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7618 (mm-30) REVERT: A 884 SER cc_start: 0.8269 (m) cc_final: 0.7834 (t) REVERT: A 900 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7797 (mtm) REVERT: A 935 GLN cc_start: 0.8408 (mm110) cc_final: 0.8167 (mm-40) REVERT: A 950 ASP cc_start: 0.8050 (t0) cc_final: 0.7699 (t0) REVERT: A 969 LYS cc_start: 0.8868 (mttt) cc_final: 0.8398 (mttm) REVERT: A 1073 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8323 (mtpp) REVERT: A 1109 PHE cc_start: 0.4567 (p90) cc_final: 0.3202 (p90) REVERT: C 190 ARG cc_start: 0.2986 (mmt90) cc_final: 0.2754 (mmt90) REVERT: C 194 PHE cc_start: 0.8312 (m-80) cc_final: 0.8041 (m-80) REVERT: C 200 TYR cc_start: 0.7361 (m-80) cc_final: 0.7058 (m-80) REVERT: C 313 TYR cc_start: 0.7924 (m-80) cc_final: 0.7403 (m-80) REVERT: C 328 ARG cc_start: 0.6048 (mmt180) cc_final: 0.5847 (mmt-90) REVERT: C 338 PHE cc_start: 0.7691 (t80) cc_final: 0.7357 (t80) REVERT: C 339 ASP cc_start: 0.8489 (m-30) cc_final: 0.8288 (t0) REVERT: C 365 TYR cc_start: 0.7574 (m-10) cc_final: 0.7122 (m-10) REVERT: C 396 TYR cc_start: 0.8508 (m-10) cc_final: 0.8097 (m-10) REVERT: C 528 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7950 (mmtm) REVERT: C 643 PHE cc_start: 0.8003 (t80) cc_final: 0.7652 (t80) REVERT: C 654 GLU cc_start: 0.7672 (tt0) cc_final: 0.7437 (tt0) REVERT: C 725 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6866 (mt-10) REVERT: C 806 LEU cc_start: 0.8481 (mt) cc_final: 0.7955 (mm) REVERT: C 816 SER cc_start: 0.8267 (p) cc_final: 0.7272 (m) REVERT: C 861 LEU cc_start: 0.8803 (mm) cc_final: 0.8515 (mt) REVERT: C 896 ILE cc_start: 0.8597 (mt) cc_final: 0.8340 (tt) REVERT: C 918 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8162 (mt-10) REVERT: C 933 LYS cc_start: 0.8242 (mttt) cc_final: 0.7919 (mmmm) REVERT: C 935 GLN cc_start: 0.8417 (tp40) cc_final: 0.8002 (tm-30) REVERT: C 957 GLN cc_start: 0.8345 (tt0) cc_final: 0.7422 (tt0) REVERT: C 969 LYS cc_start: 0.9003 (mttt) cc_final: 0.8511 (mtmm) REVERT: C 979 ASP cc_start: 0.8371 (m-30) cc_final: 0.7981 (p0) REVERT: C 983 ARG cc_start: 0.5859 (mmm160) cc_final: 0.5265 (tmt170) REVERT: C 990 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7047 (mt-10) REVERT: C 1045 LYS cc_start: 0.8147 (tttt) cc_final: 0.7911 (tppp) REVERT: C 1129 VAL cc_start: 0.9071 (t) cc_final: 0.8767 (m) REVERT: c 81 MET cc_start: 0.5398 (ttp) cc_final: 0.5136 (ttp) REVERT: c 106 TRP cc_start: 0.6202 (p90) cc_final: 0.5855 (p90) REVERT: B 33 THR cc_start: 0.8321 (p) cc_final: 0.8038 (t) REVERT: B 36 VAL cc_start: 0.8928 (t) cc_final: 0.8595 (m) REVERT: B 55 PHE cc_start: 0.7546 (m-80) cc_final: 0.6977 (m-10) REVERT: B 67 VAL cc_start: 0.6957 (OUTLIER) cc_final: 0.6620 (p) REVERT: B 106 PHE cc_start: 0.6943 (m-10) cc_final: 0.6552 (m-10) REVERT: B 119 ILE cc_start: 0.9076 (mm) cc_final: 0.8814 (mm) REVERT: B 125 ASN cc_start: 0.6064 (p0) cc_final: 0.4626 (t0) REVERT: B 129 LYS cc_start: 0.8756 (mttt) cc_final: 0.8435 (mmmm) REVERT: B 195 LYS cc_start: 0.4158 (tptt) cc_final: 0.3533 (tppt) REVERT: B 221 SER cc_start: 0.9039 (t) cc_final: 0.8662 (m) REVERT: B 298 GLU cc_start: 0.8415 (tp30) cc_final: 0.7859 (tp30) REVERT: B 364 ASP cc_start: 0.7547 (t0) cc_final: 0.7185 (t0) REVERT: B 386 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8086 (mtmt) REVERT: B 450 ASN cc_start: 0.7288 (m-40) cc_final: 0.6928 (t0) REVERT: B 515 PHE cc_start: 0.7455 (m-10) cc_final: 0.7192 (m-10) REVERT: B 603 ASN cc_start: 0.8599 (p0) cc_final: 0.8043 (p0) REVERT: B 615 VAL cc_start: 0.8462 (t) cc_final: 0.8209 (m) REVERT: B 740 MET cc_start: 0.8056 (tpp) cc_final: 0.7539 (mmm) REVERT: B 751 ASN cc_start: 0.8647 (m-40) cc_final: 0.7887 (m-40) REVERT: B 755 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8277 (mp10) REVERT: B 765 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.7952 (ttp-170) REVERT: B 773 GLU cc_start: 0.8436 (tt0) cc_final: 0.7753 (tm-30) REVERT: B 794 ILE cc_start: 0.9283 (mt) cc_final: 0.8995 (tp) REVERT: B 795 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8522 (mttm) REVERT: B 855 PHE cc_start: 0.6165 (p90) cc_final: 0.5940 (p90) REVERT: B 869 MET cc_start: 0.8910 (mtp) cc_final: 0.8629 (mtt) REVERT: B 884 SER cc_start: 0.8687 (m) cc_final: 0.8078 (t) REVERT: B 921 LYS cc_start: 0.8759 (mttt) cc_final: 0.8429 (mmtp) REVERT: B 969 LYS cc_start: 0.8841 (mttt) cc_final: 0.8232 (mtpp) REVERT: B 978 ASN cc_start: 0.8499 (p0) cc_final: 0.7892 (p0) REVERT: B 979 ASP cc_start: 0.8325 (m-30) cc_final: 0.7752 (m-30) REVERT: B 984 LEU cc_start: 