Starting phenix.real_space_refine on Fri Mar 6 10:01:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vxk_32182/03_2026/7vxk_32182.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vxk_32182/03_2026/7vxk_32182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vxk_32182/03_2026/7vxk_32182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vxk_32182/03_2026/7vxk_32182.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vxk_32182/03_2026/7vxk_32182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vxk_32182/03_2026/7vxk_32182.map" } resolution = 3.7 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= -0.000 sd= 0.145 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 144 5.16 5 C 19214 2.51 5 N 5012 2.21 5 O 5709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s 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: 30079 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} 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: "D" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8301 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 51, 'TRANS': 1007} Chain breaks: 6 Time building chain proxies: 6.10, per 1000 atoms: 0.20 Number of scatterers: 30079 At special positions: 0 Unit cell: (160.671, 149.741, 263.413, 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 144 16.00 O 5709 8.00 N 5012 7.00 C 19214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.00 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 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 B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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: 2.41 Conformation dependent library (CDL) restraints added in 1.4 seconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7156 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 47 sheets defined 31.4% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 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: 3.945A 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 386 through 389 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.758A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.696A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.544A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 removed outlier: 4.340A 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: 3.584A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.510A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 4.159A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.609A 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: 3.954A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.654A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.511A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1154 removed outlier: 4.370A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS A1154 " --> pdb=" O GLU A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 removed outlier: 3.762A pdb=" N HIS A1159 " --> pdb=" O TYR A1155 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A1160 " --> pdb=" O PHE A1156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1155 through 1160' Processing helix chain 'C' and resid 20 through 53 removed outlier: 4.045A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.765A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.543A 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: 4.151A pdb=" N LEU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.909A pdb=" N GLU C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.506A 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: 3.519A pdb=" N LYS C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.953A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 removed outlier: 3.819A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 removed outlier: 3.775A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.622A pdb=" N ARG C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 194 removed outlier: 3.645A pdb=" N MET C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 removed outlier: 3.524A pdb=" N TYR C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 204' Processing helix chain 'C' and resid 205 through 208 Processing helix chain 'C' and resid 220 through 249 removed outlier: 3.962A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.779A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 293 through 301 removed outlier: 3.766A pdb=" N ASP C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 removed outlier: 4.031A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.629A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.621A pdb=" N PHE C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 370 " --> pdb=" O MET C 366 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS C 378 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) removed outlier: 4.294A 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: 3.539A pdb=" N VAL C 404 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.692A pdb=" N ILE C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.682A pdb=" N ASN C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 466 removed outlier: 4.114A 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: 3.868A pdb=" N GLU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 removed outlier: 4.147A pdb=" N SER C 502 " --> pdb=" O CYS C 498 " (cutoff:3.500A) removed outlier: 3.902A 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: 3.502A pdb=" N THR C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.639A pdb=" N GLN C 552 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN C 556 " --> pdb=" O GLN C 552 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 removed outlier: 3.508A pdb=" N GLU C 571 " --> pdb=" O THR C 567 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.588A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.641A pdb=" N TRP C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 386 through 390 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.689A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.867A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 780 removed outlier: 3.660A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 removed outlier: 3.832A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 855 Processing helix chain 'D' and resid 866 through 882 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.729A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.860A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 3.592A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.847A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 3.872A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1160 removed outlier: 