Starting phenix.real_space_refine on Sat Mar 23 01:04:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcc_30635/03_2024/7dcc_30635.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcc_30635/03_2024/7dcc_30635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcc_30635/03_2024/7dcc_30635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcc_30635/03_2024/7dcc_30635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcc_30635/03_2024/7dcc_30635.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcc_30635/03_2024/7dcc_30635.pdb" } resolution = 4.3 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= 0.006 sd= 0.087 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 156 5.16 5 C 22230 2.51 5 N 5844 2.21 5 O 6789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "I ARG 357": "NH1" <-> "NH2" Residue "I PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 357": "NH1" <-> "NH2" Residue "K PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35019 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1691 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 204} Chain: "B" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1691 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 204} Chain: "D" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1691 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 204} Chain: "E" Number of atoms: 8310 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8304 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1061, 8304 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 6 bond proxies already assigned to first conformer: 8487 Chain: "F" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1672 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "H" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1672 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "I" Number of atoms: 8310 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8304 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1061, 8304 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 6 bond proxies already assigned to first conformer: 8487 Chain: "K" Number of atoms: 8310 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8304 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1061, 8304 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 6 bond proxies already assigned to first conformer: 8487 Chain: "M" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1672 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Time building chain proxies: 28.83, per 1000 atoms: 0.82 Number of scatterers: 35019 At special positions: 0 Unit cell: (185.64, 178.5, 201.96, 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 156 16.00 O 6789 8.00 N 5844 7.00 C 22230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 166 " distance=2.03 Simple disulfide: pdb=" SG CYS I 291 " - pdb=" SG CYS I 301 " distance=2.03 Simple disulfide: pdb=" SG CYS I 379 " - pdb=" SG CYS I 432 " distance=2.03 Simple disulfide: pdb=" SG CYS I 480 " - pdb=" SG CYS I 488 " distance=2.03 Simple disulfide: pdb=" SG CYS I 538 " - pdb=" SG CYS I 590 " distance=2.03 Simple disulfide: pdb=" SG CYS I 617 " - pdb=" SG CYS I 649 " distance=2.03 Simple disulfide: pdb=" SG CYS I 662 " - pdb=" SG CYS I 671 " distance=2.03 Simple disulfide: pdb=" SG CYS I 738 " - pdb=" SG CYS I 760 " distance=2.03 Simple disulfide: pdb=" SG CYS I 743 " - pdb=" SG CYS I 749 " distance=2.03 Simple disulfide: pdb=" SG CYS I1032 " - pdb=" SG CYS I1043 " distance=2.03 Simple disulfide: pdb=" SG CYS I1082 " - pdb=" SG CYS I1126 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.03 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.03 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.03 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.03 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 488 " distance=2.03 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.03 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.03 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.03 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.03 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.03 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.03 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " 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: 11.59 Conformation dependent library (CDL) restraints added in 10.2 seconds 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8400 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 94 sheets defined 16.5% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.515A pdb=" N ASP A 89 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 90' Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.709A pdb=" N THR B 90 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.501A pdb=" N ASP D 89 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 90 " --> pdb=" O SER D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 90' Processing helix chain 'E' and resid 297 through 304 removed outlier: 3.667A pdb=" N CYS E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR E 302 " --> pdb=" O GLU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.922A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.677A pdb=" N TYR E 505 " --> pdb=" O GLY E 502 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN E 506 " --> pdb=" O VAL E 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 502 through 506' Processing helix chain 'E' and resid 746 through 754 removed outlier: 4.124A pdb=" N SER E 750 " --> pdb=" O SER E 746 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN E 751 " --> pdb=" O THR E 747 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E 752 " --> pdb=" O GLU E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 780 removed outlier: 3.529A pdb=" N ILE E 770 " --> pdb=" O ALA E 766 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 removed outlier: 3.585A pdb=" N LEU E 821 " --> pdb=" O PHE E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 884 removed outlier: 3.533A pdb=" N ALA E 879 " --> pdb=" O SER E 875 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 908 removed outlier: 4.001A pdb=" N MET E 902 " --> pdb=" O PHE E 898 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA E 903 " --> pdb=" O ALA E 899 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR E 904 " --> pdb=" O MET E 900 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN E 907 " --> pdb=" O ALA E 903 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY E 908 " --> pdb=" O TYR E 904 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 919 removed outlier: 4.164A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 939 removed outlier: 3.502A pdb=" N ASN E 928 " --> pdb=" O ALA E 924 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER E 929 " --> pdb=" O ASN E 925 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 931 " --> pdb=" O PHE E 927 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY E 932 " --> pdb=" O ASN E 928 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS E 933 " --> pdb=" O SER E 929 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE E 934 " --> pdb=" O ALA E 930 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 954 removed outlier: 4.029A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 955 through 965 removed outlier: 3.626A pdb=" N VAL E 963 " --> pdb=" O LEU E 959 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS E 964 " --> pdb=" O ASN E 960 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 965 " --> pdb=" O THR E 961 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.639A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 981 " --> pdb=" O LEU E 977 " (cutoff:3.500A) Processing helix chain 'E' and resid 988 through 1032 removed outlier: 4.175A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP E 994 " --> pdb=" O GLU E 990 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR E1009 " --> pdb=" O GLN E1005 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1147 removed outlier: 3.551A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.539A pdb=" N ASP F 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 83' Processing helix chain 'F' and resid 121 through 128 removed outlier: 3.956A pdb=" N LEU F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR F 126 " --> pdb=" O SER F 122 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 187 removed outlier: 3.548A pdb=" N TYR F 186 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 187 " --> pdb=" O LYS F 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 182 through 187' Processing helix chain 'H' and resid 121 through 128 removed outlier: 3.980A pdb=" N LEU H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR H 126 " --> pdb=" O SER H 122 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 304 removed outlier: 3.923A pdb=" N THR I 299 " --> pdb=" O PRO I 295 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS I 300 " --> pdb=" O LEU I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 343 Processing helix chain 'I' and resid 365 through 370 removed outlier: 3.515A pdb=" N ASN I 370 " --> pdb=" O SER I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 737 through 743 removed outlier: 3.530A pdb=" N TYR I 741 " --> pdb=" O ASP I 737 " (cutoff:3.500A) Processing helix chain 'I' and resid 753 through 757 removed outlier: 3.587A pdb=" N GLY I 757 " --> pdb=" O LEU I 754 " (cutoff:3.500A) Processing helix chain 'I' and resid 758 through 782 removed outlier: 3.564A pdb=" N ALA I 771 " --> pdb=" O LEU I 767 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP I 775 " --> pdb=" O ALA I 771 " (cutoff:3.500A) Processing helix chain 'I' and resid 816 through 824 removed outlier: 3.656A pdb=" N LEU I 821 " --> pdb=" O PHE I 817 " (cutoff:3.500A) Processing helix chain 'I' and resid 866 through 882 removed outlier: 3.692A pdb=" N ILE I 882 " --> pdb=" O LEU I 878 " (cutoff:3.500A) Processing helix chain 'I' and resid 897 through 908 removed outlier: 4.028A pdb=" N ALA I 903 " --> pdb=" O ALA I 899 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE I 906 " --> pdb=" O MET I 902 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN I 907 " --> pdb=" O ALA I 903 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY I 908 " --> pdb=" O TYR I 904 " (cutoff:3.500A) Processing helix chain 'I' and resid 913 through 919 removed outlier: 4.312A pdb=" N TYR I 917 " --> pdb=" O GLN I 913 " (cutoff:3.500A) Processing helix chain 'I' and resid 919 through 941 removed outlier: 3.554A pdb=" N GLN I 926 " --> pdb=" O LEU I 922 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN I 928 " --> pdb=" O ALA I 924 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER I 929 " --> pdb=" O ASN I 925 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE I 931 " --> pdb=" O PHE I 927 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY I 932 " --> pdb=" O ASN I 928 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE I 934 " --> pdb=" O ALA I 930 " (cutoff:3.500A) Processing helix chain 'I' and resid 945 through 965 removed outlier: 