Starting phenix.real_space_refine on Fri Dec 15 12:18:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wka_32564/12_2023/7wka_32564.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wka_32564/12_2023/7wka_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_32564/12_2023/7wka_32564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wka_32564/12_2023/7wka_32564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wka_32564/12_2023/7wka_32564.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wka_32564/12_2023/7wka_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 16.27, 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: 11.24 Conformation dependent library (CDL) restraints added in 5.9 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: 3.94 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: 14.37 Time building geometry restraints manager: 12.21 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: 3.480 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: 11.150 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 82.730 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.190 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.870 ------------------------------------------------------------------------------- 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 : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 958 average time/residue: 0.4498 time to fit residues: 669.4193 Evaluate side-chains 667 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 663 time to evaluate : 3.393 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2930 time to fit residues: 7.0064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 121 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 232 optimal weight: 20.0000 chunk 362 optimal weight: 1.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 474 GLN A 505 HIS A 519 HIS ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 787 GLN A 895 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1048 HIS A1054 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 343 ASN C 394 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 644 GLN C 717 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1106 GLN C1113 GLN c 52 HIS ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 170 GLN B 207 HIS B 239 GLN B 343 ASN B 505 HIS B 544 ASN B 717 ASN B 895 GLN B 901 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1054 GLN B1113 GLN B1119 ASN a 171 HIS a 203 ASN ** b 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 32108 Z= 0.312 Angle : 0.702 9.858 43696 Z= 0.372 Chirality : 0.047 0.298 4935 Planarity : 0.006 0.236 5629 Dihedral : 4.818 31.837 4311 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.74 % Favored : 98.16 % Rotamer: Outliers : 2.45 % Allowed : 8.87 % Favored : 88.68 % 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: -1.60 (0.11), residues: 3961 helix: -2.59 (0.15), residues: 587 sheet: 0.26 (0.15), residues: 990 loop : -1.26 (0.11), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP a 161 HIS 0.008 0.002 HIS B1064 PHE 0.028 0.002 PHE C 133 TYR 0.023 0.002 TYR B1110 ARG 0.015 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 788 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 702 time to evaluate : 3.490 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 outliers start: 86 outliers final: 47 residues processed: 750 average time/residue: 0.4526 time to fit residues: 534.0426 Evaluate side-chains 644 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 597 time to evaluate : 3.640 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3143 time to fit residues: 32.2804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 201 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 246 optimal weight: 20.0000 chunk 99 optimal weight: 0.5980 chunk 362 optimal weight: 0.0870 chunk 392 optimal weight: 3.9990 chunk 323 optimal weight: 0.9980 chunk 359 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 291 optimal weight: 6.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 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 317 ASN B 334 ASN B 439 ASN ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 907 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 203 ASN ** b 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 32108 Z= 0.219 Angle : 0.598 9.193 43696 Z= 0.308 Chirality : 0.045 0.298 4935 Planarity : 0.005 0.164 5629 Dihedral : 4.535 29.618 4311 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.65 % Rotamer: Outliers : 1.54 % Allowed : 12.91 % Favored : 85.55 % 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: -0.97 (0.12), residues: 3961 helix: -1.04 (0.19), residues: 628 sheet: 0.49 (0.15), residues: 1049 loop : -1.09 (0.12), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP a 36 HIS 0.016 0.001 HIS C 49 PHE 0.029 0.002 PHE A 497 TYR 0.020 0.001 TYR B 655 ARG 0.016 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 695 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 641 time to evaluate : 3.678 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 outliers start: 54 outliers final: 28 residues processed: 670 average time/residue: 0.4904 time to fit residues: 516.0728 Evaluate side-chains 613 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 585 time to evaluate : 3.466 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3114 time to fit residues: 21.1402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 358 optimal weight: 1.9990 chunk 272 optimal weight: 0.0040 chunk 188 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 243 optimal weight: 10.0000 chunk 364 optimal weight: 6.9990 chunk 385 optimal weight: 0.0970 chunk 190 optimal weight: 1.9990 chunk 345 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 717 ASN C 926 GLN ** C1054 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 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 907 ASN B 965 GLN B1054 GLN B1088 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 32108 Z= 0.189 Angle : 0.572 11.123 43696 Z= 0.292 Chirality : 0.044 0.257 4935 Planarity : 0.004 0.150 5629 