Starting phenix.real_space_refine on Fri Mar 6 11:15:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vxd_32176/03_2026/7vxd_32176.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vxd_32176/03_2026/7vxd_32176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vxd_32176/03_2026/7vxd_32176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vxd_32176/03_2026/7vxd_32176.map" model { file = "/net/cci-nas-00/data/ceres_data/7vxd_32176/03_2026/7vxd_32176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vxd_32176/03_2026/7vxd_32176.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 sd= 0.113 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 146 5.16 5 C 19291 2.51 5 N 5028 2.21 5 O 5729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30194 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8453 Classifications: {'peptide': 1079} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 8423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8423 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 52, 'TRANS': 1022} Chain breaks: 5 Chain: "C" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 8448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8448 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 52, 'TRANS': 1025} Chain breaks: 5 Time building chain proxies: 6.07, per 1000 atoms: 0.20 Number of scatterers: 30194 At special positions: 0 Unit cell: (161.764, 148.648, 262.32, 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 146 16.00 O 5729 8.00 N 5028 7.00 C 19291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.90 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.31 Conformation dependent library (CDL) restraints added in 1.4 seconds 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7178 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 47 sheets defined 30.3% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.563A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.948A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.760A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.738A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.548A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 removed outlier: 4.349A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.523A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.602A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.138A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.626A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.947A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.509A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.525A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1152 removed outlier: 4.080A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1156 removed outlier: 4.032A pdb=" N PHE A1156 " --> pdb=" O ASP A1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1153 through 1156' Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.530A pdb=" N THR D 299 " --> pdb=" O PRO D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.116A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 747 through 755 removed outlier: 3.692A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 780 removed outlier: 3.603A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 825 removed outlier: 3.534A pdb=" N LEU D 822 " --> pdb=" O ILE D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 854 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.760A pdb=" N MET D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 3.908A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.698A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 982 removed outlier: 3.697A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.081A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1154 removed outlier: 4.244A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS D1154 " --> pdb=" O GLU D1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 53 removed outlier: 4.033A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.768A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.942A pdb=" N GLU C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 88 " --> pdb=" O LEU C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 84 through 88' Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.520A pdb=" N LYS C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.971A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 removed outlier: 3.846A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 removed outlier: 3.771A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.613A pdb=" N ARG C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 194 removed outlier: 3.643A pdb=" N MET C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.529A pdb=" N TYR C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 249 removed outlier: 3.988A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.780A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 293 through 301 removed outlier: 3.781A pdb=" N ASP C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 removed outlier: 4.025A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.634A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.644A pdb=" N PHE C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 370 " --> pdb=" O MET C 366 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.552A pdb=" N VAL C 404 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.730A pdb=" N ILE C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.658A pdb=" N ASN C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 466 removed outlier: 4.002A pdb=" N PHE C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 485 removed outlier: 3.898A pdb=" N GLU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 removed outlier: 4.123A pdb=" N SER C 502 " --> pdb=" O CYS C 498 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 503 " --> pdb=" O ASP C 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 498 through 503' Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.529A pdb=" N THR C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS C 530 " --> pdb=" O GLN C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.659A pdb=" N GLN C 552 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN C 556 " --> pdb=" O GLN C 552 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 removed outlier: 3.515A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.575A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.692A pdb=" N TRP C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.098A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.853A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.973A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.861A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.519A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.962A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 854 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.526A pdb=" N LEU B 877 " --> pdb=" O TYR B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.619A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.818A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.781A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.764A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.525A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.311A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1152 Processing helix chain 'B' and resid 1154 through 1158 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.761A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.418A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.834A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.852A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.521A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 