4.073A pdb=" N VAL I 951 " --> pdb=" O LYS I 947 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA I 958 " --> pdb=" O GLN I 954 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR I 961 " --> pdb=" O GLN I 957 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL I 963 " --> pdb=" O LEU I 959 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS I 964 " --> pdb=" O ASN I 960 " (cutoff:3.500A) Processing helix chain 'I' and resid 966 through 968 No H-bonds generated for 'chain 'I' and resid 966 through 968' Processing helix chain 'I' and resid 976 through 984 removed outlier: 3.800A pdb=" N ILE I 980 " --> pdb=" O VAL I 976 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU I 981 " --> pdb=" O LEU I 977 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER I 982 " --> pdb=" O ASN I 978 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 1032 removed outlier: 4.076A pdb=" N GLU I 990 " --> pdb=" O PRO I 986 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL I 991 " --> pdb=" O PRO I 987 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN I 992 " --> pdb=" O GLU I 988 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR I1027 " --> pdb=" O ASN I1023 " (cutoff:3.500A) Processing helix chain 'I' and resid 1140 through 1147 removed outlier: 3.834A pdb=" N GLU I1144 " --> pdb=" O PRO I1140 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 304 removed outlier: 3.893A pdb=" N THR K 299 " --> pdb=" O PRO K 295 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS K 300 " --> pdb=" O LEU K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 343 Processing helix chain 'K' and resid 365 through 370 removed outlier: 3.612A pdb=" N TYR K 369 " --> pdb=" O TYR K 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 389 removed outlier: 3.665A pdb=" N ASN K 388 " --> pdb=" O PRO K 384 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP K 389 " --> pdb=" O THR K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 410 removed outlier: 3.538A pdb=" N GLN K 409 " --> pdb=" O GLU K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 415 through 420 removed outlier: 3.996A pdb=" N ALA K 419 " --> pdb=" O THR K 415 " (cutoff:3.500A) Processing helix chain 'K' and resid 737 through 743 removed outlier: 3.616A pdb=" N TYR K 741 " --> pdb=" O ASP K 737 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE K 742 " --> pdb=" O CYS K 738 " (cutoff:3.500A) Processing helix chain 'K' and resid 747 through 752 removed outlier: 3.740A pdb=" N ASN K 751 " --> pdb=" O THR K 747 " (cutoff:3.500A) Processing helix chain 'K' and resid 753 through 757 removed outlier: 3.596A pdb=" N GLY K 757 " --> pdb=" O LEU K 754 " (cutoff:3.500A) Processing helix chain 'K' and resid 758 through 780 removed outlier: 3.523A pdb=" N ALA K 771 " --> pdb=" O LEU K 767 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR K 778 " --> pdb=" O GLN K 774 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN K 779 " --> pdb=" O ASP K 775 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 824 removed outlier: 3.605A pdb=" N LEU K 821 " --> pdb=" O PHE K 817 " (cutoff:3.500A) Processing helix chain 'K' and resid 866 through 884 removed outlier: 3.697A pdb=" N ALA K 879 " --> pdb=" O SER K 875 " (cutoff:3.500A) Processing helix chain 'K' and resid 886 through 891 removed outlier: 3.993A pdb=" N ALA K 890 " --> pdb=" O TRP K 886 " (cutoff:3.500A) Processing helix chain 'K' and resid 897 through 908 removed outlier: 3.835A pdb=" N MET K 902 " --> pdb=" O PHE K 898 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA K 903 " --> pdb=" O ALA K 899 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR K 904 " --> pdb=" O MET K 900 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG K 905 " --> pdb=" O GLN K 901 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN K 907 " --> pdb=" O ALA K 903 " (cutoff:3.500A) Processing helix chain 'K' and resid 913 through 919 removed outlier: 3.862A pdb=" N TYR K 917 " --> pdb=" O GLN K 913 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 941 removed outlier: 4.019A pdb=" N ALA K 924 " --> pdb=" O GLN K 920 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN K 928 " --> pdb=" O ALA K 924 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER K 929 " --> pdb=" O ASN K 925 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY K 932 " --> pdb=" O ASN K 928 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS K 933 " --> pdb=" O SER K 929 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE K 934 " --> pdb=" O ALA K 930 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER K 940 " --> pdb=" O ASP K 936 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR K 941 " --> pdb=" O SER K 937 " (cutoff:3.500A) Processing helix chain 'K' and resid 945 through 965 removed outlier: 4.126A pdb=" N VAL K 951 " --> pdb=" O LYS K 947 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN K 957 " --> pdb=" O ASN K 953 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA K 958 " --> pdb=" O GLN K 954 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN K 960 " --> pdb=" O ALA K 956 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR K 961 " --> pdb=" O GLN K 957 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU K 962 " --> pdb=" O ALA K 958 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL K 963 " --> pdb=" O LEU K 959 " (cutoff:3.500A) Processing helix chain 'K' and resid 966 through 968 No H-bonds generated for 'chain 'K' and resid 966 through 968' Processing helix chain 'K' and resid 976 through 982 removed outlier: 3.626A pdb=" N ILE K 980 " --> pdb=" O VAL K 976 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU K 981 " --> pdb=" O LEU K 977 " (cutoff:3.500A) Processing helix chain 'K' and resid 988 through 1032 removed outlier: 4.464A pdb=" N GLN K 992 " --> pdb=" O GLU K 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER K1003 " --> pdb=" O GLY K 999 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA K1015 " --> pdb=" O GLN K1011 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU K1017 " --> pdb=" O ILE K1013 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE K1018 " --> pdb=" O ARG K1014 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER K1030 " --> pdb=" O ALA K1026 " (cutoff:3.500A) Processing helix chain 'K' and resid 1116 through 1118 No H-bonds generated for 'chain 'K' and resid 1116 through 1118' Processing helix chain 'K' and resid 1140 through 1147 removed outlier: 4.070A pdb=" N GLU K1144 " --> pdb=" O PRO K1140 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU K1145 " --> pdb=" O LEU K1141 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER K1147 " --> pdb=" O PRO K1143 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 removed outlier: 3.885A pdb=" N LEU M 125 " --> pdb=" O SER M 121 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR M 126 " --> pdb=" O SER M 122 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 188 removed outlier: 3.807A pdb=" N GLU M 187 " --> pdb=" O LYS M 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG M 188 " --> pdb=" O ASP M 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 183 through 188' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.529A pdb=" N GLN A 3 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 47 removed outlier: 3.903A pdb=" N LYS A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 46 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 33 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 98 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 96 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 97 " --> pdb=" O TYR A 108 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 108 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 99 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 106 " --> pdb=" O TYR A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 47 removed outlier: 3.903A pdb=" N LYS A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 46 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 33 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 98 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 96 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 70 removed outlier: 3.628A pdb=" N THR A 70 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 79 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 126 through 130 removed outlier: 3.585A pdb=" N SER A 126 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 149 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 147 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 130 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 145 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 146 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 186 " --> pdb=" O HIS A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 126 through 130 removed outlier: 3.585A pdb=" N SER A 126 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 149 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 147 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 130 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 145 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 157 through 160 removed outlier: 3.835A pdb=" N CYS A 201 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 214 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 7 removed outlier: 4.272A pdb=" N GLN B 5 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 23 " --> pdb=" O GLN B 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 34 through 40 removed outlier: 7.192A pdb=" N TRP B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR B 50 " --> pdb=" O TRP B 34 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS B 44 " --> pdb=" O PHE B 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AB2, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.902A pdb=" N TYR B 93 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR B 113 " --> pdb=" O TYR B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 101 removed outlier: 3.525A pdb=" N TYR B 99 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 106 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 126 through 128 removed outlier: 3.759A pdb=" N SER B 126 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 149 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 187 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B 181 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER B 186 " --> pdb=" O HIS B 170 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS B 170 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 157 through 160 removed outlier: 4.048A pdb=" N CYS B 201 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS B 214 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 203 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.557A pdb=" N LEU D 20 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.557A pdb=" N LEU D 20 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 51 removed outlier: 3.677A pdb=" N LYS D 44 " --> pdb=" O PHE D 40 