0.7727 (mt) cc_final: 0.7237 (tp) REVERT: B 988 GLU cc_start: 0.8005 (mp0) cc_final: 0.7723 (mp0) REVERT: B 990 GLU cc_start: 0.8159 (pt0) cc_final: 0.7767 (pm20) REVERT: B 1017 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 1073 LYS cc_start: 0.8520 (tttt) cc_final: 0.8285 (mtpp) REVERT: B 1125 ASN cc_start: 0.8158 (p0) cc_final: 0.7672 (p0) REVERT: a 50 MET cc_start: 0.8012 (ttp) cc_final: 0.7770 (ttp) REVERT: a 61 ASN cc_start: 0.8687 (t0) cc_final: 0.8458 (t0) REVERT: a 83 LEU cc_start: 0.8337 (mt) cc_final: 0.7976 (mt) REVERT: a 84 SER cc_start: 0.6239 (OUTLIER) cc_final: 0.5854 (t) REVERT: b 49 LYS cc_start: 0.7833 (mttt) cc_final: 0.7492 (mttt) REVERT: b 75 PHE cc_start: 0.6860 (m-10) cc_final: 0.6649 (m-10) outliers start: 110 outliers final: 79 residues processed: 703 average time/residue: 0.4493 time to fit residues: 491.8051 Evaluate side-chains 704 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 620 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 372 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 281 optimal weight: 0.9980 chunk 218 optimal weight: 20.0000 chunk 324 optimal weight: 0.0470 chunk 215 optimal weight: 0.7980 chunk 384 optimal weight: 3.9990 chunk 240 optimal weight: 30.0000 chunk 234 optimal weight: 8.9990 chunk 177 optimal weight: 0.1980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1113 GLN C 394 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32108 Z= 0.198 Angle : 0.583 10.975 43696 Z= 0.295 Chirality : 0.044 0.267 4935 Planarity : 0.004 0.095 5629 Dihedral : 4.357 26.137 4311 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 3.22 % Allowed : 16.13 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % 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: -0.36 (0.13), residues: 3961 helix: 0.75 (0.21), residues: 639 sheet: 0.51 (0.15), residues: 1074 loop : -0.91 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP a 36 HIS 0.009 0.001 HIS B1083 PHE 0.022 0.001 PHE C 92 TYR 0.021 0.001 TYR C1138 ARG 0.010 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 642 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8759 (m) cc_final: 0.8504 (p) REVERT: A 133 PHE cc_start: 0.7298 (m-80) cc_final: 0.7019 (m-10) REVERT: A 290 ASP cc_start: 0.7520 (t0) cc_final: 0.7282 (t70) REVERT: A 304 LYS cc_start: 0.8329 (mttt) cc_final: 0.8100 (mttt) REVERT: A 309 GLU cc_start: 0.8135 (tp30) cc_final: 0.7779 (tp30) REVERT: A 313 TYR cc_start: 0.8029 (m-80) cc_final: 0.7623 (m-80) REVERT: A 338 PHE cc_start: 0.6473 (m-80) cc_final: 0.6039 (m-80) REVERT: A 339 ASP cc_start: 0.8677 (m-30) cc_final: 0.8367 (t70) REVERT: A 386 LYS cc_start: 0.8135 (mttt) cc_final: 0.7807 (mttm) REVERT: A 516 GLU cc_start: 0.6439 (mp0) cc_final: 0.6143 (mp0) REVERT: A 537 LYS cc_start: 0.8812 (tptp) cc_final: 0.8507 (tmtt) REVERT: A 543 PHE cc_start: 0.8208 (m-80) cc_final: 0.7903 (m-80) REVERT: A 546 LEU cc_start: 0.8549 (tt) cc_final: 0.8156 (tt) REVERT: A 654 GLU cc_start: 0.7796 (tt0) cc_final: 0.7460 (tt0) REVERT: A 675 GLN cc_start: 0.8504 (pp30) cc_final: 0.8156 (pp30) REVERT: A 764 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8364 (ttmm) REVERT: A 814 LYS cc_start: 0.8986 (mttt) cc_final: 0.8523 (mmmt) REVERT: A 819 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7980 (mt-10) REVERT: A 821 LEU cc_start: 0.8223 (mt) cc_final: 0.7835 (mp) REVERT: A 823 PHE cc_start: 0.8526 (t80) cc_final: 0.8030 (t80) REVERT: A 884 SER cc_start: 0.8239 (m) cc_final: 0.7889 (t) REVERT: A 900 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7847 (mtm) REVERT: A 914 ASN cc_start: 0.7870 (m-40) cc_final: 0.7198 (m-40) REVERT: A 918 GLU cc_start: 0.8156 (mp0) cc_final: 0.7475 (mp0) REVERT: A 950 ASP cc_start: 0.8050 (t0) cc_final: 0.7663 (t0) REVERT: A 969 LYS cc_start: 0.8950 (mttt) cc_final: 0.8455 (mttm) REVERT: A 1073 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8344 (mtpp) REVERT: A 1111 GLU cc_start: 0.8156 (mp0) cc_final: 0.7321 (pm20) REVERT: C 190 ARG cc_start: 0.2734 (mmt90) cc_final: 0.2505 (mmt90) REVERT: C 200 TYR cc_start: 0.7416 (m-80) cc_final: 0.7133 (m-80) REVERT: C 313 TYR cc_start: 0.7917 (m-80) cc_final: 0.7363 (m-80) REVERT: C 365 TYR cc_start: 0.7693 (m-10) cc_final: 0.7124 (m-10) REVERT: C 528 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7920 (mmtm) REVERT: C 643 PHE cc_start: 0.8000 (t80) cc_final: 0.7610 (t80) REVERT: C 654 GLU cc_start: 0.7649 (tt0) cc_final: 0.7427 (tt0) REVERT: C 806 LEU cc_start: 0.8574 (mt) cc_final: 0.8356 (mm) REVERT: C 861 LEU cc_start: 0.8816 (mm) cc_final: 