4.020A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.743A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 653 through 655 removed outlier: 5.579A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 672 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.552A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.650A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.600A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 27 through 30 removed outlier: 3.739A pdb=" N ALA D 27 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D 265 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE D 194 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 193 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.655A pdb=" N THR D 51 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE D 275 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.925A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS D 131 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AC2, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.804A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 324 through 327 removed outlier: 6.999A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE D 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 354 through 357 removed outlier: 4.324A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 434 " --> pdb=" O VAL D 511 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU D 513 " --> pdb=" O CYS D 432 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS D 432 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 378 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA D 435 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR D 376 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.151A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 701 through 702 removed outlier: 7.268A pdb=" N VAL D 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.584A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.668A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.357A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 1120 through 1122 removed outlier: 3.756A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.554A pdb=" N LEU C 142 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.126A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.571A pdb=" N THR C 347 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.128A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.128A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 48 through 52 removed outlier: 4.483A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.506A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.358A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.525A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 334 through 335 removed outlier: 7.531A pdb=" N ASN B 334 " --> pdb=" O VAL B 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 357 through 359 removed outlier: 3.988A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.509A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.633A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.580A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.463A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 3006 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: 6.04 Time building geometry restraints manager: 3.23 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: 9747 1.35 - 1.46: 7631 1.46 - 1.58: 13349 1.58 - 1.70: 0 1.70 - 1.82: 197 Bond restraints: 30924 Sorted by residual: bond pdb=" C GLN B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 1.334 1.567 -0.233 2.34e-02 1.83e+03 9.91e+01 bond pdb=" C THR B 478 " pdb=" N PRO B 479 " ideal model delta sigma weight residual 1.334 1.461 -0.127 2.34e-02 1.83e+03 2.96e+01 bond pdb=" C PRO D 25 " pdb=" N PRO D 26 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.34e-02 1.83e+03 1.87e+01 bond pdb=" C CYS D 336 " pdb=" N PRO D 337 " ideal model delta sigma weight residual 1.334 1.427 -0.094 2.34e-02 1.83e+03 1.60e+01 bond pdb=" C PRO B 25 " pdb=" N PRO B 26 " ideal model delta sigma weight residual 1.334 1.427 -0.093 2.34e-02 1.83e+03 1.57e+01 ... (remaining 30919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 41496 1.77 - 3.54: 494 3.54 - 5.31: 48 5.31 - 7.08: 10 7.08 - 8.84: 5 Bond angle restraints: 42053 Sorted by residual: angle pdb=" N VAL D 362 " pdb=" CA VAL D 362 " pdb=" C VAL D 362 " ideal model delta sigma weight residual 110.72 104.52 6.20 1.01e+00 9.80e-01 3.77e+01 angle pdb=" O ASN D 360 " pdb=" C ASN D 360 " pdb=" N CYS D 361 " ideal model delta sigma weight residual 122.59 129.55 -6.96 1.33e+00 5.65e-01 2.74e+01 angle pdb=" C ASN D 360 " pdb=" N CYS D 361 " pdb=" CA CYS D 361 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 angle pdb=" CA ASN D 360 " pdb=" C ASN D 360 " pdb=" N CYS D 361 " ideal model delta sigma weight residual 116.84 109.03 7.81 1.71e+00 3.42e-01 2.09e+01 angle pdb=" C VAL D 362 " pdb=" N ALA D 363 " pdb=" CA ALA D 363 " ideal model delta sigma weight residual 121.54 129.47 -7.93 1.91e+00 2.74e-01 1.73e+01 ... (remaining 42048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 17931 16.01 - 32.02: 302 32.02 - 48.04: 99 48.04 - 64.05: 35 64.05 - 80.06: 12 Dihedral angle restraints: 18379 sinusoidal: 7219 harmonic: 11160 Sorted by residual: dihedral pdb=" CA THR D 531 " pdb=" C THR D 531 " pdb=" N ASN D 532 " pdb=" CA ASN D 532 " ideal model delta harmonic sigma weight residual 180.00 -152.87 -27.13 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA THR B1160 " pdb=" C THR B1160 " pdb=" N SER B1161 " pdb=" CA SER B1161 " ideal model delta harmonic sigma weight residual -180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 57.14 35.86 1 1.00e+01 1.00e-02 1.82e+01 ... (remaining 18376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3980 0.055 - 0.110: 616 0.110 - 0.164: 84 0.164 - 0.219: 0 0.219 - 0.274: 4 Chirality restraints: 4684 Sorted by residual: chirality pdb=" CA CYS D 361 " pdb=" N CYS D 361 " pdb=" C CYS D 361 " pdb=" CB CYS D 361 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ALA D 363 " pdb=" N ALA D 363 " pdb=" C ALA D 363 " pdb=" CB ALA D 363 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA VAL D 362 " pdb=" N VAL D 362 " pdb=" C VAL D 362 " pdb=" CB VAL D 362 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 4681 not shown) Planarity restraints: 5455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 295 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 290 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C ASP A 290 " 0.029 2.00e-02 2.50e+03 pdb=" O ASP A 290 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS A 291 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 714 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 715 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 715 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 715 " 0.023 5.00e-02 4.00e+02 ... (remaining 5452 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 312 2.65 - 3.21: 26795 3.21 - 3.78: 43868 3.78 - 4.34: 61785 4.34 - 4.90: 100840 Nonbonded interactions: 233600 Sorted by model distance: nonbonded pdb=" NH2 ARG A 273 " pdb=" O CYS A 291 " model vdw 2.091 3.120 nonbonded pdb=" O VAL B 327 " pdb=" OG1 THR B 531 " model vdw 2.135 3.040 nonbonded pdb=" OG1 THR A 883 " pdb=" OH TYR B 707 " model vdw 2.169 3.040 nonbonded pdb=" OG1 THR D 108 " pdb=" O ASN D 234 " model vdw 2.195 3.040 nonbonded pdb=" OG SER D 