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA D 96 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 92 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR D 93 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR D 113 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AC1, first strand: chain 'D' and resid 126 through 130 removed outlier: 3.790A pdb=" N SER D 126 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 130 " --> pdb=" O GLY D 145 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 145 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 189 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 144 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 185 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL D 148 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER D 186 " --> pdb=" O HIS D 170 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS D 170 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 157 through 160 removed outlier: 3.863A pdb=" N CYS D 201 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 214 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 203 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 30 removed outlier: 3.606A pdb=" N THR E 29 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 42 through 43 removed outlier: 5.489A pdb=" N PHE E 43 " --> pdb=" O ARG K 567 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU K 585 " --> pdb=" O VAL K 576 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY K 550 " --> pdb=" O VAL K 539 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL K 539 " --> pdb=" O GLY K 550 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN K 542 " --> pdb=" O ILE K 326 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 48 through 55 removed outlier: 3.772A pdb=" N HIS E 49 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU E 277 " --> pdb=" O HIS E 49 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR E 51 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE E 275 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP E 53 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 65 through 66 removed outlier: 3.744A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR E 265 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA E 264 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR E 95 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 65 through 66 removed outlier: 3.744A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR E 265 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA E 264 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR E 95 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 90 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE E 194 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL E 193 " --> pdb=" O TYR E 204 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR E 204 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS E 195 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS E 202 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE E 197 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.577A pdb=" N ARG E 237 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY E 107 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE E 119 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 141 through 142 removed outlier: 6.972A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 311 through 319 removed outlier: 6.243A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS E 649 " --> pdb=" O TYR E 612 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 325 through 326 removed outlier: 3.752A pdb=" N ASN E 542 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 539 " --> pdb=" O GLY E 550 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR E 553 " --> pdb=" O ASP E 586 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP E 586 " --> pdb=" O THR E 553 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE E 565 " --> pdb=" O PHE I 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 356 through 358 removed outlier: 4.328A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 356 through 358 removed outlier: 4.328A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.831A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.684A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR E 695 " --> pdb=" O CYS E 671 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.684A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER E 691 " --> pdb=" O GLN E 675 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN E 675 " --> pdb=" O SER E 691 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 701 through 704 removed outlier: 5.395A pdb=" N ALA E 701 " --> pdb=" O ILE I 788 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS I 790 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN E 703 " --> pdb=" O LYS I 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 711 through 714 removed outlier: 3.667A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 718 through 728 removed outlier: 3.567A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 718 through 728 removed outlier: 3.917A pdb=" N ALA E1056 " --> pdb=" O GLY E1059 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'E' and resid 787 through 790 removed outlier: 3.809A pdb=" N LYS E 790 " --> pdb=" O ASN K 703 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 1120 through 1122 removed outlier: 3.896A pdb=" N ILE E1081 " --> pdb=" O HIS E1088 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=AE8, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.545A pdb=" N LYS F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN F 37 " --> pdb=" O LYS F 45 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 48 through 49 removed outlier: 3.657A pdb=" N TYR F 49 " --> pdb=" O THR F 53 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 85 through 86 Processing sheet with id=AF2, first strand: chain 'F' and resid 114 through 118 removed outlier: 3.975A pdb=" N ASN F 137 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER F 116 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE F 135 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE F 118 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL F 133 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA F 130 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F 136 " --> pdb=" O MET F 175 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 146 through 150 removed outlier: 3.813A pdb=" N LYS F 147 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR F 192 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE F 209 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS F 194 " --> pdb=" O LYS F 207 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS F 207 " --> pdb=" O CYS F 194 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.586A pdb=" N THR H 102 " --> pdb=" O TYR H 86 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 22 through 24 removed outlier: 3.518A pdb=" N CYS H 23 " --> pdb=" O PHE H 71 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR H 72 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER H 65 " --> pdb=" O THR H 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.722A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.643A pdb=" N THR H 114 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN H 137 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER H 116 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU H 136 " --> pdb=" O MET H 175 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER H 176 " --> pdb=" O SER H 162 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.643A pdb=" N THR H 114 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN H 137 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER H 116 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA H 130 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU H 179 " --> pdb=" O VAL H 132 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 153 through 155 removed outlier: 3.716A pdb=" N ARG H 155 " --> pdb=" O TRP H 148 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP H 148 " --> pdb=" O ARG H 155 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS H 147 " --> pdb=" O GLU H 195 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU H 195 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS H 194 " --> pdb=" O LYS H 207 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS H 207 " --> pdb=" O CYS H 194 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 28 through 30 removed outlier: 3.999A pdb=" N VAL I 267 " --> pdb=" O THR I 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA I 264 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS I 187 " --> pdb=" O ILE I 210 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR I 208 " --> pdb=" O LEU I 189 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 50 through 55 removed outlier: 4.032A pdb=" N THR I 51 " --> pdb=" O PHE I 275 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE I 275 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP I 53 " --> pdb=" O ARG I 273 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL I 289 " --> pdb=" O LEU I 276 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 84 through 85 removed outlier: 4.167A pdb=" N LEU I 84 " --> pdb=" O PHE I 238 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE I 238 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY I 103 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG I 102 " --> pdb=" O ASN I 121 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN I 121 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE I 119 " --> pdb=" O TRP I 104 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS I 131 " --> pdb=" O SER I 116 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL I 127 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE I 168 " --> pdb=" O VAL I 130 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 135 through 143 removed outlier: 6.905A pdb=" N ASP I 138 " --> pdb=" O VAL I 159 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL I 159 " --> pdb=" O ASP I 138 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE I 140 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE I 157 " --> pdb=" O PHE I 140 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY I 142 " --> pdb=" O SER I 155 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 193 through 197 removed outlier: 3.756A pdb=" N VAL I 193 " --> pdb=" O TYR I 204 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR I 204 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS I 195 " --> pdb=" O LYS I 202 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS I 202 " --> pdb=" O LYS I 195 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE I 201 " --> pdb=" O ASP I 228 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP I 228 " --> pdb=" O PHE I 201 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE I 203 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 311 through 318 removed outlier: 6.012A pdb=" N