0.8559 (mt) REVERT: C 896 ILE cc_start: 0.8579 (mt) cc_final: 0.8331 (tt) REVERT: C 933 LYS cc_start: 0.8310 (mttt) cc_final: 0.8078 (mmmm) REVERT: C 935 GLN cc_start: 0.8488 (tp40) cc_final: 0.8179 (tm-30) REVERT: C 957 GLN cc_start: 0.8352 (tt0) cc_final: 0.7493 (tt0) REVERT: C 969 LYS cc_start: 0.9014 (mttt) cc_final: 0.8393 (mtmm) REVERT: C 975 SER cc_start: 0.8630 (p) cc_final: 0.8219 (m) REVERT: C 979 ASP cc_start: 0.8364 (m-30) cc_final: 0.7581 (p0) REVERT: C 990 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7056 (mt-10) REVERT: C 1005 GLN cc_start: 0.8453 (tp40) cc_final: 0.8180 (tp40) REVERT: C 1045 LYS cc_start: 0.8194 (tttt) cc_final: 0.7928 (tppp) REVERT: C 1129 VAL cc_start: 0.9108 (t) cc_final: 0.8813 (m) REVERT: C 1139 ASP cc_start: 0.8347 (t0) cc_final: 0.7904 (t0) REVERT: c 81 MET cc_start: 0.5464 (ttp) cc_final: 0.5199 (ttp) REVERT: B 33 THR cc_start: 0.8351 (p) cc_final: 0.8059 (t) REVERT: B 36 VAL cc_start: 0.8939 (t) cc_final: 0.8590 (m) REVERT: B 55 PHE cc_start: 0.7518 (m-80) cc_final: 0.6962 (m-10) REVERT: B 67 VAL cc_start: 0.6952 (OUTLIER) cc_final: 0.6615 (p) REVERT: B 106 PHE cc_start: 0.7007 (m-10) cc_final: 0.6632 (m-10) REVERT: B 119 ILE cc_start: 0.9103 (mm) cc_final: 0.8818 (mm) REVERT: B 125 ASN cc_start: 0.6229 (p0) cc_final: 0.4807 (t0) REVERT: B 129 LYS cc_start: 0.8862 (mttt) cc_final: 0.8511 (mmtm) REVERT: B 195 LYS cc_start: 0.4215 (tptt) cc_final: 0.3686 (tppt) REVERT: B 206 LYS cc_start: 0.7780 (tptp) cc_final: 0.7550 (tptt) REVERT: B 221 SER cc_start: 0.9068 (t) cc_final: 0.8662 (m) REVERT: B 229 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8136 (mm) REVERT: B 298 GLU cc_start: 0.8467 (tp30) cc_final: 0.7905 (tp30) REVERT: B 386 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8107 (mtmt) REVERT: B 450 ASN cc_start: 0.7234 (m-40) cc_final: 0.6911 (t0) REVERT: B 577 ARG cc_start: 0.7839 (tpp80) cc_final: 0.7520 (tpp80) REVERT: B 603 ASN cc_start: 0.8618 (p0) cc_final: 0.8082 (p0) REVERT: B 654 GLU cc_start: 0.6632 (mp0) cc_final: 0.6413 (mp0) REVERT: B 740 MET cc_start: 0.8124 (tpp) cc_final: 0.7853 (mmm) REVERT: B 748 GLU cc_start: 0.8810 (pm20) cc_final: 0.8288 (pt0) REVERT: B 751 ASN cc_start: 0.8675 (m-40) cc_final: 0.7929 (m-40) REVERT: B 755 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8309 (mp10) REVERT: B 765 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.7981 (ttp-170) REVERT: B 773 GLU cc_start: 0.8372 (tt0) cc_final: 0.7763 (tm-30) REVERT: B 794 ILE cc_start: 0.9294 (mt) cc_final: 0.9012 (tp) REVERT: B 795 LYS cc_start: 0.8961 (mtpp) cc_final: 0.8576 (mttm) REVERT: B 884 SER cc_start: 0.8522 (m) cc_final: 0.7926 (t) REVERT: B 921 LYS cc_start: 0.8672 (mttt) cc_final: 0.8443 (mmtp) REVERT: B 964 LYS cc_start: 0.8855 (pttp) cc_final: 0.8444 (ttpp) REVERT: B 969 LYS cc_start: 0.8840 (mttt) cc_final: 0.8292 (mtpt) REVERT: B 978 ASN cc_start: 0.8515 (p0) cc_final: 0.7883 (p0) REVERT: B 979 ASP cc_start: 0.8305 (m-30) cc_final: 0.7720 (m-30) REVERT: B 984 LEU cc_start: 0.7764 (mt) cc_final: 0.7276 (tp) REVERT: B 1017 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7786 (tm-30) REVERT: B 1030 SER cc_start: 0.8970 (m) cc_final: 0.8355 (t) REVERT: B 1073 LYS cc_start: 0.8503 (tttt) cc_final: 0.8255 (mtpp) REVERT: B 1111 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8093 (mp0) REVERT: B 1125 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7602 (p0) REVERT: b 49 LYS cc_start: 0.7906 (mttt) cc_final: 0.7622 (mttt) REVERT: b 75 PHE cc_start: 0.6894 (m-10) cc_final: 0.6674 (m-10) outliers start: 113 outliers final: 86 residues processed: 703 average time/residue: 0.4564 time to fit residues: 505.0864 Evaluate side-chains 705 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 615 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 237 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 229 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 75 optimal weight: 0.0070 chunk 74 optimal weight: 0.9980 chunk 244 optimal weight: 0.5980 chunk 262 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B1083 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.6905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32108 Z= 0.187 Angle : 0.584 11.304 43696 Z= 0.295 Chirality : 0.044 0.257 4935 Planarity : 0.004 0.082 5629 Dihedral : 4.309 25.902 4311 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.90 % Favored : 97.02 % Rotamer: Outliers : 2.79 % Allowed : 17.16 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % 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: -0.25 (0.13), residues: 3961 helix: 0.90 (0.22), residues: 641 sheet: 0.60 (0.15), residues: 1058 loop : -0.87 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP a 36 HIS 0.003 0.001 HIS B1064 PHE 0.022 0.001 PHE C 92 TYR 0.021 0.001 TYR C1138 ARG 0.011 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 622 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8748 (m) cc_final: 0.8498 (p) REVERT: A 133 PHE cc_start: 0.7388 (m-80) cc_final: 0.7111 (m-10) REVERT: A 290 ASP cc_start: 0.7605 (t0) cc_final: 0.7351 (t70) REVERT: A 304 LYS cc_start: 0.8364 (mttt) cc_final: 0.8124 (mttt) REVERT: A 313 TYR cc_start: 0.7999 (m-80) cc_final: 0.7613 (m-80) REVERT: A 338 PHE cc_start: 0.6435 (m-80) cc_final: 0.5922 (m-80) REVERT: A 339 ASP cc_start: 0.8714 (m-30) cc_final: 0.8438 (t70) REVERT: A 386 LYS cc_start: 0.8112 (mttt) cc_final: 0.7773 (mttm) REVERT: A 537 LYS cc_start: 0.8786 (tptp) cc_final: 0.8480 (tmtt) REVERT: A 543 PHE cc_start: 0.8200 (m-80) cc_final: 0.7894 (m-80) REVERT: A 546 LEU cc_start: 0.8573 (tt) cc_final: 0.8202 (tt) REVERT: A 654 GLU cc_start: 0.7771 (tt0) cc_final: 0.7399 (tt0) REVERT: A 675 GLN cc_start: 0.8545 (pp30) cc_final: 0.8237 (pp30) REVERT: A 764 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8354 (ttmm) REVERT: A 814 LYS cc_start: 0.8998 (mttt) cc_final: 0.8508 (mmmt) REVERT: A 819 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7878 (mt-10) REVERT: A 823 PHE cc_start: 0.8519 (t80) cc_final: 0.8011 (t80) REVERT: A 884 SER cc_start: 0.8195 (m) cc_final: 0.7812 (t) REVERT: A 900 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7783 (mtm) REVERT: A 950 ASP cc_start: 0.8035 (t0) cc_final: 0.7691 (t0) REVERT: A 969 LYS cc_start: 0.8987 (mttt) cc_final: 0.8396 (mtpp) REVERT: A 1017 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8555 (tm-30) REVERT: A 1073 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8320 (mtpp) REVERT: A 1111 GLU cc_start: 0.8201 (mp0) cc_final: 0.7666 (pm20) REVERT: C 190 ARG cc_start: 0.2624 (mmt90) cc_final: 0.2409 (mmt90) REVERT: C 200 TYR cc_start: 0.7387 (m-80) cc_final: 0.7117 (m-80) REVERT: C 277 LEU cc_start: 0.8832 (mp) cc_final: 0.8587 (mm) REVERT: C 313 TYR cc_start: 0.7949 (m-80) cc_final: 0.7348 (m-80) REVERT: C 365 TYR cc_start: 0.7735 (m-10) cc_final: 0.7162 (m-10) REVERT: C 421 TYR cc_start: 0.6128 (m-10) cc_final: 0.5807 (m-10) REVERT: C 643 PHE cc_start: 0.8004 (t80) cc_final: 0.7653 (t80) REVERT: C 654 GLU cc_start: 0.7635 (tt0) cc_final: 0.7414 (tt0) REVERT: C 806 LEU cc_start: 0.8546 (mt) cc_final: 0.8305 (mm) REVERT: C 861 LEU cc_start: 0.8781 (mm) cc_final: 0.8537 (mt) REVERT: C 884 SER cc_start: 0.8359 (m) cc_final: 0.7824 (t) REVERT: C 896 ILE cc_start: 0.8555 (mt) cc_final: 0.8313 (tt) REVERT: C 935 GLN cc_start: 0.8473 (tp40) cc_final: 0.7999 (tm-30) REVERT: C 969 LYS cc_start: 0.9024 (mttt) cc_final: 0.8412 (mtmm) REVERT: C 975 SER cc_start: 0.8632 (p) cc_final: 0.8173 (m) REVERT: C 980 ILE cc_start: 0.8334 (mt) cc_final: 0.8094 (mm) REVERT: C 983 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7302 (tpp80) REVERT: C 990 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7019 (mt-10) REVERT: C 1045 LYS cc_start: 0.8205 (tttt) cc_final: 0.7911 (ttmm) REVERT: C 1111 GLU cc_start: 0.8445 (tt0) cc_final: 0.8142 (mt-10) REVERT: C 1129 VAL cc_start: 0.9110 (t) cc_final: 0.8805 (m) REVERT: C 1139 ASP cc_start: 0.8348 (t0) cc_final: 0.7808 (t0) REVERT: c 81 MET cc_start: 0.5482 (ttp) cc_final: 0.5214 (ttp) REVERT: B 33 THR cc_start: 0.8311 (p) cc_final: 0.7960 (t) REVERT: B 36 VAL cc_start: 0.8871 (t) cc_final: 0.8523 (m) REVERT: B 55 PHE cc_start: 0.7508 (m-80) cc_final: 0.6955 (m-10) REVERT: B 67 VAL cc_start: 0.6928 (OUTLIER) cc_final: 0.6588 (p) REVERT: B 106 PHE cc_start: 0.7033 (m-10) cc_final: 0.6643 (m-10) REVERT: B 119 ILE cc_start: 0.9086 (mm) cc_final: 0.8833 (mm) REVERT: B 125 ASN cc_start: 0.6796 (p0) cc_final: 0.5320 (t0) REVERT: B 129 LYS cc_start: 0.8884 (mttt) cc_final: 0.8522 (mmtm) REVERT: B 195 LYS cc_start: 0.4248 (tptt) cc_final: 0.3546 (tppt) REVERT: B 206 LYS cc_start: 0.7754 (tptp) cc_final: 0.7549 (tptt) REVERT: B 221 SER cc_start: 0.9077 (t) cc_final: 0.8675 (m) REVERT: B 229 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8004 (mm) REVERT: B 298 GLU cc_start: 0.8433 (tp30) cc_final: 0.7853 (tp30) REVERT: B 386 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8066 (mtmt) REVERT: B 450 ASN cc_start: 0.7167 (m-40) cc_final: 0.6884 (t0) REVERT: B 577 ARG cc_start: 0.7891 (tpp80) cc_final: 0.7480 (tpp80) REVERT: B 603 ASN cc_start: 