746 " pdb=" OE1 GLU D 748 " model vdw 2.205 3.040 ... (remaining 233595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 255 or resid 257 through 1157)) selection = (chain 'B' and (resid 14 through 291 or (resid 292 and (name N or name CA or nam \ e C or name O )) or resid 293 through 1157)) selection = (chain 'D' and (resid 14 through 255 or resid 257 through 291 or (resid 292 and \ (name N or name CA or name C or name O )) or resid 293 through 1157)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 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: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.520 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.233 30962 Z= 0.136 Angle : 0.526 27.614 42129 Z= 0.310 Chirality : 0.041 0.274 4684 Planarity : 0.003 0.055 5455 Dihedral : 7.889 80.060 11087 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.96 % Favored : 95.86 % Rotamer: Outliers : 0.03 % Allowed : 0.15 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.11), residues: 3791 helix: -3.17 (0.10), residues: 944 sheet: -0.49 (0.17), residues: 665 loop : -1.03 (0.12), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 34 TYR 0.016 0.001 TYR A 495 PHE 0.018 0.001 PHE B 464 TRP 0.019 0.001 TRP B 152 HIS 0.006 0.001 HIS D 242 Details of bonding type rmsd covalent geometry : bond 0.00256 (30924) covalent geometry : angle 0.50218 (42053) SS BOND : bond 0.02185 ( 38) SS BOND : angle 3.68835 ( 76) hydrogen bonds : bond 0.29660 ( 1051) hydrogen bonds : angle 10.08483 ( 3006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 929 time to evaluate : 1.168 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: A 54 LEU cc_start: 0.8742 (mp) cc_final: 0.8427 (mm) REVERT: A 177 MET cc_start: 0.1855 (ttm) cc_final: -0.0367 (mtm) REVERT: A 280 ASN cc_start: 0.6734 (p0) cc_final: 0.6437 (p0) REVERT: A 408 ARG cc_start: 0.7332 (ptt180) cc_final: 0.6890 (tpt-90) REVERT: A 732 THR cc_start: 0.8983 (m) cc_final: 0.8638 (p) REVERT: A 775 ASP cc_start: 0.8930 (m-30) cc_final: 0.7603 (m-30) REVERT: A 992 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8714 (mm-40) REVERT: A 1001 LEU cc_start: 0.9354 (mt) cc_final: 0.9111 (mt) REVERT: A 1011 GLN cc_start: 0.9076 (mm110) cc_final: 0.8617 (mp10) REVERT: A 1028 LYS cc_start: 0.9149 (mmtp) cc_final: 0.8915 (mmmm) REVERT: A 1029 MET cc_start: 0.9197 (tpp) cc_final: 0.8697 (tpp) REVERT: A 1055 SER cc_start: 0.9233 (t) cc_final: 0.8576 (p) REVERT: A 1064 HIS cc_start: 0.7000 (m-70) cc_final: 0.4985 (m-70) REVERT: D 55 PHE cc_start: 0.7893 (m-10) cc_final: 0.7431 (m-10) REVERT: D 133 PHE cc_start: 0.4777 (m-10) cc_final: 0.4025 (m-10) REVERT: D 224 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7578 (pt0) REVERT: D 284 THR cc_start: 0.9324 (m) cc_final: 0.9024 (p) REVERT: D 377 PHE cc_start: 0.5635 (m-10) cc_final: 0.2437 (t80) REVERT: D 598 ILE cc_start: 0.9399 (mp) cc_final: 0.9188 (mp) REVERT: D 721 SER cc_start: 0.8645 (t) cc_final: 0.8326 (p) REVERT: D 730 SER cc_start: 0.9079 (p) cc_final: 0.8546 (t) REVERT: D 761 THR cc_start: 0.8304 (m) cc_final: 0.8000 (m) REVERT: D 770 ILE cc_start: 0.9332 (mt) cc_final: 0.8586 (mm) REVERT: D 780 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7889 (mt-10) REVERT: D 797 PHE cc_start: 0.6085 (m-10) cc_final: 0.5872 (m-80) REVERT: D 954 GLN cc_start: 0.8536 (tp40) cc_final: 0.8128 (tp40) REVERT: D 1023 ASN cc_start: 0.9248 (m-40) cc_final: 0.9016 (m-40) REVERT: D 1033 VAL cc_start: 0.9237 (t) cc_final: 0.8753 (t) REVERT: D 1040 VAL cc_start: 0.7253 (t) cc_final: 0.6644 (m) REVERT: C 37 GLU cc_start: 0.6519 (tt0) cc_final: 0.6238 (tt0) REVERT: C 62 MET cc_start: 0.7437 (ttp) cc_final: 0.7197 (mtp) REVERT: C 64 ASN cc_start: 0.8070 (m-40) cc_final: 0.7699 (t0) REVERT: C 106 SER cc_start: 0.7435 (m) cc_final: 0.6848 (m) REVERT: C 274 PHE cc_start: 0.8228 (p90) cc_final: 0.7971 (m-80) REVERT: C 383 MET cc_start: 0.2560 (mtp) cc_final: 0.1311 (ppp) REVERT: C 555 PHE cc_start: 0.3751 (t80) cc_final: 0.3297 (t80) REVERT: C 585 LEU cc_start: 0.7484 (tp) cc_final: 0.7089 (pp) REVERT: B 86 PHE cc_start: 0.7449 (t80) cc_final: 0.6687 (t80) REVERT: B 92 PHE cc_start: 0.7456 (m-10) cc_final: 0.6925 (m-80) REVERT: B 106 PHE cc_start: 0.9051 (m-10) cc_final: 0.8343 (m-80) REVERT: B 117 LEU cc_start: 0.8951 (tp) cc_final: 0.8537 (mt) REVERT: B 180 GLU cc_start: 0.6949 (tt0) cc_final: 0.6667 (mm-30) REVERT: B 194 PHE cc_start: 0.6717 (m-10) cc_final: 0.6177 (m-10) REVERT: B 302 THR cc_start: 0.8764 (m) cc_final: 0.8546 (m) REVERT: B 315 THR cc_start: 0.8565 (p) cc_final: 0.8364 (m) REVERT: B 417 ASN cc_start: 0.9106 (m-40) cc_final: 0.8756 (p0) REVERT: B 449 TYR cc_start: 0.8474 (m-10) cc_final: 0.8241 (m-80) REVERT: B 802 PHE cc_start: 0.8844 (m-80) cc_final: 0.8584 (m-80) REVERT: B 819 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 867 ASP cc_start: 0.8660 (m-30) cc_final: 0.8389 (p0) REVERT: B 868 GLU cc_start: 0.8265 (tp30) cc_final: 0.7878 (tp30) REVERT: B 959 LEU cc_start: 0.9498 (mt) cc_final: 0.9252 (mm) REVERT: B 1029 MET cc_start: 0.8939 (tpp) cc_final: 0.8633 (tpp) REVERT: B 1043 CYS cc_start: 0.3797 (m) cc_final: 0.3311 (m) REVERT: B 1104 VAL cc_start: 0.9158 (t) cc_final: 0.8828 (p) outliers start: 1 outliers final: 0 residues processed: 930 average time/residue: 0.2024 time to fit residues: 299.3287 Evaluate side-chains 507 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 544 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS D 148 ASN D 317 ASN D 360 ASN D 563 GLN D 925 ASN D 949 GLN D 955 ASN D 965 GLN D1064 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN C 388 GLN C 401 HIS C 417 HIS C 526 GLN C 535 HIS C 552 GLN C 580 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 556 ASN B 703 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.114320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.096639 restraints weight = 238291.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.098188 restraints weight = 124516.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.099106 restraints weight = 77153.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.099821 restraints weight = 54737.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.100258 restraints weight = 42447.381| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30962 Z= 0.219 Angle : 0.713 10.206 42129 Z= 0.377 Chirality : 0.047 0.206 4684 Planarity : 0.005 0.052 5455 Dihedral : 4.420 28.982 4105 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.06 % Favored : 97.92 % Rotamer: Outliers : 2.89 % Allowed : 9.54 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.12), residues: 3791 helix: -0.54 (0.15), residues: 986 sheet: -0.13 (0.18), residues: 635 loop : -0.78 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 214 TYR 0.023 0.002 TYR A 279 PHE 0.038 0.002 PHE C 438 TRP 0.028 0.002 TRP A 436 HIS 0.008 0.002 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00463 (30924) covalent geometry : angle 0.71089 (42053) SS BOND : bond 0.00571 ( 38) SS BOND : angle 1.54466 ( 76) hydrogen bonds : bond 0.05473 ( 1051) hydrogen bonds : angle 6.39033 ( 3006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 509 time to evaluate : 1.123 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: A 177 MET cc_start: 0.1590 (ttm) cc_final: 0.0549 (mtm) REVERT: A 762 GLN cc_start: 0.9137 (pt0) cc_final: 0.8787 (pt0) REVERT: A 776 LYS cc_start: 0.9453 (tppt) cc_final: 0.9067 (tppt) REVERT: A 904 TYR cc_start: 0.7289 (m-10) cc_final: 0.6701 (m-10) REVERT: A 945 LEU cc_start: 0.8933 (tp) cc_final: 0.8727 (tp) REVERT: A 955 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8615 (m-40) REVERT: A 1011 GLN