ILE I 312 " --> pdb=" O THR I 599 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N THR I 599 " --> pdb=" O ILE I 312 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN I 314 " --> pdb=" O VAL I 597 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL I 597 " --> pdb=" O GLN I 314 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY I 594 " --> pdb=" O GLN I 613 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 356 through 358 removed outlier: 4.004A pdb=" N ASN I 394 " --> pdb=" O GLU I 516 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU I 516 " --> pdb=" O ASN I 394 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 356 through 358 removed outlier: 4.004A pdb=" N ASN I 394 " --> pdb=" O GLU I 516 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU I 516 " --> pdb=" O ASN I 394 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 452 through 454 Processing sheet with id=AH1, first strand: chain 'I' and resid 473 through 474 removed outlier: 3.659A pdb=" N TYR I 473 " --> pdb=" O TYR I 489 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR I 489 " --> pdb=" O TYR I 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'I' and resid 538 through 542 removed outlier: 3.907A pdb=" N GLY I 548 " --> pdb=" O PHE I 541 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR I 553 " --> pdb=" O ASP I 586 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 565 through 566 removed outlier: 7.211A pdb=" N PHE I 565 " --> pdb=" O PHE K 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'I' and resid 654 through 655 removed outlier: 5.786A pdb=" N GLU I 654 " --> pdb=" O ALA I 694 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR I 696 " --> pdb=" O GLU I 654 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN I 675 " --> pdb=" O SER I 691 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER I 673 " --> pdb=" O ILE I 693 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE I 670 " --> pdb=" O ILE I 666 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 701 through 703 removed outlier: 5.698A pdb=" N ALA I 701 " --> pdb=" O ILE K 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'I' and resid 711 through 714 removed outlier: 3.747A pdb=" N LYS I1073 " --> pdb=" O ILE I 714 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE I1095 " --> pdb=" O ALA I1078 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 718 through 728 removed outlier: 3.799A pdb=" N SER I 721 " --> pdb=" O THR I1066 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU I1063 " --> pdb=" O SER I1051 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER I1051 " --> pdb=" O LEU I1063 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL I1065 " --> pdb=" O LEU I1049 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR I1047 " --> pdb=" O TYR I1067 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 718 through 728 removed outlier: 3.799A pdb=" N SER I 721 " --> pdb=" O THR I1066 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA I1056 " --> pdb=" O GLY I1059 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 733 through 736 removed outlier: 4.308A pdb=" N LYS I 733 " --> pdb=" O LEU I 861 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 1081 through 1082 removed outlier: 3.644A pdb=" N ILE I1081 " --> pdb=" O HIS I1088 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA I1087 " --> pdb=" O SER I1123 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 28 through 30 removed outlier: 7.337A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL K 267 " --> pdb=" O THR K 63 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 28 through 30 removed outlier: 7.337A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL K 267 " --> pdb=" O THR K 63 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA K 264 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR K 95 " --> pdb=" O ALA K 264 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR K 266 " --> pdb=" O ALA K 93 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL K 90 " --> pdb=" O PHE K 194 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE K 194 " --> pdb=" O VAL K 90 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 48 through 55 removed outlier: 3.721A pdb=" N HIS K 49 " --> pdb=" O LEU K 277 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE K 275 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP K 53 " --> pdb=" O ARG K 273 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR K 274 " --> pdb=" O ASP K 290 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASP K 290 " --> pdb=" O THR K 274 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU K 276 " --> pdb=" O ALA K 288 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA K 288 " --> pdb=" O LEU K 276 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LYS K 278 " --> pdb=" O THR K 286 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 84 through 85 removed outlier: 4.081A pdb=" N LEU K 84 " --> pdb=" O PHE K 238 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE K 238 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY K 107 " --> pdb=" O ARG K 237 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS K 131 " --> pdb=" O SER K 116 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE K 168 " --> pdb=" O VAL K 130 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 158 through 160 removed outlier: 3.668A pdb=" N ARG K 158 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE K 140 " --> pdb=" O ARG K 158 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N TYR K 160 " --> pdb=" O ASP K 138 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N ASP K 138 " --> pdb=" O TYR K 160 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N LEU K 242 " --> pdb=" O ASN K 137 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU K 244 " --> pdb=" O PRO K 139 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU K 141 " --> pdb=" O LEU K 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'K' and resid 196 through 197 removed outlier: 3.686A pdb=" N ILE K 197 " --> pdb=" O TYR K 200 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 311 through 318 removed outlier: 6.264A pdb=" N ILE K 312 " --> pdb=" O THR K 599 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR K 599 " --> pdb=" O ILE K 312 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN K 314 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL K 597 " --> pdb=" O GLN K 314 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER K 316 " --> pdb=" O VAL K 595 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR K 612 " --> pdb=" O CYS K 649 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS K 649 " --> pdb=" O TYR K 612 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 356 through 358 removed outlier: 3.586A pdb=" N LYS K 356 " --> pdb=" O ALA K 397 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL K 395 " --> pdb=" O ILE K 358 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN K 394 " --> pdb=" O GLU K 516 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU K 516 " --> pdb=" O ASN K 394 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE K 402 " --> pdb=" O TYR K 508 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG K 509 " --> pdb=" O TRP K 436 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TRP K 436 " --> pdb=" O ARG K 509 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AJ2, first strand: chain 'K' and resid 473 through 474 removed outlier: 3.960A pdb=" N TYR K 473 " --> pdb=" O TYR K 489 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR K 489 " --> pdb=" O TYR K 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'K' and resid 654 through 655 removed outlier: 5.766A pdb=" N GLU K 654 " --> pdb=" O ALA K 694 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR K 696 " --> pdb=" O GLU K 654 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN K 675 " --> pdb=" O SER K 691 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER K 673 " --> pdb=" O ILE K 693 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'K' and resid 712 through 714 Processing sheet with id=AJ5, first strand: chain 'K' and resid 718 through 728 removed outlier: 3.513A pdb=" N VAL K1068 " --> pdb=" O THR K 719 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA K1056 " --> pdb=" O GLY K1059 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET K1050 " --> pdb=" O VAL K1065 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'K' and resid 734 through 736 Processing sheet with id=AJ7, first strand: chain 'K' and resid 1120 through 1122 removed outlier: 3.858A pdb=" N ILE K1081 " --> pdb=" O HIS K1088 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'K' and resid 1094 through 1097 Processing sheet with id=AJ9, first strand: chain 'M' and resid 4 through 6 removed outlier: 3.667A pdb=" N LYS M 24 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE M 21 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'M' and resid 10 through 13 Processing sheet with id=AK2, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.708A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'M' and resid 116 through 118 removed outlier: 3.645A pdb=" N VAL M 133 " --> pdb=" O PHE M 118 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'M' and resid 153 through 154 removed outlier: 3.641A pdb=" N ASN M 145 " --> pdb=" O THR M 197 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS M 194 " --> pdb=" O LYS M 207 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS M 207 " --> pdb=" O CYS M 194 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA M 196 " --> pdb=" O ILE M 205 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE M 205 " --> pdb=" O ALA M 196 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2514 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.66 Time building geometry restraints manager: 12.