Dihedral : 4.351 27.853 4311 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.60 % Rotamer: Outliers : 1.91 % Allowed : 13.94 % Favored : 84.15 % 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: -0.67 (0.12), residues: 3961 helix: -0.21 (0.21), residues: 632 sheet: 0.56 (0.15), residues: 1037 loop : -1.01 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP a 36 HIS 0.013 0.001 HIS C 49 PHE 0.026 0.002 PHE A 515 TYR 0.016 0.001 TYR C1138 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 696 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 629 time to evaluate : 3.620 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 outliers start: 67 outliers final: 34 residues processed: 654 average time/residue: 0.4637 time to fit residues: 476.3751 Evaluate side-chains 613 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 579 time to evaluate : 3.349 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2932 time to fit residues: 23.2234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 321 optimal weight: 0.8980 chunk 218 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 329 optimal weight: 0.9980 chunk 266 optimal weight: 0.0670 chunk 0 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 346 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 207 HIS A 474 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 907 ASN B 965 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 17 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32108 Z= 0.222 Angle : 0.584 9.486 43696 Z= 0.298 Chirality : 0.044 0.331 4935 Planarity : 0.004 0.107 5629 Dihedral : 4.369 26.894 4311 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Rotamer: Outliers : 1.82 % Allowed : 14.28 % Favored : 83.89 % 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: -0.47 (0.13), residues: 3961 helix: 0.34 (0.21), residues: 636 sheet: 0.62 (0.15), residues: 1064 loop : -0.97 (0.12), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP a 36 HIS 0.013 0.001 HIS C 49 PHE 0.035 0.002 PHE A 135 TYR 0.018 0.001 TYR A 170 ARG 0.012 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 682 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 618 time to evaluate : 3.122 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 outliers start: 64 outliers final: 40 residues processed: 654 average time/residue: 0.4522 time to fit residues: 465.8381 Evaluate side-chains 638 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 598 time to evaluate : 3.298 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3057 time to fit residues: 27.8285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 129 optimal weight: 0.9990 chunk 347 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 226 optimal weight: 40.0000 chunk 95 optimal weight: 0.7980 chunk 386 optimal weight: 6.9990 chunk 320 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 202 optimal weight: 0.0040 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN C 49 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 751 ASN B 784 GLN B 907 ASN B1113 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 32108 Z= 0.161 Angle : 0.562 10.226 43696 Z= 0.284 Chirality : 0.044 0.326 4935 Planarity : 0.004 0.111 5629 Dihedral : 4.242 26.231 4311 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.35 % Favored : 97.58 % Rotamer: Outliers : 1.23 % Allowed : 15.74 % Favored : 83.04 % 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: 0.64 (0.22), residues: 625 sheet: 0.61 (0.15), residues: 1083 loop : -0.93 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 104 HIS 0.011 0.001 HIS C 49 PHE 0.026 0.002 PHE C 192 TYR 0.025 0.001 TYR A 660 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 669 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 626 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 25 residues processed: 644 average time/residue: 0.4763 time to fit residues: 480.4496 Evaluate side-chains 631 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 606 time to evaluate : 3.383 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3366 time to fit residues: 22.1073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 372 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 chunk 218 optimal weight: 20.0000 chunk 324 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 384 optimal weight: 4.9990 chunk 240 optimal weight: 40.0000 chunk 234 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 188 ASN A 207 HIS A 474 GLN A 901 GLN A1054 GLN A1088 HIS A1113 GLN C 188 ASN C 196 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 641 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B1002 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.7461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 32108 Z= 0.564 Angle : 0.841 13.133 43696 Z= 0.443 Chirality : 0.052 0.331 4935 Planarity : 0.006 0.143 5629 Dihedral : 5.339 27.738 4311 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 2.45 % Allowed : 16.25 % Favored : 81.30 % 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: -0.95 (0.13), residues: 3961 helix: -0.01 (0.20), residues: 653 sheet: 0.31 (0.16), residues: 1016 loop : -1.29 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.003 TRP A 104 HIS 0.016 0.003 HIS B1064 PHE 0.039 0.003 PHE B 559 TYR 0.030 0.003 TYR C 269 ARG 0.014 0.001 ARG B1107 *********************** 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 748 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 662 time to evaluate : 3.337 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 outliers start: 86 outliers final: 61 residues processed: 694 average time/residue: 0.4771 time to fit residues: 517.3824 Evaluate side-chains 687 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 626 time to evaluate : 3.935 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.4083 time to fit residues: 50.2630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 229 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 chunk 190 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 302 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 207 HIS ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 HIS ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 784 GLN B 907 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.7625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32108 Z= 0.271 Angle : 0.667 12.051 43696 Z= 0.342 Chirality : 0.046 0.320 4935 Planarity : 0.005 0.118 5629 Dihedral : 4.979 34.222 4311 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 0.97 % Allowed : 18.22 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.75 (0.13), residues: 3961 helix: 0.30 (0.21), residues: 655 sheet: 0.39 (0.16), residues: 1025 loop : -1.19 (0.12), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP A 104 HIS 0.009 0.001 HIS C1083 PHE 0.035 0.002 PHE C 541 TYR 0.019 0.002 TYR A1138 ARG 0.012 0.001 ARG A 237 *********************** 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 656 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 622 time to evaluate : 3.280 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 outliers start: 34 outliers final: 26 residues processed: 637 average time/residue: 0.4785 time to fit residues: 473.7574 Evaluate side-chains 612 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 586 time to evaluate : 3.065 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3111 time to fit residues: 19.0676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 349 optimal weight: 0.7980 chunk 368 optimal weight: 0.1980 chunk 336 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 281 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 323 optimal weight: 1.9990 chunk 338 optimal weight: 2.9990 chunk 357 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1106 GLN ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** 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: 0.7059 moved from start: 0.7744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32108 Z= 0.214 Angle : 0.662 12.473 43696 Z= 0.337 Chirality : 0.046 0.311 4935 Planarity : 0.005 0.105 5629 Dihedral : 4.818 43.685 4311 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 0.88 % Allowed : 19.41 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.60 (0.13), residues: 3961 helix: 0.66 (0.21), residues: 647 sheet: 0.33 (0.16), residues: 1047 loop : -1.09 (0.12), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP A 104 HIS 0.008 0.001 HIS C1083 PHE 0.064 0.002 PHE A 194 TYR 0.025 0.001 TYR C 796 ARG 0.012 0.001 ARG A 190 *********************** 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 635 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 604 time to evaluate : 3.262 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 outliers start: 31 outliers final: 17 residues processed: 614 average time/residue: 0.4864 time to fit residues: 463.0853 Evaluate side-chains 608 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 591 time to evaluate : 3.389 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3337 time to fit residues: 15.3853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 231 optimal weight: 30.0000 chunk 179 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 397 optimal weight: 9.9990 chunk 365 optimal weight: 1.9990 chunk 316 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 194 optimal weight: 0.0020 overall best weight: 1.4794 ------------------------------------------------------------------------------- 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 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 762 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7119 moved from start: 0.8067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32108 Z= 0.308 Angle : 0.709 11.558 43696 Z= 0.364 Chirality : 0.047 0.306 4935 Planarity : 0.005 0.110 5629 Dihedral : 4.972 37.398 4311 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.54 % Favored : 95.41 % Rotamer: Outliers : 0.43 % Allowed : 20.27 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.70 (0.13), residues: 3961 helix: 0.55 (0.21), residues: 645 sheet: 0.23 (0.16), residues: 1049 loop : -1.12 (0.12), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 104 HIS 0.008 0.001 HIS A 505 PHE 0.043 0.002 PHE A 194 TYR 0.026 0.002 TYR B 904 ARG 0.014 0.001 ARG C1019 ********************** 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 615 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 600 time to evaluate : 3.364 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 outliers start: 15 outliers final: 5 residues processed: 604 average time/residue: 0.5100 time to fit residues: 479.9286 Evaluate side-chains 588 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 583 time to evaluate : 3.363 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3102 time to fit residues: 7.7051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 251 optimal weight: 10.0000 chunk 337 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 317 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 325 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 354 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.165223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.124162 restraints weight = 73456.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.127616 restraints weight = 36571.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.129833 restraints weight = 22571.952| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.8392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 32108 Z= 0.315 Angle : 0.714 12.293 43696 Z= 0.368 Chirality : 0.047 0.276 4935 Planarity : 0.005 0.092 5629 Dihedral : 5.078 34.115 4311 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 0.86 % Allowed : 20.21 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.79 (0.13), residues: 3961 helix: 0.63 (0.22), residues: 627 sheet: 0.20 (0.16), residues: 1033 loop : -1.22 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP a 36 HIS 0.008 0.001 HIS B 49 PHE 0.045 0.002 PHE A 817 TYR 0.023 0.002 TYR C 796 ARG 0.014 0.001 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8715.97 seconds wall clock time: 159 minutes 17.98 seconds (9557.98 seconds total)