cc_start: 0.9305 (mm110) cc_final: 0.8677 (mp10) REVERT: A 1029 MET cc_start: 0.9471 (tpp) cc_final: 0.8961 (tpp) REVERT: A 1068 VAL cc_start: 0.9053 (t) cc_final: 0.8764 (p) REVERT: D 133 PHE cc_start: 0.5559 (m-10) cc_final: 0.4589 (m-10) REVERT: D 602 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8045 (p) REVERT: D 730 SER cc_start: 0.9310 (p) cc_final: 0.7880 (t) REVERT: D 770 ILE cc_start: 0.9387 (mt) cc_final: 0.9155 (mm) REVERT: D 776 LYS cc_start: 0.9444 (ttmm) cc_final: 0.9137 (ttpt) REVERT: D 777 ASN cc_start: 0.9211 (m-40) cc_final: 0.8920 (t0) REVERT: D 797 PHE cc_start: 0.6684 (m-10) cc_final: 0.6225 (m-80) REVERT: D 869 MET cc_start: 0.9231 (mtp) cc_final: 0.8804 (mtt) REVERT: D 948 LEU cc_start: 0.9222 (mt) cc_final: 0.8960 (mp) REVERT: D 955 ASN cc_start: 0.9234 (m110) cc_final: 0.8772 (m110) REVERT: D 1004 LEU cc_start: 0.9352 (tp) cc_final: 0.8821 (mt) REVERT: D 1029 MET cc_start: 0.9487 (tpp) cc_final: 0.9230 (tpp) REVERT: D 1040 VAL cc_start: 0.7689 (t) cc_final: 0.7245 (t) REVERT: D 1050 MET cc_start: 0.8267 (ptp) cc_final: 0.7949 (mtp) REVERT: D 1122 VAL cc_start: 0.8814 (p) cc_final: 0.8607 (p) REVERT: C 64 ASN cc_start: 0.8061 (m-40) cc_final: 0.7755 (t0) REVERT: C 152 MET cc_start: -0.1914 (mtt) cc_final: -0.3105 (mmt) REVERT: C 270 MET cc_start: -0.0479 (mpp) cc_final: -0.0745 (mpp) REVERT: C 274 PHE cc_start: 0.8203 (p90) cc_final: 0.7995 (m-80) REVERT: C 383 MET cc_start: 0.2636 (mtp) cc_final: 0.1873 (ppp) REVERT: C 585 LEU cc_start: 0.7537 (tp) cc_final: 0.7301 (pp) REVERT: B 86 PHE cc_start: 0.6155 (t80) cc_final: 0.5807 (t80) REVERT: B 117 LEU cc_start: 0.8855 (tp) cc_final: 0.8241 (mp) REVERT: B 180 GLU cc_start: 0.7134 (tt0) cc_final: 0.6920 (tp30) REVERT: B 302 THR cc_start: 0.8924 (m) cc_final: 0.8581 (m) REVERT: B 417 ASN cc_start: 0.9117 (m-40) cc_final: 0.8581 (t0) REVERT: B 565 PHE cc_start: 0.7637 (p90) cc_final: 0.7426 (p90) REVERT: B 661 GLU cc_start: 0.8058 (tp30) cc_final: 0.7744 (tp30) REVERT: B 904 TYR cc_start: 0.8494 (t80) cc_final: 0.8219 (t80) REVERT: B 905 ARG cc_start: 0.9216 (mtt-85) cc_final: 0.8905 (mmm-85) REVERT: B 936 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8757 (p0) REVERT: B 1010 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8937 (tm-30) REVERT: B 1023 ASN cc_start: 0.9412 (t0) cc_final: 0.9027 (t0) REVERT: B 1040 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8765 (p) outliers start: 97 outliers final: 57 residues processed: 568 average time/residue: 0.1787 time to fit residues: 166.9959 Evaluate side-chains 428 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 367 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 726 ILE Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 821 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 925 ASN Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 156 optimal weight: 3.9990 chunk 353 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 340 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 544 ASN A 949 GLN A 953 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS D 188 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN C 42 GLN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 61 ASN B 282 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1106 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.111156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.093502 restraints weight = 240400.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.095024 restraints weight = 125647.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.095888 restraints weight = 77829.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.096562 restraints weight = 55546.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.097053 restraints weight = 43408.017| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 30962 Z= 0.169 Angle : 0.622 10.529 42129 Z= 0.325 Chirality : 0.045 0.188 4684 Planarity : 0.004 0.067 5455 Dihedral : 4.301 25.297 4105 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.59 % Favored : 97.39 % Rotamer: Outliers : 3.28 % Allowed : 10.97 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 3791 helix: 0.25 (0.16), residues: 1005 sheet: -0.01 (0.18), residues: 676 loop : -0.75 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1019 TYR 0.029 0.002 TYR D 873 PHE 0.023 0.002 PHE C 438 TRP 0.032 0.002 TRP B 886 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00360 (30924) covalent geometry : angle 0.61994 (42053) SS BOND : bond 0.00523 ( 38) SS BOND : angle 1.37336 ( 76) hydrogen bonds : bond 0.04919 ( 1051) hydrogen bonds : angle 5.87586 ( 3006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 402 time to evaluate : 1.568 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 177 MET cc_start: 0.1941 (ttm) cc_final: -0.0263 (mtp) REVERT: A 663 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7108 (p0) REVERT: A 740 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8242 (mmm) REVERT: A 747 THR cc_start: 0.9341 (m) cc_final: 0.9004 (p) REVERT: A 762 GLN cc_start: 0.9330 (pt0) cc_final: 0.9111 (pt0) REVERT: A 776 LYS cc_start: 0.9506 (tppt) cc_final: 0.9113 (tppt) REVERT: A 878 LEU cc_start: 0.9647 (tp) cc_final: 0.9430 (tp) REVERT: A 1011 GLN cc_start: 0.9388 (mm110) cc_final: 0.8952 (mm110) REVERT: A 1029 MET cc_start: 0.9583 (tpp) cc_final: 0.9364 (tpp) REVERT: A 1030 SER cc_start: 0.9667 (m) cc_final: 0.9424 (p) REVERT: A 1068 VAL cc_start: 0.9254 (t) cc_final: 0.8976 (p) REVERT: A 1138 TYR cc_start: 0.8548 (m-80) cc_final: 0.8199 (m-80) REVERT: D 133 PHE cc_start: 0.5996 (m-10) cc_final: 0.5118 (m-10) REVERT: D 296 LEU cc_start: 0.9221 (pp) cc_final: 0.8995 (tt) REVERT: D 563 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7461 (mm110) REVERT: D 770 ILE cc_start: 0.9500 (mt) cc_final: 0.9099 (mm) REVERT: D 775 ASP cc_start: 0.9290 (m-30) cc_final: 0.8893 (t0) REVERT: D 777 ASN cc_start: 0.9297 (m-40) cc_final: 0.9047 (t0) REVERT: D 797 PHE cc_start: 0.6955 (m-10) cc_final: 0.6687 (m-80) REVERT: D 869 MET cc_start: 0.9194 (mtp) cc_final: 0.8955 (mtt) REVERT: D 955 ASN cc_start: 0.9070 (m110) cc_final: 0.8640 (m110) REVERT: D 1014 ARG cc_start: 0.8826 (mmt-90) cc_final: 0.8564 (tpp-160) REVERT: D 1029 MET cc_start: 0.9585 (tpp) cc_final: 0.9354 (tpp) REVERT: C 152 MET cc_start: -0.0703 (mtt) cc_final: -0.2154 (mmt) REVERT: C 383 MET cc_start: 0.2298 (mtp) cc_final: 0.1642 (ppp) REVERT: B 86 PHE cc_start: 0.6261 (t80) cc_final: 0.5628 (t80) REVERT: B 117 LEU cc_start: 0.8868 (tp) cc_final: 0.8084 (mp) REVERT: B 118 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8884 (mp) REVERT: B 194 PHE cc_start: 0.6521 (m-10) cc_final: 0.6288 (m-10) REVERT: B 417 ASN cc_start: 0.9142 (m-40) cc_final: 0.8637 (t0) REVERT: B 725 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7778 (mt-10) REVERT: B 909 ILE cc_start: 0.9196 (pt) cc_final: 0.8962 (tp) REVERT: B 954 GLN cc_start: 0.9109 (mt0) cc_final: 0.8856 (mt0) REVERT: B 1010 GLN cc_start: 0.9296 (mm-40) cc_final: 0.9088 (tm-30) REVERT: B 1040 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.9007 (p) REVERT: B 1043 CYS cc_start: 0.5209 (m) cc_final: 0.5001 (m) REVERT: B 1045 LYS cc_start: 0.8489 (tptt) cc_final: 0.8149 (tptt) outliers start: 110 outliers final: 65 residues processed: 471 average time/residue: 0.1796 time to fit residues: 139.9937 Evaluate side-chains 396 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 327 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain D residue 1137 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1096 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 334 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 256 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 371 optimal weight: 0.9980 chunk 242 optimal weight: 8.9990 chunk 353 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 318 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN A 787 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS B1083 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.110079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.092498 restraints weight = 238469.