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 11272 1.35 - 1.47: 8892 1.47 - 1.59: 15491 1.59 - 1.70: 0 1.70 - 1.82: 201 Bond restraints: 35856 Sorted by residual: bond pdb=" C GLY E 526 " pdb=" N PRO E 527 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.60e+00 bond pdb=" CA GLN K1142 " pdb=" C GLN K1142 " ideal model delta sigma weight residual 1.521 1.537 -0.016 1.14e-02 7.69e+03 2.01e+00 bond pdb=" C GLN I1142 " pdb=" N PRO I1143 " ideal model delta sigma weight residual 1.337 1.354 -0.017 1.24e-02 6.50e+03 1.78e+00 bond pdb=" C GLN K1142 " pdb=" N PRO K1143 " ideal model delta sigma weight residual 1.337 1.353 -0.016 1.24e-02 6.50e+03 1.62e+00 bond pdb=" C GLN E1142 " pdb=" N PRO E1143 " ideal model delta sigma weight residual 1.336 1.352 -0.016 1.25e-02 6.40e+03 1.61e+00 ... (remaining 35851 not shown) Histogram of bond angle deviations from ideal: 100.72 - 107.56: 1341 107.56 - 114.41: 20606 114.41 - 121.25: 16357 121.25 - 128.10: 10313 128.10 - 134.94: 199 Bond angle restraints: 48816 Sorted by residual: angle pdb=" C LYS I 150 " pdb=" N SER I 151 " pdb=" CA SER I 151 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 angle pdb=" N GLY E 526 " pdb=" CA GLY E 526 " pdb=" C GLY E 526 " ideal model delta sigma weight residual 112.34 120.13 -7.79 2.04e+00 2.40e-01 1.46e+01 angle pdb=" C TYR F 94 " pdb=" N PRO F 95 " pdb=" CA PRO F 95 " ideal model delta sigma weight residual 127.00 134.94 -7.94 2.40e+00 1.74e-01 1.09e+01 angle pdb=" N THR I 333 " pdb=" CA THR I 333 " pdb=" C THR I 333 " ideal model delta sigma weight residual 113.02 116.83 -3.81 1.20e+00 6.94e-01 1.01e+01 angle pdb=" C TRP M 50 " pdb=" N ALA M 51 " pdb=" CA ALA M 51 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.54e+00 ... (remaining 48811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 20760 17.15 - 34.31: 504 34.31 - 51.46: 85 51.46 - 68.62: 7 68.62 - 85.77: 1 Dihedral angle restraints: 21357 sinusoidal: 8277 harmonic: 13080 Sorted by residual: dihedral pdb=" CB CYS K1032 " pdb=" SG CYS K1032 " pdb=" SG CYS K1043 " pdb=" CB CYS K1043 " ideal model delta sinusoidal sigma weight residual 93.00 136.15 -43.15 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CB CYS E1032 " pdb=" SG CYS E1032 " pdb=" SG CYS E1043 " pdb=" CB CYS E1043 " ideal model delta sinusoidal sigma weight residual 93.00 134.63 -41.63 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 128.20 -35.20 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 21354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3778 0.036 - 0.071: 1103 0.071 - 0.107: 478 0.107 - 0.143: 139 0.143 - 0.179: 4 Chirality restraints: 5502 Sorted by residual: chirality pdb=" CA THR I 333 " pdb=" N THR I 333 " pdb=" C THR I 333 " pdb=" CB THR I 333 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA ILE I 332 " pdb=" N ILE I 332 " pdb=" C ILE I 332 " pdb=" CB ILE I 332 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA GLN I1142 " pdb=" N GLN I1142 " pdb=" C GLN I1142 " pdb=" CB GLN I1142 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01 ... (remaining 5499 not shown) Planarity restraints: 6303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO I 986 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO I 987 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO I 987 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 987 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY I 526 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO I 527 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO I 527 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 527 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 986 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO K 987 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO K 987 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 987 " -0.038 5.00e-02 4.00e+02 ... (remaining 6300 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 9210 2.80 - 3.33: 26076 3.33 - 3.85: 56342 3.85 - 4.38: 61466 4.38 - 4.90: 109522 Nonbonded interactions: 262616 Sorted by model distance: nonbonded pdb=" O THR I 333 " pdb=" CB ASN I 334 " model vdw 2.279 3.440 nonbonded pdb=" O GLN K 957 " pdb=" OG1 THR K 961 " model vdw 2.312 2.440 nonbonded pdb=" O GLY K 880 " pdb=" OG SER K 884 " model vdw 2.320 2.440 nonbonded pdb=" O ASN K 439 " pdb=" OG SER K 443 " model vdw 2.326 2.440 nonbonded pdb=" O ASN I 439 " pdb=" OG SER I 443 " model vdw 2.329 2.440 ... (remaining 262611 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 'D' } ncs_group { reference = (chain 'E' and (resid 14 through 492 or resid 494 through 1147)) selection = (chain 'I' and (resid 14 through 492 or resid 494 through 1147)) selection = (chain 'K' and (resid 14 through 492 or resid 494 through 1147)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } 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=0.50 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: 5.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 23.530 Check model and map are aligned: 0.460 Set scattering table: 0.300 Process input model: 103.640 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.230 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 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 : 0.002 0.045 35856 Z= 0.135 Angle : 0.481 7.940 48816 Z= 0.283 Chirality : 0.042 0.179 5502 Planarity : 0.005 0.073 6303 Dihedral : 7.377 85.773 12810 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.26 % Favored : 97.70 % Rotamer: Outliers : 1.39 % Allowed : 3.04 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % 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: -4.06 (0.10), residues: 4434 helix: -4.75 (0.05), residues: 606 sheet: -1.89 (0.15), residues: 1004 loop : -2.65 (0.09), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 64 HIS 0.002 0.000 HIS E1064 PHE 0.014 0.001 PHE K 329 TYR 0.011 0.001 TYR B 104 ARG 0.002 0.000 ARG I 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 898 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.2841 (tt) cc_final: 0.2588 (tt) REVERT: A 141 MET cc_start: -0.2496 (mtm) cc_final: -0.3212 (ptm) REVERT: A 180 LEU cc_start: -0.2640 (OUTLIER) cc_final: -0.3115 (mm) REVERT: B 172 PHE cc_start: 0.2413 (m-10) cc_final: 0.1952 (m-80) REVERT: D 159 THR cc_start: 0.7206 (p) cc_final: 0.6912 (t) REVERT: D 220 ASP cc_start: 0.6362 (m-30) cc_final: 0.5097 (t0) REVERT: E 277 LEU cc_start: 0.9121 (mt) cc_final: 0.8909 (pp) REVERT: E 462 LYS cc_start: 0.7597 (mtmt) cc_final: 0.7260 (mmtt) REVERT: E 747 THR cc_start: 0.8562 (m) cc_final: 0.8283 (t) REVERT: E 761 THR cc_start: 0.8367 (m) cc_final: 0.8083 (p) REVERT: E 763 LEU cc_start: 0.8660 (mt) cc_final: 0.7804 (mt) REVERT: E 770 ILE cc_start: 0.9129 (mt) cc_final: 0.8127 (mm) REVERT: E 869 MET cc_start: 0.8261 (mmt) cc_final: 0.7899 (mmt) REVERT: E 1033 VAL cc_start: 0.8763 (t) cc_final: 0.8429 (t) REVERT: E 1052 PHE cc_start: 0.7822 (m-10) cc_final: 0.7302 (m-10) REVERT: F 134 CYS cc_start: 0.4421 (t) cc_final: 0.3786 (m) REVERT: F 175 MET cc_start: 0.2551 (ppp) cc_final: 0.1608 (ppp) REVERT: H 117 ILE cc_start: 0.0742 (tt) cc_final: 0.0476 (tt) REVERT: H 124 GLN cc_start: 0.1257 (tt0) cc_final: 0.1015 (mt0) REVERT: H 172 THR cc_start: 0.4476 (p) cc_final: 0.3774 (t) REVERT: I 269 TYR cc_start: 0.6594 (m-10) cc_final: 0.5676 (m-80) REVERT: I 335 LEU cc_start: 0.8034 (mt) cc_final: 0.7631 (tp) REVERT: I 614 ASP cc_start: 0.7847 (m-30) cc_final: 0.7644 (t0) REVERT: I 777 ASN cc_start: 0.8275 (m-40) cc_final: 0.5501 (p0) REVERT: I 1007 TYR cc_start: 0.7100 (t80) cc_final: 0.6784 (t80) REVERT: I 1023 ASN cc_start: 0.8827 (m-40) cc_final: 0.8349 (t0) REVERT: I 1104 VAL cc_start: 0.7012 (OUTLIER) cc_final: 0.6756 (p) REVERT: K 110 LEU cc_start: 0.7763 (mp) cc_final: 0.6845 (mt) REVERT: K 650 LEU cc_start: 0.7461 (tp) cc_final: 0.7070 (pp) REVERT: K 699 LEU cc_start: 0.9096 (mt) cc_final: 0.8693 (tp) REVERT: K 925 ASN cc_start: 0.7565 (m-40) cc_final: 0.7149 (t0) REVERT: K 1033 VAL cc_start: 0.9181 (t) cc_final: 0.8339 (t) REVERT: K 1141 LEU cc_start: 0.8989 (mt) cc_final: 0.8774 (tp) REVERT: M 206 VAL cc_start: 0.6237 (OUTLIER) cc_final: 0.5983 (p) outliers start: 55 outliers final: 7 residues processed: 946 average time/residue: 0.4898 time to fit residues: 732.1549 Evaluate side-chains 410 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 400 time to evaluate : 3.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 377 optimal weight: 4.9990 chunk 338 optimal weight: 6.9990 chunk 187 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 181 optimal weight: 7.9990 chunk 350 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 213 optimal weight: 0.2980 chunk 260 optimal weight: 9.9990 chunk 405 optimal weight: 6.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN ** D 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN E 580 GLN E 751 ASN E 919 ASN E 949 GLN ** E1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1101 HIS F 8 HIS ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN F 189 HIS H 17 HIS H 212 ASN I 23 GLN I 49 HIS ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 ASN ** I 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 580 GLN I 655 HIS ** I 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 935 GLN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 992 GLN I1011 GLN ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 354 ASN K 394 ASN K 540 ASN K 542 ASN ** K 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 919 ASN ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1108 ASN M 157 ASN ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.146 35856 Z= 0.464 Angle : 0.921 14.235 48816 Z= 0.485 Chirality : 0.051 0.280 5502 Planarity : 0.007 0.079 6303 Dihedral : 5.017 24.860 4827 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 24.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % 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: -2.86 (0.11), residues: 4434 helix: -1.95 (0.17), residues: 681 sheet: -1.54 (0.15), residues: 1124 loop : -2.09 (0.11), residues: 2629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 160 HIS 0.015 0.003 HIS D 170 PHE 0.032 0.003 PHE I 43 TYR 0.039 0.003 TYR K 449 ARG 0.013 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 457 time to evaluate : 3.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TRP cc_start: 0.5826 (m100) cc_final: 0.5132 (m-90) REVERT: A 141 MET cc_start: -0.2120 (mtm) cc_final: -0.2951 (ppp) REVERT: D 159 THR cc_start: 0.7409 (p) cc_final: 0.7088 (t) REVERT: E 277 LEU cc_start: 0.9168 (mt) cc_final: 0.8878 (pp) REVERT: E 303 LEU cc_start: 0.9275 (tp) cc_final: 0.9037 (tp) REVERT: E 450 ASN cc_start: 0.8891 (t0) cc_final: 0.8577 (p0) REVERT: E 747 THR cc_start: 0.9228 (m) cc_final: 0.8943 (p) REVERT: E 802 PHE cc_start: 0.6667 (m-80) cc_final: 0.6368 (m-80) REVERT: E 869 MET cc_start: 0.8746 (mmt) cc_final: 0.8330 (mmt) REVERT: E 1017 GLU cc_start: 0.8066 (tp30) cc_final: 0.7050 (tp30) REVERT: E 1023 ASN cc_start: 0.8762 (m110) cc_final: 0.8533 (m110) REVERT: E 1041 ASP cc_start: 0.7206 (t0) cc_final: 0.6910 (t0) REVERT: E 1050 MET cc_start: 0.8428 (ptp) cc_final: 0.8198 (ptp) REVERT: F 8 HIS cc_start: 0.8484 (m90) cc_final: 0.8108 (t-170) REVERT: F 11 MET cc_start: 0.3970 (mtt) cc_final: 0.2934 (mtt) REVERT: F 175 MET cc_start: 0.3537 (ppp) cc_final: 0.2546 (ppp) REVERT: H 184 ASP cc_start: 0.8101 (m-30) cc_final: 0.7801 (p0) REVERT: I 763 LEU cc_start: 0.9233 (pp) cc_final: 0.9009 (tt) REVERT: I 950 ASP cc_start: 0.8670 (p0) cc_final: 0.8453 (p0) REVERT: I 1002 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7362 (tm-30) REVERT: I 1030 SER cc_start: 0.8976 (p) cc_final: 0.8762 (t) REVERT: K 54 LEU cc_start: 0.8613 (tp) cc_final: 0.8347 (tp) REVERT: K 228 ASP cc_start: 0.7406 (m-30) cc_final: 0.7137 (m-30) REVERT: K 229 LEU cc_start: 0.8079 (mt) cc_final: 0.7785 (mt) REVERT: K 305 SER cc_start: 0.8403 (t) cc_final: 0.8194 (t) REVERT: K 346 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8093 (tmt170) REVERT: K 697 MET cc_start: 0.8644 (ptm) cc_final: 0.8243 (ptm) REVERT: K 699 LEU cc_start: 0.9048 (mt) cc_final: 0.8682 (mt) REVERT: K 727 LEU cc_start: 0.9146 (mt) cc_final: 0.8557 (mt) REVERT: K 864 LEU cc_start: 0.9391 (pt) cc_final: 0.7323 (pt) REVERT: K 882 ILE cc_start: 0.8243 (mt) cc_final: 0.7877 (mt) REVERT: K 925 ASN cc_start: 0.8001 (m-40) cc_final: 0.7462 (t0) REVERT: K 950 ASP cc_start: 0.8244 (p0) cc_final: 0.7976 (p0) REVERT: K 1050 MET cc_start: 0.8078 (pmm) cc_final: 0.7761 (pmm) REVERT: M 11 MET cc_start: 0.6015 (ppp) cc_final: 0.4321 (mtm) outliers start: 1 outliers final: 0 residues processed: 458 average time/residue: 0.4751 time to fit residues: 352.3989 Evaluate side-chains 282 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 3.