0.8599 (p0) cc_final: 0.8095 (p0) REVERT: B 740 MET cc_start: 0.8142 (tpp) cc_final: 0.7880 (mmm) REVERT: B 748 GLU cc_start: 0.8781 (pm20) cc_final: 0.8367 (pt0) REVERT: B 751 ASN cc_start: 0.8680 (m-40) cc_final: 0.7984 (m-40) REVERT: B 755 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8325 (mp10) REVERT: B 765 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8146 (ttm170) REVERT: B 773 GLU cc_start: 0.8313 (tt0) cc_final: 0.7718 (tm-30) REVERT: B 795 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8669 (mttm) REVERT: B 869 MET cc_start: 0.8935 (mtp) cc_final: 0.8655 (mtt) REVERT: B 884 SER cc_start: 0.8519 (m) cc_final: 0.7924 (t) REVERT: B 921 LYS cc_start: 0.8691 (mttt) cc_final: 0.8474 (mmtp) REVERT: B 964 LYS cc_start: 0.8881 (pttp) cc_final: 0.8466 (ttpp) REVERT: B 969 LYS cc_start: 0.8845 (mttt) cc_final: 0.8293 (mtpt) REVERT: B 978 ASN cc_start: 0.8485 (p0) cc_final: 0.7823 (p0) REVERT: B 979 ASP cc_start: 0.8266 (m-30) cc_final: 0.7670 (m-30) REVERT: B 984 LEU cc_start: 0.7780 (mt) cc_final: 0.7272 (tp) REVERT: B 988 GLU cc_start: 0.8020 (mp0) cc_final: 0.7701 (mp0) REVERT: B 1017 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 1030 SER cc_start: 0.8955 (m) cc_final: 0.8483 (t) REVERT: B 1073 LYS cc_start: 0.8513 (tttt) cc_final: 0.8270 (mtpp) REVERT: B 1125 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7426 (p0) REVERT: a 83 LEU cc_start: 0.8326 (mt) cc_final: 0.8072 (mt) REVERT: a 84 SER cc_start: 0.6349 (OUTLIER) cc_final: 0.5913 (t) REVERT: a 142 MET cc_start: 0.6101 (mmm) cc_final: 0.4934 (ppp) REVERT: b 49 LYS cc_start: 0.7932 (mttt) cc_final: 0.7647 (mttt) REVERT: b 59 GLU cc_start: 0.7711 (tp30) cc_final: 0.7273 (tm-30) REVERT: b 75 PHE cc_start: 0.6955 (m-10) cc_final: 0.6730 (m-10) outliers start: 98 outliers final: 83 residues processed: 676 average time/residue: 0.4320 time to fit residues: 457.6558 Evaluate side-chains 697 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 609 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 349 optimal weight: 0.9990 chunk 368 optimal weight: 1.9990 chunk 336 optimal weight: 8.9990 chunk 358 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 281 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 323 optimal weight: 0.0770 chunk 338 optimal weight: 2.9990 chunk 357 optimal weight: 1.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.7239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32108 Z= 0.253 Angle : 0.631 12.068 43696 Z= 0.321 Chirality : 0.045 0.271 4935 Planarity : 0.004 0.080 5629 Dihedral : 4.498 26.860 4311 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 3.16 % Allowed : 17.16 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % 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: -0.36 (0.13), residues: 3961 helix: 0.76 (0.21), residues: 671 sheet: 0.50 (0.16), residues: 1055 loop : -0.93 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP a 36 HIS 0.012 0.001 HIS B1083 PHE 0.024 0.002 PHE C 92 TYR 0.028 0.002 TYR B 707 ARG 0.013 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 634 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8773 (m) cc_final: 0.8518 (p) REVERT: A 133 PHE cc_start: 0.7556 (m-80) cc_final: 0.7225 (m-10) REVERT: A 290 ASP cc_start: 0.7682 (t0) cc_final: 0.7464 (t0) REVERT: A 304 LYS cc_start: 0.8411 (mttt) cc_final: 0.8148 (mptt) REVERT: A 309 GLU cc_start: 0.8176 (tp30) cc_final: 0.7797 (tp30) REVERT: A 313 TYR cc_start: 0.8077 (m-80) cc_final: 0.7648 (m-80) REVERT: A 338 PHE cc_start: 0.6513 (m-80) cc_final: 0.5938 (m-80) REVERT: A 339 ASP cc_start: 0.8692 (m-30) cc_final: 0.8415 (t70) REVERT: A 386 LYS cc_start: 0.8174 (mttt) cc_final: 0.7659 (mttm) REVERT: A 537 LYS cc_start: 0.8770 (tptp) cc_final: 0.8396 (tmtt) REVERT: A 543 PHE cc_start: 0.8234 (m-80) cc_final: 0.7933 (m-80) REVERT: A 546 LEU cc_start: 0.8716 (tt) cc_final: 0.8382 (tt) REVERT: A 654 GLU cc_start: 0.7827 (tt0) cc_final: 0.7474 (tt0) REVERT: A 703 ASN cc_start: 0.8781 (t0) cc_final: 0.8538 (t0) REVERT: A 711 SER cc_start: 0.8751 (t) cc_final: 0.8096 (p) REVERT: A 764 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8388 (ttmm) REVERT: A 814 LYS cc_start: 0.8991 (mttt) cc_final: 0.8526 (mmmt) REVERT: A 823 PHE cc_start: 0.8548 (t80) cc_final: 0.8041 (t80) REVERT: A 884 SER cc_start: 0.8495 (m) cc_final: 0.8077 (t) REVERT: A 900 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7783 (mtm) REVERT: A 935 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8130 (mm-40) REVERT: A 950 ASP cc_start: 0.8089 (t0) cc_final: 0.7698 (t0) REVERT: A 969 LYS cc_start: 0.9069 (mttt) cc_final: 0.8520 (mtpp) REVERT: A 1017 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8556 (tm-30) REVERT: A 1073 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8353 (mtpp) REVERT: A 1111 GLU cc_start: 0.8271 (mp0) cc_final: 0.7531 (pm20) REVERT: C 33 THR cc_start: 0.8222 (p) cc_final: 0.7912 (p) REVERT: C 190 ARG cc_start: 0.2730 (mmt90) cc_final: 0.1975 (mmt90) REVERT: C 200 TYR cc_start: 0.7452 (m-80) cc_final: 0.7168 (m-80) REVERT: C 277 LEU cc_start: 0.8900 (mp) cc_final: 0.8604 (mm) REVERT: C 313 TYR cc_start: 0.7967 (m-80) cc_final: 0.7469 (m-80) REVERT: C 392 PHE cc_start: 0.7940 (m-80) cc_final: 0.7582 (m-80) REVERT: C 643 PHE cc_start: 0.8038 (t80) cc_final: 0.7684 (t80) REVERT: C 654 GLU cc_start: 0.7604 (tt0) cc_final: 0.7386 (tt0) REVERT: C 861 LEU cc_start: 0.8854 (mm) cc_final: 0.8616 (mt) REVERT: C 884 SER cc_start: 0.8428 (m) cc_final: 0.7888 (t) REVERT: C 886 TRP cc_start: 0.8656 (OUTLIER) cc_final: 0.8155 (p90) REVERT: C 896 ILE cc_start: 0.8603 (mt) cc_final: 0.8390 (tt) REVERT: C 935 GLN cc_start: 0.8515 (tp40) cc_final: 0.8181 (tm-30) REVERT: C 969 LYS cc_start: 0.9070 (mttt) cc_final: 0.8454 (mtmm) REVERT: C 975 SER cc_start: 0.8588 (p) cc_final: 0.8182 (m) REVERT: C 983 ARG cc_start: 0.7662 (tpp80) cc_final: 0.7256 (tpp80) REVERT: C 990 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7048 (mt-10) REVERT: C 1040 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8291 (m) REVERT: C 1041 ASP cc_start: 0.8638 (m-30) cc_final: 0.7871 (m-30) REVERT: C 1045 LYS cc_start: 0.8239 (tttt) cc_final: 0.7972 (ttmm) REVERT: C 1129 VAL cc_start: 0.9212 (t) cc_final: 0.8928 (m) REVERT: C 1139 ASP cc_start: 0.8479 (t0) cc_final: 0.7987 (t0) REVERT: c 81 MET cc_start: 0.5548 (ttp) cc_final: 0.5254 (ttp) REVERT: B 33 THR cc_start: 0.8364 (p) cc_final: 0.8105 (t) REVERT: B 36 VAL cc_start: 0.8865 (t) cc_final: 0.8539 (m) REVERT: B 55 PHE cc_start: 0.7558 (m-80) cc_final: 0.7009 (m-10) REVERT: B 67 VAL cc_start: 0.6992 (OUTLIER) cc_final: 0.6649 (p) REVERT: B 106 PHE cc_start: 0.7157 (m-10) cc_final: 0.6767 (m-10) REVERT: B 119 ILE cc_start: 0.9100 (mm) cc_final: 0.8831 (mm) REVERT: B 125 ASN cc_start: 0.6948 (p0) cc_final: 0.5378 (t0) REVERT: B 129 LYS cc_start: 0.8924 (mttt) cc_final: 0.8538 (mmtm) REVERT: B 195 LYS cc_start: 0.4526 (tptt) cc_final: 0.3761 (tppt) REVERT: B 206 LYS cc_start: 0.7767 (tptp) cc_final: 0.7554 (tptt) REVERT: B 221 SER cc_start: 0.9114 (t) cc_final: 0.8772 (m) REVERT: B 229 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8126 (mm) REVERT: B 298 GLU cc_start: 0.8484 (tp30) cc_final: 0.7887 (tp30) REVERT: B 386 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8271 (mtpt) REVERT: B 450 ASN cc_start: 0.7132 (m-40) cc_final: 0.6862 (t0) REVERT: B 603 ASN cc_start: 0.8624 (p0) cc_final: 0.8173 (p0) REVERT: B 740 MET cc_start: 0.8135 (tpp) cc_final: 0.7902 (mmm) REVERT: B 748 GLU cc_start: 0.8767 (pm20) cc_final: 0.8427 (pt0) REVERT: B 751 ASN cc_start: 0.8813 (m-40) cc_final: 0.8215 (m-40) REVERT: B 755 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8519 (mp10) REVERT: B 765 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.8113 (ttm-80) REVERT: B 773 GLU cc_start: 0.8396 (tt0) cc_final: 0.7733 (tm-30) REVERT: B 784 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8080 (tp40) REVERT: B 795 LYS cc_start: 0.8994 (mtpp) cc_final: 0.8701 (mttm) REVERT: B 918 GLU cc_start: 0.8440 (mp0) cc_final: 0.8149 (mp0) REVERT: B 921 LYS cc_start: 0.8658 (mttt) cc_final: 0.8431 (mmmm) REVERT: B 964 LYS cc_start: 0.8913 (pttp) cc_final: 0.8499 (ttpp) REVERT: B 969 LYS cc_start: 0.8890 (mttt) cc_final: 0.8362 (mtpt) REVERT: B 978 ASN cc_start: 0.8515 (p0) cc_final: 0.7856 (p0) REVERT: B 979 ASP cc_start: 0.8312 (m-30) cc_final: 0.7734 (m-30) REVERT: B 984 LEU cc_start: 0.7670 (mt) cc_final: 0.7135 (tp) REVERT: B 988 GLU cc_start: 0.8083 (mp0) cc_final: 0.7721 (mp0) REVERT: B 1017 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7778 (tm-30) REVERT: B 1030 SER cc_start: 0.8982 (m) cc_final: 0.8343 (t) REVERT: B 1073 LYS cc_start: 0.8556 (tttt) cc_final: 0.8314 (mtpp) REVERT: B 1125 ASN cc_start: 0.8135 (p0) cc_final: 0.7526 (p0) REVERT: a 83 LEU cc_start: 0.8362 (mt) cc_final: 0.8074 (mt) REVERT: a 142 MET cc_start: 0.6267 (mmm) cc_final: 0.5144 (ppp) REVERT: b 49 LYS cc_start: 0.8037 (mttt) cc_final: 0.7753 (mttt) REVERT: b 59 GLU cc_start: 0.7846 (tp30) cc_final: 0.7440 (tm-30) REVERT: b 75 PHE cc_start: 0.7036 (m-10) cc_final: 0.6742 (m-10) outliers start: 111 