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.094005 restraints weight = 123382.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.094877 restraints weight = 76011.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.095565 restraints weight = 53860.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.095918 restraints weight = 42118.553| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30962 Z= 0.145 Angle : 0.582 8.807 42129 Z= 0.303 Chirality : 0.044 0.174 4684 Planarity : 0.004 0.064 5455 Dihedral : 4.285 24.971 4105 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 2.56 % Allowed : 12.55 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 3791 helix: 0.42 (0.16), residues: 1025 sheet: -0.03 (0.19), residues: 683 loop : -0.75 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1019 TYR 0.016 0.001 TYR A 495 PHE 0.025 0.001 PHE A 759 TRP 0.047 0.002 TRP D 104 HIS 0.007 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00313 (30924) covalent geometry : angle 0.58010 (42053) SS BOND : bond 0.00338 ( 38) SS BOND : angle 1.24347 ( 76) hydrogen bonds : bond 0.04290 ( 1051) hydrogen bonds : angle 5.64520 ( 3006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 367 time to evaluate : 1.167 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 177 MET cc_start: 0.1697 (ttm) cc_final: -0.0245 (mtp) REVERT: A 773 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8740 (mm-30) REVERT: A 776 LYS cc_start: 0.9546 (tppt) cc_final: 0.9181 (tppt) REVERT: A 1011 GLN cc_start: 0.9328 (mm110) cc_final: 0.8862 (mm110) REVERT: A 1068 VAL cc_start: 0.9348 (t) cc_final: 0.9077 (p) REVERT: A 1138 TYR cc_start: 0.8566 (m-80) cc_final: 0.8255 (m-80) REVERT: D 55 PHE cc_start: 0.7730 (m-10) cc_final: 0.7469 (m-10) REVERT: D 133 PHE cc_start: 0.5864 (m-10) cc_final: 0.5012 (m-10) REVERT: D 326 ILE cc_start: 0.2897 (mm) cc_final: 0.2553 (mt) REVERT: D 563 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7786 (mm-40) REVERT: D 755 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8296 (tp-100) REVERT: D 770 ILE cc_start: 0.9524 (mt) cc_final: 0.9118 (mm) REVERT: D 775 ASP cc_start: 0.9184 (m-30) cc_final: 0.8968 (t0) REVERT: D 869 MET cc_start: 0.9157 (mtp) cc_final: 0.8880 (mtt) REVERT: D 955 ASN cc_start: 0.8887 (m110) cc_final: 0.8574 (m110) REVERT: D 965 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8494 (mm110) REVERT: D 1011 GLN cc_start: 0.9243 (mm110) cc_final: 0.8607 (mm-40) REVERT: D 1029 MET cc_start: 0.9550 (tpp) cc_final: 0.9336 (tpp) REVERT: C 152 MET cc_start: -0.1364 (mtt) cc_final: -0.2434 (mmt) REVERT: C 383 MET cc_start: 0.1877 (mtp) cc_final: 0.1269 (ppp) REVERT: C 473 TRP cc_start: -0.1284 (m-10) cc_final: -0.1573 (m100) REVERT: B 117 LEU cc_start: 0.8814 (tp) cc_final: 0.8130 (mp) REVERT: B 417 ASN cc_start: 0.9118 (m-40) cc_final: 0.8595 (t0) REVERT: B 661 GLU cc_start: 0.8194 (tp30) cc_final: 0.7948 (tp30) REVERT: B 776 LYS cc_start: 0.9517 (tmtt) cc_final: 0.9224 (tptm) REVERT: B 954 GLN cc_start: 0.9048 (mt0) cc_final: 0.8759 (mt0) REVERT: B 1045 LYS cc_start: 0.8527 (tptt) cc_final: 0.8193 (tptt) outliers start: 86 outliers final: 61 residues processed: 421 average time/residue: 0.1762 time to fit residues: 124.0407 Evaluate side-chains 393 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 332 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 225 optimal weight: 2.9990 chunk 366 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 333 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 493 GLN A1048 HIS ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 GLN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.109968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.093693 restraints weight = 239310.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.095324 restraints weight = 125761.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.096358 restraints weight = 67138.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.096304 restraints weight = 53933.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.096263 restraints weight = 45711.165| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30962 Z= 0.125 Angle : 0.561 7.671 42129 Z= 0.291 Chirality : 0.044 0.224 4684 Planarity : 0.004 0.063 5455 Dihedral : 4.177 23.567 4105 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 2.68 % Allowed : 12.79 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 3791 helix: 0.58 (0.16), residues: 1017 sheet: -0.08 (0.19), residues: 660 loop : -0.72 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1019 TYR 0.016 0.001 TYR B 904 PHE 0.035 0.001 PHE D 306 TRP 0.034 0.001 TRP D 104 HIS 0.026 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00269 (30924) covalent geometry : angle 0.55928 (42053) SS BOND : bond 0.00374 ( 38) SS BOND : angle 1.12397 ( 76) hydrogen bonds : bond 0.04113 ( 1051) hydrogen bonds : angle 5.48647 ( 3006) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 359 time to evaluate : 1.149 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 177 MET cc_start: 0.2186 (ttm) cc_final: 0.0401 (mtp) REVERT: A 651 ILE cc_start: 0.9248 (pt) cc_final: 0.9019 (mp) REVERT: A 776 LYS cc_start: 0.9558 (tppt) cc_final: 0.9282 (tppt) REVERT: A 1068 VAL cc_start: 0.9333 (t) cc_final: 0.9047 (p) REVERT: A 1138 TYR cc_start: 0.8796 (m-80) cc_final: 0.8440 (m-80) REVERT: D 55 PHE cc_start: 0.7867 (m-10) cc_final: 0.7560 (m-10) REVERT: D 133 PHE cc_start: 0.6046 (m-10) cc_final: 0.5134 (m-10) REVERT: D 177 MET cc_start: 0.2475 (tpp) cc_final: 0.1930 (tpp) REVERT: D 296 LEU cc_start: 0.9258 (pp) cc_final: 0.8969 (tt) REVERT: D 326 ILE cc_start: 0.3174 (mm) cc_final: 0.2893 (mt) REVERT: D 563 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7810 (mm-40) REVERT: D 726 ILE cc_start: 0.8960 (mm) cc_final: 0.8584 (tt) REVERT: D 869 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8860 (mtt) REVERT: D 955 ASN cc_start: 0.8929 (m110) cc_final: 0.8563 (m110) REVERT: D 1011 GLN cc_start: 0.9257 (mm110) cc_final: 0.8599 (mm-40) REVERT: D 1029 MET cc_start: 0.9564 (tpp) cc_final: 0.9345 (tpp) REVERT: C 152 MET cc_start: -0.5766 (mtt) cc_final: -0.5988 (mmt) REVERT: C 332 MET cc_start: 0.5642 (ppp) cc_final: 0.5389 (ppp) REVERT: C 383 MET cc_start: 0.1480 (mtp) cc_final: 0.0660 (tmm) REVERT: B 117 LEU cc_start: 0.8994 (tp) cc_final: 0.8242 (mp) REVERT: B 118 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9029 (pt) REVERT: B 318 PHE cc_start: 0.8075 (p90) cc_final: 0.7822 (p90) REVERT: B 417 ASN cc_start: 0.9128 (m-40) cc_final: 0.8592 (t0) REVERT: B 661 GLU cc_start: 0.8150 (tp30) cc_final: 0.7920 (tp30) REVERT: B 774 GLN cc_start: 0.9401 (mm-40) cc_final: 0.8800 (mm110) REVERT: B 904 TYR cc_start: 0.8497 (t80) cc_final: 0.8206 (t80) REVERT: B 954 GLN cc_start: 0.9104 (mt0) cc_final: 0.8790 (mt0) REVERT: B 1010 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8519 (tm-30) REVERT: B 1045 LYS cc_start: 0.8788 (tptt) cc_final: 0.8471 (tptt) REVERT: B 1092 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 1113 GLN cc_start: 0.8513 (mm-40) cc_final: 0.7907 (mm-40) outliers start: 90 outliers final: 61 residues processed: 418 average time/residue: 0.1726 time to fit residues: 121.0878 Evaluate side-chains 384 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 321 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 902 MET Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1137 VAL Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1023 ASN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1103 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 296 optimal weight: 8.9990 chunk 344 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 339 optimal weight: 0.1980 chunk 185 optimal weight: 0.5980 chunk 260 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 287 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 103 optimal weight: 0.0030 chunk 347 optimal weight: 0.0030 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 762 GLN A 935 GLN A1011 GLN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS C 61 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.110580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.094426 restraints weight = 237682.