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 225 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 337 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 406 optimal weight: 0.8980 chunk 439 optimal weight: 4.9990 chunk 362 optimal weight: 9.9990 chunk 403 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 326 optimal weight: 0.0980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN D 100 HIS E 49 HIS ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN E 690 GLN ** E 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN E1005 GLN E1083 HIS ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS F 145 ASN H 17 HIS I 49 HIS I 125 ASN I 580 GLN ** I 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 965 GLN I1054 GLN I1108 ASN K 125 ASN ** K 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 544 ASN K 613 GLN K 675 GLN K 762 GLN ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 954 GLN K1002 GLN K1011 GLN ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35856 Z= 0.174 Angle : 0.552 12.951 48816 Z= 0.286 Chirality : 0.044 0.300 5502 Planarity : 0.004 0.072 6303 Dihedral : 4.114 21.832 4827 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.08 % Allowed : 1.32 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % 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: -2.41 (0.12), residues: 4434 helix: -1.08 (0.18), residues: 688 sheet: -1.38 (0.15), residues: 1125 loop : -1.88 (0.11), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 64 HIS 0.006 0.001 HIS D 78 PHE 0.016 0.001 PHE E 275 TYR 0.019 0.001 TYR E 145 ARG 0.011 0.001 ARG I1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 431 time to evaluate : 3.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TRP cc_start: 0.5341 (m100) cc_final: 0.4721 (m-90) REVERT: A 141 MET cc_start: -0.2143 (mtm) cc_final: -0.3120 (ppp) REVERT: D 159 THR cc_start: 0.7275 (p) cc_final: 0.6963 (t) REVERT: E 32 PHE cc_start: 0.7778 (t80) cc_final: 0.7501 (t80) REVERT: E 194 PHE cc_start: 0.8667 (m-80) cc_final: 0.8086 (m-80) REVERT: E 303 LEU cc_start: 0.9287 (tp) cc_final: 0.8985 (tp) REVERT: E 450 ASN cc_start: 0.8630 (t0) cc_final: 0.8330 (p0) REVERT: E 747 THR cc_start: 0.9184 (m) cc_final: 0.8900 (p) REVERT: E 802 PHE cc_start: 0.6151 (m-80) cc_final: 0.5864 (m-80) REVERT: E 869 MET cc_start: 0.8651 (mmt) cc_final: 0.8166 (mmt) REVERT: E 1002 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7358 (tm-30) REVERT: E 1041 ASP cc_start: 0.7107 (t0) cc_final: 0.6718 (t0) REVERT: F 134 CYS cc_start: 0.6103 (t) cc_final: 0.5336 (m) REVERT: F 140 TYR cc_start: 0.5055 (t80) cc_final: 0.4329 (t80) REVERT: F 175 MET cc_start: 0.3266 (ppp) cc_final: 0.2346 (ppp) REVERT: H 184 ASP cc_start: 0.8067 (m-30) cc_final: 0.7760 (p0) REVERT: I 780 GLU cc_start: 0.7336 (tp30) cc_final: 0.6960 (tp30) REVERT: I 950 ASP cc_start: 0.8660 (p0) cc_final: 0.8384 (p0) REVERT: I 1002 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7470 (tm-30) REVERT: I 1018 ILE cc_start: 0.9643 (mm) cc_final: 0.9403 (mm) REVERT: I 1023 ASN cc_start: 0.8937 (m-40) cc_final: 0.8652 (t0) REVERT: I 1030 SER cc_start: 0.9043 (p) cc_final: 0.8605 (t) REVERT: I 1064 HIS cc_start: 0.6337 (m-70) cc_final: 0.3857 (m-70) REVERT: K 54 LEU cc_start: 0.8881 (tp) cc_final: 0.8594 (tp) REVERT: K 153 MET cc_start: 0.4916 (mtm) cc_final: 0.4493 (mtm) REVERT: K 305 SER cc_start: 0.8367 (t) cc_final: 0.8118 (t) REVERT: K 346 ARG cc_start: 0.8444 (mtp85) cc_final: 0.7916 (tmt170) REVERT: K 546 LEU cc_start: 0.7966 (tp) cc_final: 0.7297 (mm) REVERT: K 697 MET cc_start: 0.8481 (ptm) cc_final: 0.8190 (ptm) REVERT: K 699 LEU cc_start: 0.9132 (mt) cc_final: 0.8482 (mt) REVERT: K 727 LEU cc_start: 0.9109 (mt) cc_final: 0.8577 (mt) REVERT: K 759 PHE cc_start: 0.6847 (m-10) cc_final: 0.6637 (m-10) REVERT: K 867 ASP cc_start: 0.7756 (m-30) cc_final: 0.7333 (t70) REVERT: K 882 ILE cc_start: 0.8211 (mt) cc_final: 0.7934 (mt) REVERT: K 925 ASN cc_start: 0.7933 (m-40) cc_final: 0.7401 (t0) REVERT: K 1018 ILE cc_start: 0.9283 (tp) cc_final: 0.9079 (tp) REVERT: K 1050 MET cc_start: 0.8213 (pmm) cc_final: 0.7760 (pmm) REVERT: K 1110 TYR cc_start: 0.6439 (t80) cc_final: 0.6189 (t80) outliers start: 3 outliers final: 0 residues processed: 434 average time/residue: 0.4451 time to fit residues: 315.4605 Evaluate side-chains 287 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 401 optimal weight: 0.6980 chunk 305 optimal weight: 5.9990 chunk 211 optimal weight: 0.0980 chunk 45 optimal weight: 0.0570 chunk 194 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 408 optimal weight: 2.9990 chunk 432 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 386 optimal weight: 0.9990 chunk 116 optimal weight: 0.0040 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN D 100 HIS E 125 ASN ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 751 ASN ** E 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 777 ASN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN ** E1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1023 ASN E1108 ASN F 8 HIS F 17 HIS F 55 HIS I 49 HIS ** I 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 675 GLN ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 957 GLN K1023 ASN K1083 HIS ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 35856 Z= 0.134 Angle : 0.506 8.131 48816 Z= 0.260 Chirality : 0.043 0.253 5502 Planarity : 0.004 0.063 6303 Dihedral : 3.783 19.506 4827 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.03 % Allowed : 1.22 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % 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: -2.07 (0.12), residues: 4434 helix: -0.65 (0.19), residues: 687 sheet: -1.13 (0.15), residues: 1134 loop : -1.71 (0.11), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 64 HIS 0.009 0.001 HIS I1064 PHE 0.018 0.001 PHE E1109 TYR 0.027 0.001 TYR I1007 ARG 0.011 0.001 ARG I 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 427 time to evaluate : 4.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: -0.2153 (mtm) cc_final: -0.3172 (ppp) REVERT: D 159 THR cc_start: 0.7169 (p) cc_final: 0.6816 (t) REVERT: E 32 PHE cc_start: 0.7750 (t80) cc_final: 0.7451 (t80) REVERT: E 194 PHE cc_start: 0.8460 (m-80) cc_final: 0.7961 (m-80) REVERT: E 303 LEU cc_start: 0.9278 (tp) cc_final: 0.9001 (tp) REVERT: E 450 ASN cc_start: 0.8653 (t0) cc_final: 0.8362 (p0) REVERT: E 747 THR cc_start: 0.9108 (m) cc_final: 0.8833 (p) REVERT: E 869 MET cc_start: 0.8527 (mmt) cc_final: 0.8133 (mmt) REVERT: E 1002 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7267 (tm-30) REVERT: F 18 ARG cc_start: 0.4461 (tpt170) cc_final: 0.4210 (mmt180) REVERT: F 134 CYS cc_start: 0.5588 (t) cc_final: 0.4907 (m) REVERT: F 140 TYR cc_start: 0.4939 (t80) cc_final: 0.4295 (t80) REVERT: F 175 MET cc_start: 0.3325 (ppp) cc_final: 0.2444 (ppp) REVERT: H 184 ASP cc_start: 0.8046 (m-30) cc_final: 0.7756 (p0) REVERT: I 198 ASP cc_start: 0.7757 (m-30) cc_final: 0.6791 (p0) REVERT: I 767 LEU cc_start: 0.8937 (mt) cc_final: 0.8718 (pp) REVERT: I 777 ASN cc_start: 0.8994 (m-40) cc_final: 0.8586 (m-40) REVERT: I 898 PHE cc_start: 0.7135 (t80) cc_final: 0.6543 (t80) REVERT: I 950 ASP cc_start: 0.8682 (p0) cc_final: 0.8115 (p0) REVERT: I 1001 LEU cc_start: 0.9223 (pp) cc_final: 0.8922 (pp) REVERT: I 1002 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7469 (tm-30) REVERT: I 1018 ILE cc_start: 0.9615 (mm) cc_final: 0.9386 (mt) REVERT: K 54 LEU cc_start: 0.8872 (tp) cc_final: 0.8546 (tp) REVERT: K 224 GLU cc_start: 0.7581 (pp20) cc_final: 0.7122 (pp20) REVERT: K 305 SER cc_start: 0.8326 (t) cc_final: 0.8089 (t) REVERT: K 346 ARG cc_start: 0.8432 (mtp85) cc_final: 0.7892 (tmt170) REVERT: K 546 LEU cc_start: 0.7858 (tp) cc_final: 0.7233 (mm) REVERT: K 699 LEU cc_start: 0.8829 (mt) cc_final: 0.8017 (mt) REVERT: K 727 LEU cc_start: 0.9135 (mt) cc_final: 0.8549 (mt) REVERT: K 867 ASP cc_start: 0.7641 (m-30) cc_final: 0.7232 (t70) REVERT: K 925 ASN cc_start: 0.8016 (m-40) cc_final: 0.7496 (t0) REVERT: K 950 ASP cc_start: 0.7890 (p0) cc_final: 0.7624 (p0) REVERT: K 1050 MET cc_start: 0.8197 (pmm) cc_final: 0.7804 (pmm) REVERT: M 11 MET cc_start: 0.5403 (ppp) cc_final: 0.3357 (mtm) outliers start: 1 outliers final: 0 residues processed: 428 average time/residue: 0.4545 time to fit residues: 321.6514 Evaluate side-chains 281 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 4.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 359 optimal weight: 0.5980 chunk 245 optimal weight: 0.0470 chunk 6 optimal weight: 0.0000 chunk 321 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 368 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 220 optimal weight: 0.9980 chunk 387 optimal weight: 0.1980 chunk 109 optimal weight: 0.9990 overall best weight: 0.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN D 100 HIS ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 777 ASN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1023 ASN E1108 ASN F 17 HIS F 55 HIS I 49 HIS I 317 ASN ** I 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 ASN ** I1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN ** K 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 913 GLN K 919 ASN ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 955 ASN K1083 HIS ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35856 Z= 0.126 Angle : 0.486 7.513 48816 Z= 0.250 Chirality : 0.043 0.217 5502 Planarity : 0.004 0.058 6303 Dihedral : 3.604 18.834 4827 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.05 % Allowed : 0.79 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % 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: -1.81 (0.12), residues: 4434 helix: -0.38 (0.20), residues: 685 sheet: -0.93 (0.15), residues: 1148 loop : -1.57 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 64 HIS 0.006 0.001 HIS H 55 PHE 0.014 0.001 PHE K1062 TYR 0.020 0.001 TYR E 145 ARG 0.005 0.000 ARG K 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 410 time to evaluate : 3.