outliers final: 94 residues processed: 698 average time/residue: 0.4502 time to fit residues: 491.4537 Evaluate side-chains 710 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 611 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 182 TYR Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 235 optimal weight: 6.9990 chunk 378 optimal weight: 10.0000 chunk 231 optimal weight: 30.0000 chunk 179 optimal weight: 0.9980 chunk 263 optimal weight: 0.9980 chunk 397 optimal weight: 10.0000 chunk 365 optimal weight: 4.9990 chunk 316 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.7675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 32108 Z= 0.317 Angle : 0.683 11.590 43696 Z= 0.351 Chirality : 0.046 0.301 4935 Planarity : 0.005 0.077 5629 Dihedral : 4.782 28.380 4311 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.63 % Rotamer: Outliers : 2.99 % Allowed : 17.87 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % 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: -0.43 (0.13), residues: 3961 helix: 0.82 (0.21), residues: 643 sheet: 0.48 (0.16), residues: 1004 loop : -0.97 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP a 36 HIS 0.013 0.001 HIS B1083 PHE 0.055 0.002 PHE A 817 TYR 0.022 0.002 TYR B 707 ARG 0.012 0.001 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 629 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8763 (m) cc_final: 0.8542 (p) REVERT: A 133 PHE cc_start: 0.7551 (m-80) cc_final: 0.7277 (m-10) REVERT: A 290 ASP cc_start: 0.7834 (t0) cc_final: 0.7520 (t70) REVERT: A 304 LYS cc_start: 0.8481 (mttt) cc_final: 0.8245 (mptt) REVERT: A 309 GLU cc_start: 0.8199 (tp30) cc_final: 0.7950 (tp30) REVERT: A 313 TYR cc_start: 0.8113 (m-80) cc_final: 0.7666 (m-80) REVERT: A 338 PHE cc_start: 0.6636 (m-80) cc_final: 0.5905 (m-80) REVERT: A 339 ASP cc_start: 0.8788 (m-30) cc_final: 0.8529 (t70) REVERT: A 386 LYS cc_start: 0.8089 (mttt) cc_final: 0.7660 (mttm) REVERT: A 537 LYS cc_start: 0.8769 (tptp) cc_final: 0.8387 (tmtt) REVERT: A 546 LEU cc_start: 0.8773 (tt) cc_final: 0.8470 (tt) REVERT: A 654 GLU cc_start: 0.7859 (tt0) cc_final: 0.7523 (tt0) REVERT: A 703 ASN cc_start: 0.8749 (t0) cc_final: 0.8528 (t0) REVERT: A 711 SER cc_start: 0.8810 (t) cc_final: 0.8185 (p) REVERT: A 804 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7988 (tp40) REVERT: A 814 LYS cc_start: 0.9003 (mttt) cc_final: 0.8566 (mmmt) REVERT: A 823 PHE cc_start: 0.8606 (t80) cc_final: 0.8011 (t80) REVERT: A 884 SER cc_start: 0.8450 (m) cc_final: 0.8040 (t) REVERT: A 900 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7807 (mtm) REVERT: A 902 MET cc_start: 0.8080 (mmm) cc_final: 0.7284 (mmm) REVERT: A 918 GLU cc_start: 0.8112 (mp0) cc_final: 0.7703 (mp0) REVERT: A 950 ASP cc_start: 0.8050 (t0) cc_final: 0.7673 (t0) REVERT: A 969 LYS cc_start: 0.9113 (mttt) cc_final: 0.8563 (mtpp) REVERT: A 1017 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8557 (tm-30) REVERT: A 1073 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8366 (mtpp) REVERT: A 1111 GLU cc_start: 0.8291 (mp0) cc_final: 0.7533 (pm20) REVERT: C 33 THR cc_start: 0.8302 (p) cc_final: 0.7986 (p) REVERT: C 190 ARG cc_start: 0.3223 (mmt90) cc_final: 0.2438 (mmt90) REVERT: C 200 TYR cc_start: 0.7585 (m-80) cc_final: 0.7381 (m-80) REVERT: C 205 SER cc_start: 0.8753 (p) cc_final: 0.8439 (p) REVERT: C 224 GLU cc_start: 0.8263 (mp0) cc_final: 0.7941 (mp0) REVERT: C 313 TYR cc_start: 0.7962 (m-80) cc_final: 0.7466 (m-80) REVERT: C 392 PHE cc_start: 0.8130 (m-80) cc_final: 0.7856 (m-80) REVERT: C 528 LYS cc_start: 0.7530 (mmtm) cc_final: 0.7293 (mmtm) REVERT: C 562 PHE cc_start: 0.6868 (p90) cc_final: 0.6441 (p90) REVERT: C 643 PHE cc_start: 0.8171 (t80) cc_final: 0.7848 (t80) REVERT: C 654 GLU cc_start: 0.7590 (tt0) cc_final: 0.7365 (tt0) REVERT: C 755 GLN cc_start: 0.8428 (mt0) cc_final: 0.8123 (mt0) REVERT: C 775 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7616 (t0) REVERT: C 861 LEU cc_start: 0.8880 (mm) cc_final: 0.8635 (mt) REVERT: C 896 ILE cc_start: 0.8637 (mt) cc_final: 0.8374 (tt) REVERT: C 935 GLN cc_start: 0.8530 (tp40) cc_final: 0.7983 (tm-30) REVERT: C 969 LYS cc_start: 0.9102 (mttt) cc_final: 0.8463 (mtmm) REVERT: C 975 SER cc_start: 0.8439 (p) cc_final: 0.8094 (m) REVERT: C 988 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7937 (mt-10) REVERT: C 990 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7086 (mt-10) REVERT: C 1040 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8448 (m) REVERT: C 1045 LYS cc_start: 0.8260 (tttt) cc_final: 0.8034 (tppp) REVERT: C 1129 VAL cc_start: 0.9253 (t) cc_final: 0.9009 (m) REVERT: C 1139 ASP cc_start: 0.8579 (t0) cc_final: 0.8145 (t0) REVERT: c 81 MET cc_start: 0.5630 (ttp) cc_final: 0.5354 (ttp) REVERT: B 33 THR cc_start: 0.8324 (p) cc_final: 0.8040 (t) REVERT: B 36 VAL cc_start: 0.8909 (t) cc_final: 0.8599 (m) REVERT: B 55 PHE cc_start: 0.7597 (m-80) cc_final: 0.7084 (m-10) REVERT: B 106 PHE cc_start: 0.7288 (m-10) cc_final: 0.6989 (m-10) REVERT: B 119 ILE cc_start: 0.9107 (mm) cc_final: 0.8833 (mm) REVERT: B 129 LYS cc_start: 0.8862 (mttt) cc_final: 0.8553 (mmmm) REVERT: B 195 LYS cc_start: 0.4935 (tptt) cc_final: 0.4200 (tppt) REVERT: B 200 TYR cc_start: 0.6263 (OUTLIER) cc_final: 0.5249 (m-80) REVERT: B 206 LYS cc_start: 0.7803 (tptp) cc_final: 0.7539 (tptt) REVERT: B 229 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8125 (mm) REVERT: B 238 PHE cc_start: 0.7228 (p90) cc_final: 0.6857 (p90) REVERT: B 298 GLU cc_start: 0.8491 (tp30) cc_final: 0.7919 (tp30) REVERT: B 450 ASN cc_start: 0.6983 (m-40) cc_final: 0.6670 (t0) REVERT: B 603 ASN cc_start: 0.8643 (p0) cc_final: 0.8248 (p0) REVERT: B 673 SER cc_start: 0.8798 (t) cc_final: 0.8070 (p) REVERT: B 740 MET cc_start: 0.8122 (tpp) cc_final: 0.7872 (tpp) REVERT: B 751 ASN cc_start: 0.8882 (m-40) cc_final: 0.8214 (m110) REVERT: B 755 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8621 (mp10) REVERT: B 765 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.8143 (ttm-80) REVERT: B 773 GLU cc_start: 0.8417 (tt0) cc_final: 0.7782 (tm-30) REVERT: B 784 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8361 (tp40) REVERT: B 795 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8705 (mttm) REVERT: B 804 GLN cc_start: 0.8233 (mp10) cc_final: 0.7761 (mp10) REVERT: B 921 LYS cc_start: 0.8669 (mttt) cc_final: 0.8443 (mmmm) REVERT: B 964 LYS cc_start: 0.8933 (pttp) cc_final: 0.8428 (tmmt) REVERT: B 969 LYS cc_start: 0.8894 (mttt) cc_final: 0.8296 (mtpp) REVERT: B 978 ASN cc_start: 0.8503 (p0) cc_final: 0.7859 (p0) REVERT: B 979 ASP cc_start: 0.8337 (m-30) cc_final: 0.7796 (m-30) REVERT: B 984 LEU cc_start: 0.7683 (mt) cc_final: 0.7156 (tp) REVERT: B 988 GLU cc_start: 0.8103 (mp0) cc_final: 0.7700 (mp0) REVERT: B 1017 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7809 (tm-30) REVERT: B 1030 SER cc_start: 0.9011 (m) cc_final: 0.8396 (t) REVERT: B 1073 LYS cc_start: 0.8583 (tttt) cc_final: 0.8339 (mtpp) REVERT: B 1125 ASN cc_start: 0.8423 (p0) cc_final: 0.7944 (p0) REVERT: a 83 LEU cc_start: 0.8342 (mt) cc_final: 0.7921 (mt) REVERT: a 84 SER cc_start: 0.6168 (OUTLIER) cc_final: 0.5653 (t) REVERT: a 142 MET cc_start: 0.6272 (mmm) cc_final: 0.5187 (ppp) REVERT: b 49 LYS cc_start: 0.8090 (mttt) cc_final: 0.7809 (mttt) REVERT: b 59 GLU cc_start: 0.7867 (tp30) cc_final: 0.7471 (tm-30) outliers start: 105 outliers final: 90 residues processed: 689 average time/residue: 0.4509 time to fit residues: 487.2575 Evaluate side-chains 714 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 617 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 182 TYR Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 251 optimal weight: 50.0000 chunk 337 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 291 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 317 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 325 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B1083 HIS B1101 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.168181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.127575 restraints weight = 74874.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.131392 restraints weight = 37006.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.133843 restraints weight = 22365.515| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.7823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32108 Z= 0.237 Angle : 0.644 11.877 43696 Z= 0.328 Chirality : 0.045 0.272 4935 Planarity : 0.004 0.076 5629 Dihedral : 4.705 28.655 4311 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 2.57 % Allowed : 19.04 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % 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: -0.40 (0.13), residues: 3961 helix: 0.91 (0.22), residues: 634 sheet: 0.52 (0.16), residues: 970 loop : -0.96 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP a 36 HIS 0.009 0.001 HIS B1101 PHE 0.041 0.002 PHE A 817 TYR 0.020 0.001 TYR C1138 ARG 0.012 0.001 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8843.72 seconds wall clock time: 161 minutes 57.54 seconds (9717.54 seconds total)