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.096062 restraints weight = 124473.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.097148 restraints weight = 65328.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.097132 restraints weight = 51067.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.097054 restraints weight = 43568.428| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30962 Z= 0.107 Angle : 0.555 10.083 42129 Z= 0.281 Chirality : 0.043 0.253 4684 Planarity : 0.004 0.066 5455 Dihedral : 4.032 22.294 4105 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.97 % Rotamer: Outliers : 2.09 % Allowed : 13.12 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 3791 helix: 0.73 (0.16), residues: 1003 sheet: -0.06 (0.19), residues: 662 loop : -0.66 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1000 TYR 0.018 0.001 TYR D 873 PHE 0.033 0.001 PHE D 306 TRP 0.032 0.001 TRP D 104 HIS 0.006 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00231 (30924) covalent geometry : angle 0.55332 (42053) SS BOND : bond 0.00356 ( 38) SS BOND : angle 1.07387 ( 76) hydrogen bonds : bond 0.03907 ( 1051) hydrogen bonds : angle 5.32157 ( 3006) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 374 time to evaluate : 1.342 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 55 PHE cc_start: 0.7217 (m-80) cc_final: 0.6925 (m-10) REVERT: A 177 MET cc_start: 0.2083 (ttm) cc_final: 0.0235 (mtp) REVERT: A 651 ILE cc_start: 0.9230 (pt) cc_final: 0.9005 (mp) REVERT: A 776 LYS cc_start: 0.9538 (tppt) cc_final: 0.9338 (tppt) REVERT: A 1028 LYS cc_start: 0.9496 (mmmm) cc_final: 0.9227 (mmmt) REVERT: A 1029 MET cc_start: 0.9359 (tpp) cc_final: 0.9127 (tpt) REVERT: A 1068 VAL cc_start: 0.9327 (t) cc_final: 0.9030 (p) REVERT: A 1138 TYR cc_start: 0.8852 (m-80) cc_final: 0.8500 (m-80) REVERT: D 55 PHE cc_start: 0.7988 (m-10) cc_final: 0.7627 (m-10) REVERT: D 133 PHE cc_start: 0.5874 (m-10) cc_final: 0.4988 (m-10) REVERT: D 177 MET cc_start: 0.2428 (OUTLIER) cc_final: 0.1878 (tpp) REVERT: D 296 LEU cc_start: 0.9252 (pp) cc_final: 0.8989 (tt) REVERT: D 326 ILE cc_start: 0.3197 (mm) cc_final: 0.2775 (mt) REVERT: D 563 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7754 (mm-40) REVERT: D 726 ILE cc_start: 0.8888 (mm) cc_final: 0.8469 (tt) REVERT: D 869 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8941 (mtm) REVERT: D 955 ASN cc_start: 0.8884 (m110) cc_final: 0.8529 (m110) REVERT: D 970 PHE cc_start: 0.8152 (m-10) cc_final: 0.7902 (m-10) REVERT: D 1011 GLN cc_start: 0.9256 (mm110) cc_final: 0.8600 (mm-40) REVERT: D 1014 ARG cc_start: 0.8724 (tpp-160) cc_final: 0.8266 (tpp-160) REVERT: C 332 MET cc_start: 0.5492 (ppp) cc_final: 0.5071 (ppp) REVERT: C 383 MET cc_start: 0.1520 (mtp) cc_final: 0.0558 (tmm) REVERT: B 117 LEU cc_start: 0.8965 (tp) cc_final: 0.8206 (mp) REVERT: B 118 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9027 (pt) REVERT: B 318 PHE cc_start: 0.8032 (p90) cc_final: 0.7824 (p90) REVERT: B 417 ASN cc_start: 0.9115 (m-40) cc_final: 0.8567 (t0) REVERT: B 661 GLU cc_start: 0.8202 (tp30) cc_final: 0.7936 (tp30) REVERT: B 751 ASN cc_start: 0.9055 (p0) cc_final: 0.8851 (p0) REVERT: B 774 GLN cc_start: 0.9402 (mm-40) cc_final: 0.8972 (mm110) REVERT: B 775 ASP cc_start: 0.8799 (m-30) cc_final: 0.8465 (t0) REVERT: B 904 TYR cc_start: 0.8477 (t80) cc_final: 0.8136 (t80) REVERT: B 954 GLN cc_start: 0.9152 (mt0) cc_final: 0.8817 (mt0) REVERT: B 1010 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8439 (tm-30) REVERT: B 1045 LYS cc_start: 0.8809 (tptt) cc_final: 0.8527 (tptt) REVERT: B 1050 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7882 (ptp) REVERT: B 1092 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7753 (tm-30) REVERT: B 1113 GLN cc_start: 0.8587 (mm-40) cc_final: 0.7947 (mm110) outliers start: 70 outliers final: 54 residues processed: 418 average time/residue: 0.1767 time to fit residues: 123.6955 Evaluate side-chains 395 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 337 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1137 VAL Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1023 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1103 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 46 optimal weight: 7.9990 chunk 354 optimal weight: 0.9980 chunk 256 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 328 optimal weight: 8.9990 chunk 311 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 655 HIS A 658 ASN A 762 GLN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 901 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.105641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.088065 restraints weight = 239912.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.089497 restraints weight = 125885.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.090341 restraints weight = 78370.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.091007 restraints weight = 55880.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.091294 restraints weight = 43914.732| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 30962 Z= 0.204 Angle : 0.640 9.130 42129 Z= 0.335 Chirality : 0.045 0.232 4684 Planarity : 0.004 0.064 5455 Dihedral : 4.423 24.017 4105 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.89 % Allowed : 13.36 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.13), residues: 3791 helix: 0.49 (0.16), residues: 1014 sheet: -0.20 (0.19), residues: 679 loop : -0.77 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 765 TYR 0.021 0.002 TYR B 904 PHE 0.031 0.002 PHE A 759 TRP 0.039 0.002 TRP B 886 HIS 0.008 0.002 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00440 (30924) covalent geometry : angle 0.63795 (42053) SS BOND : bond 0.00605 ( 38) SS BOND : angle 1.27974 ( 76) hydrogen bonds : bond 0.04321 ( 1051) hydrogen bonds : angle 5.57502 ( 3006) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 330 time to evaluate : 1.171 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 177 MET cc_start: 0.2265 (ttm) cc_final: 0.1824 (ttm) REVERT: A 776 LYS cc_start: 0.9563 (tppt) cc_final: 0.9347 (tppt) REVERT: A 822 LEU cc_start: 0.9585 (mt) cc_final: 0.9161 (tt) REVERT: A 902 MET cc_start: 0.9530 (mmp) cc_final: 0.9111 (tpp) REVERT: A 1011 GLN cc_start: 0.9259 (mm-40) cc_final: 0.9048 (mm110) REVERT: A 1029 MET cc_start: 0.9485 (tpp) cc_final: 0.9202 (tpp) REVERT: A 1068 VAL cc_start: 0.9341 (t) cc_final: 0.9132 (p) REVERT: D 55 PHE cc_start: 0.8081 (m-10) cc_final: 0.7821 (m-10) REVERT: D 177 MET cc_start: 0.2249 (tpp) cc_final: 0.1837 (tpp) REVERT: D 296 LEU cc_start: 0.9208 (pp) cc_final: 0.8980 (tt) REVERT: D 726 ILE cc_start: 0.8780 (mm) cc_final: 0.8491 (tt) REVERT: D 776 LYS cc_start: 0.9217 (tmmt) cc_final: 0.9009 (tmmt) REVERT: D 796 ASP cc_start: 0.7598 (t0) cc_final: 0.7356 (t0) REVERT: D 869 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8923 (mtt) REVERT: D 955 ASN cc_start: 0.8917 (m110) cc_final: 0.8471 (m110) REVERT: D 970 PHE cc_start: 0.8419 (m-10) cc_final: 0.8196 (m-10) REVERT: D 1011 GLN cc_start: 0.9222 (mm110) cc_final: 0.8579 (mm-40) REVERT: C 323 MET cc_start: 0.2038 (mmt) cc_final: 0.0344 (mmm) REVERT: C 332 MET cc_start: 0.7152 (ppp) cc_final: 0.6712 (ppp) REVERT: C 360 MET cc_start: 0.5244 (OUTLIER) cc_final: 0.5025 (mtm) REVERT: C 383 MET cc_start: 0.1183 (mtp) cc_final: 0.0686 (ttp) REVERT: B 117 LEU cc_start: 0.8874 (tp) cc_final: 0.8136 (mp) REVERT: B 417 ASN cc_start: 0.9091 (m-40) cc_final: 0.8499 (t0) REVERT: B 557 LYS cc_start: 0.7240 (mmtt) cc_final: 0.6982 (mmtm) REVERT: B 774 GLN cc_start: 0.9417 (mm-40) cc_final: 0.9153 (mm110) REVERT: B 954 GLN cc_start: 0.9090 (mt0) cc_final: 0.8842 (mt0) REVERT: B 1045 LYS cc_start: 0.8870 (tptt) cc_final: 0.8615 (tptt) outliers start: 97 outliers final: 70 residues processed: 397 average time/residue: 0.1789 time to fit residues: 119.1331 Evaluate side-chains 358 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 286 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 607 GLN Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain D residue 1137 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 266 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 333 optimal weight: 10.0000 chunk 290 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 341 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 762 GLN A 935 GLN ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 ASN B 282 ASN B 487 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.105108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.088983 restraints weight = 240973.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.090075 restraints weight = 141808.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.090465 restraints weight = 86560.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.090647 restraints weight = 68672.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.090767 restraints weight = 69139.194| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.7153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30962 Z= 0.181 Angle : 0.638 10.107 42129 Z= 0.331 Chirality : 0.045 0.269 4684 Planarity : 0.004 0.065 5455 Dihedral : 4.500 23.265 4105 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.80 % Allowed : 14.28 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.13), residues: 3791 helix: 0.52 (0.16), residues: 1007 sheet: -0.33 (0.19), residues: 685 loop : -0.81 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 765 TYR 0.036 0.002 TYR B 904 PHE 0.027 0.002 PHE A 759 TRP 0.049 0.002 TRP D 104 HIS 0.009 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00398 (30924) covalent geometry : angle 0.63391 (42053) SS BOND : bond 0.00464 ( 38) SS BOND : angle 1.80547 ( 76) hydrogen bonds : bond 0.04231 ( 1051) hydrogen bonds : angle 5.57856 ( 3006) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 318 time to evaluate : 1.277 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: A 173 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7373 (pm20) REVERT: A 177 MET cc_start: 0.2511 (ttm) cc_final: 0.2129 (ttm) REVERT: A 258 TRP cc_start: 0.4123 (OUTLIER) cc_final: 0.3659 (m100) REVERT: A 287 ASP cc_start: 0.6879 (t0) cc_final: 0.6634 (t0) REVERT: A 822 LEU cc_start: 0.9620 (mt) cc_final: 0.9264 (tp) REVERT: A 912 THR cc_start: 0.8693 (m) cc_final: 0.8434 (p) REVERT: D 55 PHE cc_start: 0.8200 (m-10) cc_final: 0.7953 (m-10) REVERT: D 177 MET cc_start: 0.2833 (tpp) cc_final: 0.2155 (tpp) REVERT: D 296 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8985 (tt) REVERT: D 726 ILE cc_start: 0.8980 (mm) cc_final: 0.8534 (tt) REVERT: D 727 LEU cc_start: 0.9124 (mm) cc_final: 0.8919 (mp) REVERT: D 796 ASP cc_start: 0.7366 (t0) cc_final: 0.6722 (t0) REVERT: D 869 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8900 (mtt) REVERT: D 955 ASN cc_start: 0.8887 (m110) cc_final: 0.8505 (m110) REVERT: D 970 PHE cc_start: 0.8485 (m-10) cc_final: 0.8246 (m-10) REVERT: D 984 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8618 (tp) REVERT: D 1011 GLN cc_start: 0.9237 (mm110) cc_final: 0.8906 (tp40) REVERT: D 1014 ARG cc_start: 0.8664 (tpp-160) cc_final: 0.8285 (tpp-160) REVERT: C 323 MET cc_start: -0.1032 (mmt) cc_final: -0.2449 (mmm) REVERT: C 332 MET cc_start: 0.5553 (ppp) cc_final: 0.5062 (ppp) REVERT: C 383 MET cc_start: 0.1344 (mtp) cc_final: 0.0566 (ttp) REVERT: B 117 LEU cc_start: 0.9001 (tp) cc_final: 0.8217 (mp) REVERT: B 417 ASN cc_start: 0.9026 (m-40) cc_final: 0.8457 (t0) REVERT: B 557 LYS cc_start: 0.7418 (mmtt) cc_final: 0.7037 (mmtm) REVERT: B 774 GLN cc_start: 0.9322 (mm-40) cc_final: 0.9061 (mm-40) REVERT: B 954 GLN cc_start: 0.9123 (mt0) cc_final: 0.8835 (mt0) REVERT: B 1045 LYS cc_start: 0.8877 (tptt) cc_final: 0.8590 (tptt) outliers start: 94 outliers final: 68 residues processed: 384 average time/residue: 0.1879 time to fit residues: 120.1551 Evaluate side-chains 362 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 290 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1137 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 580 ASN Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 171 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 362 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 233 optimal weight: 20.0000 chunk 269 optimal weight: 0.3980 chunk 210 optimal weight: 5.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 762 GLN A1159 HIS D 173 GLN ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 925 ASN ** C 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS C 265 HIS C 505 HIS ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 ASN B 242 HIS B 655 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.101156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.083799 restraints weight = 238861.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.085194 restraints weight = 124283.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.085991 restraints weight = 76943.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.086558 restraints weight = 55125.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.086965 restraints weight = 44116.727| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.8026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 30962 Z= 0.252 Angle : 0.735 10.463 42129 Z= 0.386 Chirality : 0.047 0.280 4684 Planarity : 0.005 0.068 5455 Dihedral : 5.085 27.251 4105 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.16 % Allowed : 14.34 % Favored : 82.