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: -0.2154 (mtm) cc_final: -0.3187 (ppp) REVERT: D 159 THR cc_start: 0.7127 (p) cc_final: 0.6774 (t) REVERT: E 32 PHE cc_start: 0.7749 (t80) cc_final: 0.7464 (t80) REVERT: E 194 PHE cc_start: 0.8390 (m-80) cc_final: 0.7911 (m-80) REVERT: E 303 LEU cc_start: 0.9298 (tp) cc_final: 0.9003 (tp) REVERT: E 450 ASN cc_start: 0.8682 (t0) cc_final: 0.8375 (p0) REVERT: E 747 THR cc_start: 0.9146 (m) cc_final: 0.8850 (p) REVERT: E 869 MET cc_start: 0.8431 (mmt) cc_final: 0.8159 (mmp) REVERT: E 1002 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7259 (tm-30) REVERT: E 1041 ASP cc_start: 0.6741 (t0) cc_final: 0.6420 (t0) REVERT: E 1052 PHE cc_start: 0.7812 (m-10) cc_final: 0.7574 (m-10) REVERT: F 134 CYS cc_start: 0.5663 (t) cc_final: 0.4601 (m) REVERT: F 140 TYR cc_start: 0.4793 (t80) cc_final: 0.4153 (t80) REVERT: H 184 ASP cc_start: 0.8063 (m-30) cc_final: 0.7774 (p0) REVERT: I 198 ASP cc_start: 0.7754 (m-30) cc_final: 0.6824 (p0) REVERT: I 898 PHE cc_start: 0.7093 (t80) cc_final: 0.6402 (t80) REVERT: I 950 ASP cc_start: 0.8519 (p0) cc_final: 0.8280 (p0) REVERT: I 985 ASP cc_start: 0.7509 (p0) cc_final: 0.7193 (p0) REVERT: I 1001 LEU cc_start: 0.9207 (pp) cc_final: 0.8868 (pp) REVERT: I 1002 GLN cc_start: 0.8503 (tm-30) cc_final: 0.7769 (tm-30) REVERT: I 1018 ILE cc_start: 0.9575 (mm) cc_final: 0.9135 (mm) REVERT: I 1030 SER cc_start: 0.8931 (p) cc_final: 0.8449 (p) REVERT: K 54 LEU cc_start: 0.8834 (tp) cc_final: 0.8496 (tp) REVERT: K 224 GLU cc_start: 0.7589 (pp20) cc_final: 0.7134 (pp20) REVERT: K 287 ASP cc_start: 0.7260 (m-30) cc_final: 0.7055 (m-30) REVERT: K 346 ARG cc_start: 0.8447 (mtp85) cc_final: 0.7965 (tmt170) REVERT: K 546 LEU cc_start: 0.7864 (tp) cc_final: 0.7257 (mm) REVERT: K 699 LEU cc_start: 0.8533 (mt) cc_final: 0.7266 (mt) REVERT: K 727 LEU cc_start: 0.9127 (mt) cc_final: 0.8536 (mt) REVERT: K 925 ASN cc_start: 0.8070 (m-40) cc_final: 0.7521 (t0) REVERT: K 950 ASP cc_start: 0.7943 (p0) cc_final: 0.7678 (p0) REVERT: K 1050 MET cc_start: 0.8335 (pmm) cc_final: 0.7934 (pmm) REVERT: M 4 MET cc_start: 0.1931 (tmm) cc_final: 0.1364 (tmm) REVERT: M 77 ASN cc_start: 0.6804 (m-40) cc_final: 0.6403 (p0) outliers start: 2 outliers final: 0 residues processed: 411 average time/residue: 0.4487 time to fit residues: 306.7494 Evaluate side-chains 272 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 3.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 145 optimal weight: 0.7980 chunk 389 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 253 optimal weight: 0.0570 chunk 106 optimal weight: 10.0000 chunk 432 optimal weight: 0.0170 chunk 359 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 35 optimal weight: 0.1980 chunk 143 optimal weight: 0.4980 chunk 227 optimal weight: 8.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN D 77 GLN D 100 HIS ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1023 ASN F 55 HIS I 49 HIS ** I 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 ASN ** I1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN ** K 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 955 ASN K1083 HIS ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35856 Z= 0.123 Angle : 0.478 7.414 48816 Z= 0.245 Chirality : 0.043 0.303 5502 Planarity : 0.004 0.060 6303 Dihedral : 3.537 18.124 4827 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.08 % Allowed : 0.66 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % 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: -1.65 (0.12), residues: 4434 helix: -0.28 (0.20), residues: 685 sheet: -0.85 (0.15), residues: 1148 loop : -1.45 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 64 HIS 0.007 0.001 HIS I1064 PHE 0.026 0.001 PHE I 823 TYR 0.028 0.001 TYR I1007 ARG 0.008 0.000 ARG K 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 405 time to evaluate : 4.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: -0.2190 (mtm) cc_final: -0.3195 (ppp) REVERT: E 32 PHE cc_start: 0.7764 (t80) cc_final: 0.7461 (t80) REVERT: E 194 PHE cc_start: 0.8379 (m-80) cc_final: 0.7937 (m-80) REVERT: E 200 TYR cc_start: 0.9623 (m-80) cc_final: 0.9273 (m-80) REVERT: E 303 LEU cc_start: 0.9260 (tp) cc_final: 0.8982 (tp) REVERT: E 450 ASN cc_start: 0.8642 (t0) cc_final: 0.8376 (p0) REVERT: E 1002 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7358 (tm-30) REVERT: E 1041 ASP cc_start: 0.6517 (t0) cc_final: 0.6203 (t0) REVERT: F 140 TYR cc_start: 0.4827 (t80) cc_final: 0.4204 (t80) REVERT: F 175 MET cc_start: 0.3302 (ppp) cc_final: 0.2154 (ppp) REVERT: H 184 ASP cc_start: 0.8081 (m-30) cc_final: 0.7797 (p0) REVERT: I 56 LEU cc_start: 0.8495 (tp) cc_final: 0.8232 (tt) REVERT: I 776 LYS cc_start: 0.8680 (tptp) cc_final: 0.7561 (tptp) REVERT: I 858 LEU cc_start: 0.8133 (mp) cc_final: 0.7910 (mp) REVERT: I 898 PHE cc_start: 0.7154 (t80) cc_final: 0.6648 (t80) REVERT: I 950 ASP cc_start: 0.8444 (p0) cc_final: 0.8226 (p0) REVERT: I 985 ASP cc_start: 0.7546 (p0) cc_final: 0.7184 (p0) REVERT: I 1002 GLN cc_start: 0.8564 (tm-30) cc_final: 0.7494 (tm-30) REVERT: I 1018 ILE cc_start: 0.9604 (mm) cc_final: 0.9160 (mm) REVERT: I 1030 SER cc_start: 0.8901 (p) cc_final: 0.8232 (p) REVERT: K 54 LEU cc_start: 0.8856 (tp) cc_final: 0.8525 (tp) REVERT: K 224 GLU cc_start: 0.7627 (pp20) cc_final: 0.7198 (pp20) REVERT: K 287 ASP cc_start: 0.7191 (m-30) cc_final: 0.6971 (m-30) REVERT: K 346 ARG cc_start: 0.8466 (mtp85) cc_final: 0.7990 (tmt170) REVERT: K 546 LEU cc_start: 0.7984 (tp) cc_final: 0.7356 (mm) REVERT: K 724 THR cc_start: 0.8157 (t) cc_final: 0.7940 (p) REVERT: K 925 ASN cc_start: 0.8074 (m-40) cc_final: 0.7472 (t0) REVERT: K 1050 MET cc_start: 0.8231 (pmm) cc_final: 0.7849 (pmm) REVERT: K 1118 ASP cc_start: 0.8596 (p0) cc_final: 0.8302 (p0) REVERT: M 11 MET cc_start: 0.5141 (ppp) cc_final: 0.3275 (ttp) REVERT: M 77 ASN cc_start: 0.6791 (m-40) cc_final: 0.6378 (p0) outliers start: 3 outliers final: 0 residues processed: 407 average time/residue: 0.4532 time to fit residues: 305.4511 Evaluate side-chains 282 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 4.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 416 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 315 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 364 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 chunk 430 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 262 optimal weight: 0.9980 chunk 198 optimal weight: 0.0470 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 777 ASN ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS F 79 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 HIS I 239 GLN I 317 ASN I 474 GLN ** I 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 804 GLN ** I 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 978 ASN ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 ASN I1108 ASN ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 474 GLN ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 919 ASN ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 955 ASN K1083 HIS ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 35856 Z= 0.290 Angle : 0.667 10.172 48816 Z= 0.350 Chirality : 0.046 0.214 5502 Planarity : 0.005 0.065 6303 Dihedral : 4.542 21.956 4827 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.03 % Allowed : 0.68 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % 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: -1.83 (0.12), residues: 4434 helix: -0.56 (0.19), residues: 693 sheet: -1.03 (0.15), residues: 1132 loop : -1.49 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 160 HIS 0.011 0.002 HIS D 170 PHE 0.023 0.002 PHE I 43 TYR 0.025 0.002 TYR E 873 ARG 0.056 0.001 ARG K 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 386 time to evaluate : 3.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TRP cc_start: 0.5529 (m100) cc_final: 0.4869 (m-90) REVERT: A 141 MET cc_start: -0.1764 (mtm) cc_final: -0.2663 (ppp) REVERT: E 32 PHE cc_start: 0.8072 (t80) cc_final: 0.7821 (t80) REVERT: E 198 ASP cc_start: 0.8168 (t70) cc_final: 0.7967 (t0) REVERT: E 200 TYR cc_start: 0.9650 (m-80) cc_final: 0.9317 (m-80) REVERT: E 303 LEU cc_start: 0.9346 (tp) cc_final: 0.9090 (tp) REVERT: E 450 ASN cc_start: 0.8983 (t0) cc_final: 0.8549 (p0) REVERT: E 736 VAL cc_start: 0.8480 (t) cc_final: 0.8193 (m) REVERT: E 894 LEU cc_start: 0.8999 (tp) cc_final: 0.8667 (tp) REVERT: E 1017 GLU cc_start: 0.8153 (tp30) cc_final: 0.7255 (tp30) REVERT: E 1019 ARG cc_start: 0.8309 (tmm-80) cc_final: 0.7950 (tmm-80) REVERT: F 140 TYR cc_start: 0.4919 (t80) cc_final: 0.4481 (t80) REVERT: F 175 MET cc_start: 0.4061 (ppp) cc_final: 0.2931 (ppp) REVERT: I 33 THR cc_start: 0.6085 (p) cc_final: 0.4335 (p) REVERT: I 56 LEU cc_start: 0.8688 (tp) cc_final: 0.8404 (tt) REVERT: I 321 GLN cc_start: 0.8889 (tp40) cc_final: 0.8505 (tm-30) REVERT: I 456 PHE cc_start: 0.7734 (m-80) cc_final: 0.7524 (m-80) REVERT: I 950 ASP cc_start: 0.8642 (p0) cc_final: 0.8351 (p0) REVERT: I 1002 GLN cc_start: 0.8671 (tm-30) cc_final: 0.7853 (tm-30) REVERT: I 1018 ILE cc_start: 0.9623 (mm) cc_final: 0.9194 (mm) REVERT: K 54 LEU cc_start: 0.8926 (tp) cc_final: 0.8671 (tp) REVERT: K 228 ASP cc_start: 0.7727 (m-30) cc_final: 0.7280 (m-30) REVERT: K 346 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8054 (tmt170) REVERT: K 697 MET cc_start: 0.8790 (ptm) cc_final: 0.8436 (ptm) REVERT: K 699 LEU cc_start: 0.8598 (mt) cc_final: 0.7326 (mt) REVERT: K 727 LEU cc_start: 0.9063 (mt) cc_final: 0.8752 (mt) REVERT: K 729 VAL cc_start: 0.8165 (t) cc_final: 0.7824 (t) REVERT: K 1050 MET cc_start: 0.8832 (pmm) cc_final: 0.8251 (pmm) REVERT: M 11 MET cc_start: 0.5493 (ppp) cc_final: 0.3460 (ttp) REVERT: M 77 ASN cc_start: 0.6896 (m-40) cc_final: 0.6452 (p0) outliers start: 1 outliers final: 0 residues processed: 387 average time/residue: 0.4567 time to fit residues: 293.7523 Evaluate side-chains 262 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 3.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 266 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 257 optimal weight: 6.9990 chunk 129 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 273 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 338 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 111 GLN D 100 HIS D 202 ASN ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS I 30 ASN I 317 ASN ** I 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 474 GLN ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 925 ASN K 935 GLN ** K 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 955 ASN K 957 GLN K1023 ASN K1083 HIS ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.7145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35856 Z= 0.228 Angle : 0.583 8.504 48816 Z= 0.305 Chirality : 0.044 0.205 5502 Planarity : 0.005 0.062 6303 Dihedral : 4.498 21.384 4827 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.05 % Allowed : 0.58 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % 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: -1.77 (0.12), residues: 4434 helix: -0.35 (0.19), residues: 697 sheet: -0.95 (0.16), residues: 1109 loop : -1.53 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 64 HIS 0.011 0.001 HIS I1064 PHE 0.020 0.002 PHE I 898 TYR 0.033 0.002 TYR K1110 ARG 0.008 0.001 ARG K 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 368 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TRP cc_start: 0.5683 (m100) cc_final: 0.5456 (m100) REVERT: A 141 MET cc_start: -0.1529 (mtm) cc_final: -0.2460 (ppp) REVERT: B 43 ASN cc_start: 0.5990 (OUTLIER) cc_final: 0.5713 (t0) REVERT: E 32 PHE cc_start: 0.8116 (t80) cc_final: 