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 3791 helix: 0.07 (0.16), residues: 1036 sheet: -0.55 (0.19), residues: 668 loop : -1.11 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 765 TYR 0.041 0.002 TYR A 741 PHE 0.031 0.002 PHE D 194 TRP 0.042 0.002 TRP D 104 HIS 0.012 0.002 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00547 (30924) covalent geometry : angle 0.73127 (42053) SS BOND : bond 0.00532 ( 38) SS BOND : angle 1.97996 ( 76) hydrogen bonds : bond 0.04634 ( 1051) hydrogen bonds : angle 6.00070 ( 3006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 301 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.7902 (m-10) cc_final: 0.7346 (m-80) REVERT: A 773 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8851 (mm-30) REVERT: A 822 LEU cc_start: 0.9593 (mt) cc_final: 0.9272 (tp) REVERT: A 912 THR cc_start: 0.8700 (m) cc_final: 0.8424 (p) REVERT: D 177 MET cc_start: 0.2298 (tpp) cc_final: 0.1927 (tpp) REVERT: D 296 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8668 (tt) REVERT: D 869 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8957 (mtt) REVERT: D 984 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8571 (tp) REVERT: D 995 ARG cc_start: 0.9384 (mtt180) cc_final: 0.8828 (ttp-110) REVERT: D 1011 GLN cc_start: 0.9222 (mm110) cc_final: 0.8941 (tp40) REVERT: D 1014 ARG cc_start: 0.8699 (tpp-160) cc_final: 0.8374 (tpp-160) REVERT: C 323 MET cc_start: 0.2055 (mmt) cc_final: 0.0930 (mmm) REVERT: C 332 MET cc_start: 0.6892 (ppp) cc_final: 0.6606 (ppp) REVERT: C 360 MET cc_start: 0.4821 (mtm) cc_final: 0.4585 (mtm) REVERT: C 383 MET cc_start: 0.1179 (mtp) cc_final: 0.0469 (ppp) REVERT: B 117 LEU cc_start: 0.8770 (tp) cc_final: 0.8088 (mp) REVERT: B 153 MET cc_start: -0.0833 (ptt) cc_final: -0.1120 (ptt) REVERT: B 417 ASN cc_start: 0.8995 (m-40) cc_final: 0.8423 (t0) REVERT: B 557 LYS cc_start: 0.7281 (mmtt) cc_final: 0.6790 (mmtm) REVERT: B 774 GLN cc_start: 0.9385 (mm-40) cc_final: 0.8973 (mm-40) REVERT: B 797 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6129 (m-10) REVERT: B 936 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8714 (p0) REVERT: B 954 GLN cc_start: 0.9119 (mt0) cc_final: 0.8830 (mt0) REVERT: B 1041 ASP cc_start: 0.7620 (m-30) cc_final: 0.6857 (m-30) outliers start: 106 outliers final: 77 residues processed: 375 average time/residue: 0.1744 time to fit residues: 110.2571 Evaluate side-chains 357 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 275 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 607 GLN Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1137 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 797 PHE Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 145 optimal weight: 0.0670 chunk 191 optimal weight: 0.8980 chunk 318 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 0.0000 chunk 351 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 280 ASN A 580 GLN A1159 HIS D 196 ASN D 360 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 935 GLN B1005 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.105802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.089647 restraints weight = 236176.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.091001 restraints weight = 122994.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.091007 restraints weight = 84055.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.091680 restraints weight = 64766.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.091948 restraints weight = 46766.400| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.7835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30962 Z= 0.123 Angle : 0.647 12.112 42129 Z= 0.330 Chirality : 0.046 0.301 4684 Planarity : 0.004 0.066 5455 Dihedral : 4.593 22.214 4105 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.70 % Allowed : 16.37 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.13), residues: 3791 helix: 0.48 (0.16), residues: 1019 sheet: -0.38 (0.20), residues: 638 loop : -0.92 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 765 TYR 0.027 0.001 TYR D 873 PHE 0.031 0.002 PHE D 92 TRP 0.058 0.002 TRP D 104 HIS 0.007 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00269 (30924) covalent geometry : angle 0.64402 (42053) SS BOND : bond 0.00377 ( 38) SS BOND : angle 1.50325 ( 76) hydrogen bonds : bond 0.04072 ( 1051) hydrogen bonds : angle 5.59688 ( 3006) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 340 time to evaluate : 1.257 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 173 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7126 (pm20) REVERT: A 287 ASP cc_start: 0.7497 (t0) cc_final: 0.7283 (t0) REVERT: A 773 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8839 (mp0) REVERT: A 902 MET cc_start: 0.9513 (mmp) cc_final: 0.9307 (tpp) REVERT: A 912 THR cc_start: 0.8700 (m) cc_final: 0.8441 (p) REVERT: D 55 PHE cc_start: 0.8119 (m-10) cc_final: 0.7744 (m-10) REVERT: D 104 TRP cc_start: 0.6953 (m-90) cc_final: 0.6659 (m100) REVERT: D 148 ASN cc_start: 0.8460 (m-40) cc_final: 0.7562 (t0) REVERT: D 177 MET cc_start: 0.2356 (tpp) cc_final: 0.1815 (tpp) REVERT: D 726 ILE cc_start: 0.8780 (mm) cc_final: 0.8486 (tt) REVERT: D 730 SER cc_start: 0.9486 (p) cc_final: 0.9137 (t) REVERT: D 869 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8725 (mtm) REVERT: D 995 ARG cc_start: 0.9332 (mtt180) cc_final: 0.8760 (ttp-110) REVERT: D 1011 GLN cc_start: 0.9243 (mm110) cc_final: 0.8966 (tp40) REVERT: D 1014 ARG cc_start: 0.8766 (tpp-160) cc_final: 0.8331 (tpp-160) REVERT: C 323 MET cc_start: -0.0583 (mmt) cc_final: -0.1990 (mmm) REVERT: C 332 MET cc_start: 0.5004 (ppp) cc_final: 0.4688 (ppp) REVERT: C 355 ASP cc_start: 0.5942 (t0) cc_final: 0.5048 (m-30) REVERT: C 360 MET cc_start: 0.4304 (mtm) cc_final: 0.3995 (mtm) REVERT: C 383 MET cc_start: 0.1344 (mtp) cc_final: 0.0114 (tmm) REVERT: B 117 LEU cc_start: 0.8801 (tp) cc_final: 0.8153 (mp) REVERT: B 201 PHE cc_start: 0.9333 (m-10) cc_final: 0.9073 (m-80) REVERT: B 417 ASN cc_start: 0.8994 (m-40) cc_final: 0.8471 (t0) REVERT: B 557 LYS cc_start: 0.7208 (mmtt) cc_final: 0.6704 (mmtm) REVERT: B 895 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8255 (pp30) REVERT: B 936 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8611 (p0) REVERT: B 947 LYS cc_start: 0.9085 (tptt) cc_final: 0.8728 (tppt) REVERT: B 954 GLN cc_start: 0.9099 (mt0) cc_final: 0.8786 (mt0) REVERT: B 1092 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7835 (tm-30) REVERT: B 1146 ASP cc_start: 0.8049 (m-30) cc_final: 0.7788 (t0) outliers start: 57 outliers final: 42 residues processed: 386 average time/residue: 0.1795 time to fit residues: 116.4026 Evaluate side-chains 355 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 310 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1137 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 190 optimal weight: 0.9980 chunk 248 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.096637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.074095 restraints weight = 193865.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.075739 restraints weight = 109500.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.076776 restraints weight = 72628.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.077421 restraints weight = 54137.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.077809 restraints weight = 44266.112| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.7863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.254 30962 Z= 0.233 Angle : 0.838 59.196 42129 Z= 0.457 Chirality : 0.050 0.968 4684 Planarity : 0.005 0.183 5455 Dihedral : 4.567 22.381 4105 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.76 % Allowed : 16.73 % Favored : 81.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 3791 helix: 0.47 (0.16), residues: 1019 sheet: -0.39 (0.20), residues: 634 loop : -0.92 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 765 TYR 0.028 0.001 TYR A1007 PHE 0.028 0.002 PHE B 201 TRP 0.046 0.002 TRP D 104 HIS 0.007 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00526 (30924) covalent geometry : angle 0.83611 (42053) SS BOND : bond 0.00358 ( 38) SS BOND : angle 1.50769 ( 76) hydrogen bonds : bond 0.04131 ( 1051) hydrogen bonds : angle 5.61217 ( 3006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7245.71 seconds wall clock time: 125 minutes 26.68 seconds (7526.68 seconds total)