0.7885 (t80) REVERT: E 200 TYR cc_start: 0.9696 (m-80) cc_final: 0.9381 (m-80) REVERT: E 303 LEU cc_start: 0.9359 (tp) cc_final: 0.9139 (tp) REVERT: E 450 ASN cc_start: 0.9017 (t0) cc_final: 0.8541 (p0) REVERT: E 736 VAL cc_start: 0.8473 (t) cc_final: 0.8229 (m) REVERT: E 894 LEU cc_start: 0.9047 (tp) cc_final: 0.8700 (tp) REVERT: F 140 TYR cc_start: 0.5114 (t80) cc_final: 0.4729 (t80) REVERT: F 175 MET cc_start: 0.4011 (ppp) cc_final: 0.2875 (ppp) REVERT: I 33 THR cc_start: 0.6120 (p) cc_final: 0.4408 (p) REVERT: I 56 LEU cc_start: 0.8687 (tp) cc_final: 0.8333 (tt) REVERT: I 898 PHE cc_start: 0.7990 (t80) cc_final: 0.7759 (t80) REVERT: I 950 ASP cc_start: 0.8593 (p0) cc_final: 0.8384 (p0) REVERT: I 1002 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8389 (tm-30) REVERT: I 1018 ILE cc_start: 0.9614 (mm) cc_final: 0.9396 (tp) REVERT: K 54 LEU cc_start: 0.8913 (tp) cc_final: 0.8583 (tp) REVERT: K 228 ASP cc_start: 0.7785 (m-30) cc_final: 0.7377 (m-30) REVERT: K 287 ASP cc_start: 0.7246 (m-30) cc_final: 0.7033 (m-30) REVERT: K 346 ARG cc_start: 0.8658 (mtp85) cc_final: 0.8291 (tmt170) REVERT: K 697 MET cc_start: 0.8718 (ptm) cc_final: 0.8378 (ptm) REVERT: K 699 LEU cc_start: 0.8399 (mt) cc_final: 0.7004 (mt) REVERT: K 882 ILE cc_start: 0.8566 (mt) cc_final: 0.8149 (mt) REVERT: K 950 ASP cc_start: 0.8038 (p0) cc_final: 0.7825 (p0) REVERT: K 1018 ILE cc_start: 0.9097 (tp) cc_final: 0.8660 (tt) REVERT: K 1050 MET cc_start: 0.8842 (pmm) cc_final: 0.8269 (pmm) REVERT: M 11 MET cc_start: 0.5424 (ppp) cc_final: 0.4377 (ttp) REVERT: M 77 ASN cc_start: 0.6882 (m-40) cc_final: 0.6428 (p0) outliers start: 2 outliers final: 0 residues processed: 370 average time/residue: 0.4652 time to fit residues: 289.4225 Evaluate side-chains 269 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 391 optimal weight: 0.8980 chunk 412 optimal weight: 2.9990 chunk 376 optimal weight: 9.9990 chunk 401 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 315 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 chunk 379 optimal weight: 4.9990 chunk 400 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 HIS ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN I 317 ASN ** I 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 ASN ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 ASN ** K 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 751 ASN ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 955 ASN K 957 GLN K1011 GLN K1083 HIS ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 35856 Z= 0.296 Angle : 0.693 13.016 48816 Z= 0.362 Chirality : 0.047 0.213 5502 Planarity : 0.005 0.076 6303 Dihedral : 5.087 23.346 4827 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 25.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.03 % Allowed : 0.58 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % 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: -2.00 (0.12), residues: 4434 helix: -0.54 (0.19), residues: 693 sheet: -1.13 (0.16), residues: 1106 loop : -1.67 (0.12), residues: 2635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 64 HIS 0.014 0.002 HIS I1048 PHE 0.025 0.002 PHE I 497 TYR 0.027 0.002 TYR K 707 ARG 0.016 0.001 ARG I 815 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 341 time to evaluate : 4.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: -0.1239 (mtm) cc_final: -0.2019 (ppp) REVERT: E 32 PHE cc_start: 0.8239 (t80) cc_final: 0.8005 (t80) REVERT: E 200 TYR cc_start: 0.9733 (m-80) cc_final: 0.9460 (m-80) REVERT: E 450 ASN cc_start: 0.9144 (t0) cc_final: 0.8619 (p0) REVERT: E 894 LEU cc_start: 0.9145 (tp) cc_final: 0.8864 (tp) REVERT: E 1002 GLN cc_start: 0.8287 (tm-30) cc_final: 0.8050 (tm-30) REVERT: E 1019 ARG cc_start: 0.8826 (ptt90) cc_final: 0.8492 (tmm-80) REVERT: E 1041 ASP cc_start: 0.6798 (t0) cc_final: 0.6035 (t0) REVERT: F 140 TYR cc_start: 0.5685 (t80) cc_final: 0.5360 (t80) REVERT: F 175 MET cc_start: 0.4493 (ppp) cc_final: 0.3433 (ppp) REVERT: H 107 LYS cc_start: 0.4268 (mtpt) cc_final: 0.3931 (tptt) REVERT: I 33 THR cc_start: 0.6228 (p) cc_final: 0.4581 (p) REVERT: I 456 PHE cc_start: 0.7772 (m-80) cc_final: 0.7567 (m-80) REVERT: I 747 THR cc_start: 0.9606 (m) cc_final: 0.9403 (t) REVERT: I 983 ARG cc_start: 0.9389 (ttm110) cc_final: 0.9091 (mtm110) REVERT: I 1002 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8394 (tm-30) REVERT: I 1018 ILE cc_start: 0.9642 (mm) cc_final: 0.9246 (mm) REVERT: I 1030 SER cc_start: 0.9347 (p) cc_final: 0.8721 (t) REVERT: K 54 LEU cc_start: 0.8968 (tp) cc_final: 0.8687 (tp) REVERT: K 200 TYR cc_start: 0.8502 (m-80) cc_final: 0.8192 (m-80) REVERT: K 228 ASP cc_start: 0.8139 (m-30) cc_final: 0.7894 (m-30) REVERT: K 346 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8167 (tmt170) REVERT: K 697 MET cc_start: 0.8856 (ptm) cc_final: 0.8422 (ptm) REVERT: K 699 LEU cc_start: 0.8498 (mt) cc_final: 0.8069 (mt) REVERT: K 950 ASP cc_start: 0.8024 (p0) cc_final: 0.7791 (p0) REVERT: K 1050 MET cc_start: 0.9003 (pmm) cc_final: 0.8366 (pmm) REVERT: M 11 MET cc_start: 0.5386 (ppp) cc_final: 0.4473 (ttp) REVERT: M 77 ASN cc_start: 0.6971 (m-40) cc_final: 0.6514 (p0) outliers start: 1 outliers final: 0 residues processed: 342 average time/residue: 0.4475 time to fit residues: 255.6485 Evaluate side-chains 237 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 3.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 263 optimal weight: 10.0000 chunk 424 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 295 optimal weight: 0.7980 chunk 445 optimal weight: 7.9990 chunk 409 optimal weight: 0.0070 chunk 354 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 273 optimal weight: 0.4980 chunk 217 optimal weight: 8.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN D 100 HIS ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 HIS F 55 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN ** K 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 949 GLN K 955 ASN K1010 GLN K1083 HIS ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.7869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35856 Z= 0.172 Angle : 0.562 8.744 48816 Z= 0.290 Chirality : 0.045 0.199 5502 Planarity : 0.004 0.060 6303 Dihedral : 4.612 21.342 4827 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.03 % Allowed : 0.15 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % 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: -1.80 (0.12), residues: 4434 helix: -0.21 (0.20), residues: 690 sheet: -1.09 (0.16), residues: 1129 loop : -1.54 (0.12), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP K 64 HIS 0.011 0.001 HIS I1048 PHE 0.021 0.001 PHE K 898 TYR 0.033 0.002 TYR K 269 ARG 0.013 0.001 ARG I 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 346 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: -0.1588 (mtm) cc_final: -0.2410 (ppp) REVERT: B 64 LYS cc_start: 0.7894 (pttm) cc_final: 0.6910 (mmmt) REVERT: E 32 PHE cc_start: 0.8215 (t80) cc_final: 0.7991 (t80) REVERT: E 200 TYR cc_start: 0.9704 (m-80) cc_final: 0.9438 (m-80) REVERT: E 450 ASN cc_start: 0.9079 (t0) cc_final: 0.8539 (p0) REVERT: E 802 PHE cc_start: 0.6825 (m-10) cc_final: 0.6509 (m-80) REVERT: E 894 LEU cc_start: 0.9039 (tp) cc_final: 0.8739 (tp) REVERT: E 1019 ARG cc_start: 0.8811 (ptt90) cc_final: 0.8525 (tmm-80) REVERT: F 134 CYS cc_start: 0.6551 (t) cc_final: 0.5678 (m) REVERT: F 140 TYR cc_start: 0.5530 (t80) cc_final: 0.5149 (t80) REVERT: F 175 MET cc_start: 0.4082 (ppp) cc_final: 0.2871 (ppp) REVERT: H 4 MET cc_start: -0.1492 (mtt) cc_final: -0.1745 (mtt) REVERT: I 33 THR cc_start: 0.6154 (p) cc_final: 0.4676 (p) REVERT: I 456 PHE cc_start: 0.7879 (m-80) cc_final: 0.7598 (m-80) REVERT: I 543 PHE cc_start: 0.7936 (t80) cc_final: 0.7165 (t80) REVERT: I 546 LEU cc_start: 0.8204 (tt) cc_final: 0.7953 (tt) REVERT: I 898 PHE cc_start: 0.7786 (t80) cc_final: 0.7578 (t80) REVERT: I 983 ARG cc_start: 0.9174 (ttm110) cc_final: 0.8815 (mtm180) REVERT: I 1018 ILE cc_start: 0.9624 (mm) cc_final: 0.9218 (mm) REVERT: K 54 LEU cc_start: 0.8910 (tp) cc_final: 0.8636 (tp) REVERT: K 56 LEU cc_start: 0.9240 (tp) cc_final: 0.8847 (tt) REVERT: K 228 ASP cc_start: 0.7987 (m-30) cc_final: 0.7762 (m-30) REVERT: K 346 ARG cc_start: 0.8597 (mtp85) cc_final: 0.8191 (tmt170) REVERT: K 697 MET cc_start: 0.8781 (ptm) cc_final: 0.8415 (ptm) REVERT: K 699 LEU cc_start: 0.8394 (mt) cc_final: 0.7974 (mt) REVERT: K 707 TYR cc_start: 0.6781 (t80) cc_final: 0.6422 (t80) REVERT: K 950 ASP cc_start: 0.7886 (p0) cc_final: 0.7560 (p0) REVERT: K 1018 ILE cc_start: 0.9037 (tp) cc_final: 0.8649 (tt) REVERT: K 1050 MET cc_start: 0.8841 (pmm) cc_final: 0.8274 (pmm) REVERT: K 1118 ASP cc_start: 0.8643 (p0) cc_final: 0.8095 (m-30) REVERT: M 11 MET cc_start: 0.5370 (ppp) cc_final: 0.3777 (ttp) REVERT: M 77 ASN cc_start: 0.6865 (m-40) cc_final: 0.6403 (p0) outliers start: 1 outliers final: 0 residues processed: 347 average time/residue: 0.4419 time to fit residues: 257.7775 Evaluate side-chains 255 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 3.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 281 optimal weight: 4.9990 chunk 377 optimal weight: 0.0020 chunk 108 optimal weight: 6.9990 chunk 326 optimal weight: 0.0040 chunk 52 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 355 optimal weight: 0.5980 chunk 148 optimal weight: 0.4980 chunk 364 optimal weight: 0.0470 chunk 44 optimal weight: 10.0000 chunk 65 optimal weight: 0.4980 overall best weight: 0.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN D 100 HIS E 165 ASN E 183 GLN ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 HIS F 55 HIS H 6 GLN I 239 GLN ** I 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 ASN ** K 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 919 ASN K 955 ASN K1083 HIS ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.100734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.083462 restraints weight = 420661.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.086016 restraints weight = 254413.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.086068 restraints weight = 162612.357| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4033 r_free = 0.4033 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4033 r_free = 0.4033 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.7675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35856 Z= 0.140 Angle : 0.531 10.351 48816 Z= 0.271 Chirality : 0.044 0.171 5502 Planarity : 0.004 0.056 6303 Dihedral : 4.191 29.506 4827 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.03 % Allowed : 0.15 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % 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 (0.12), residues: 4434 helix: -0.03 (0.20), residues: 679 sheet: -0.88 (0.16), residues: 1102 loop : -1.43 (0.12), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 64 HIS 0.008 0.001 HIS H 55 PHE 0.018 0.001 PHE K 898 TYR 0.031 0.001 TYR B 181 ARG 0.014 0.001 ARG I 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7849.32 seconds wall clock time: 144 minutes 23.71 seconds (8663.71 seconds total)