4.296A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.530A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.193A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.119A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.501A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.748A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.645A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.694A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.922A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.339A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.900A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.531A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.849A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 984 removed outlier: 3.624A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.445A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.835A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.767A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.298A 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: 4.355A 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: 3.573A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.553A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.518A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.548A 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: 3.876A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.965A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.566A 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: 5.713A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 672 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 4.005A 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: 3.546A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.727A 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: 3.648A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.769A 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: 3.578A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.534A pdb=" N LEU C 142 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.156A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.539A pdb=" N THR C 347 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 27 through 30 removed outlier: 3.835A pdb=" N ALA D 27 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.538A pdb=" N VAL D 47 " --> pdb=" O TYR D 279 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.506A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL D 126 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN D 134 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N ASN D 164 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AC5, first strand: chain 'D' and resid 311 through 319 removed outlier: 3.650A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 325 through 327 removed outlier: 3.511A pdb=" N VAL D 539 " --> pdb=" O GLY D 550 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE D 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 354 through 359 removed outlier: 3.578A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 513 " --> pdb=" O CYS D 432 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N CYS D 432 " --> pdb=" O LEU D 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'D' and resid 654 through 660 removed outlier: 6.232A 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) removed outlier: 8.780A pdb=" N VAL D 656 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 701 through 702 removed outlier: 6.621A pdb=" N VAL D 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.693A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.555A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.646A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.574A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.395A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.828A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.877A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.449A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.900A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AE8, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.627A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.518A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'B' and resid 1094 through 1097 1132 hydrogen bonds defined for protein. 3198 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: 6.95 Time building geometry restraints manager: 3.22 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: 9717 1.35 - 1.46: 7581 1.46 - 1.58: 13311 1.58 - 1.70: 0 1.70 - 1.82: 195 Bond restraints: 30804 Sorted by residual: bond pdb=" C LEU D 229 " pdb=" N PRO D 230 " ideal model delta sigma weight residual 1.334 1.425 -0.092 2.34e-02 1.83e+03 1.53e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.49e+00 bond pdb=" C PRO A 25 " pdb=" N PRO A 26 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.20e+00 bond pdb=" C GLY B 142 " pdb=" O GLY B 142 " ideal model delta sigma weight residual 1.243 1.229 0.013 9.30e-03 1.16e+04 2.08e+00 bond pdb=" N ILE B 410 " pdb=" CA ILE B 410 " ideal model delta sigma weight residual 1.459 1.474 -0.016 1.19e-02 7.06e+03 1.78e+00 ... (remaining 30799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 41497 2.02 - 4.03: 353 4.03 - 6.05: 31 6.05 - 8.07: 6 8.07 - 10.09: 2 Bond angle restraints: 41889 Sorted by residual: angle pdb=" C LYS A 790 " pdb=" N THR A 791 " pdb=" CA THR A 791 " ideal model delta sigma weight residual 120.94 130.64 -9.70 1.90e+00 2.77e-01 2.61e+01 angle pdb=" N CYS A 291 " pdb=" CA CYS A 291 " pdb=" C CYS A 291 " ideal model delta sigma weight residual 108.41 116.23 -7.82 1.61e+00 3.86e-01 2.36e+01 angle pdb=" N ALA A 292 " pdb=" CA ALA A 292 " pdb=" C ALA A 292 " ideal model delta sigma weight residual 110.80 100.71 10.09 2.13e+00 2.20e-01 2.24e+01 angle pdb=" C HIS B 242 " pdb=" N ILE B 243 " pdb=" CA ILE B 243 " ideal model delta sigma weight residual 121.97 127.90 -5.93 1.80e+00 3.09e-01 1.09e+01 angle pdb=" CA GLY D 667 " pdb=" C GLY D 667 " pdb=" O GLY D 667 " ideal model delta sigma weight residual 122.22 120.24 1.98 6.50e-01 2.37e+00 9.32e+00 ... (remaining 41884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 17875 15.99 - 31.98: 303 31.98 - 47.97: 109 47.97 - 63.97: 22 63.97 - 79.96: 8 Dihedral angle restraints: 18317 sinusoidal: 7197 harmonic: 11120 Sorted by residual: 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 54.15 38.85 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CA HIS D 242 " pdb=" C HIS D 242 " pdb=" N ILE D 243 " pdb=" CA ILE D 243 " ideal model delta harmonic sigma weight residual -180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA HIS B 242 " pdb=" C HIS B 242 " pdb=" N ILE B 243 " pdb=" CA ILE B 243 " ideal model delta harmonic sigma weight residual -180.00 -158.72 -21.28 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 18314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3626 0.044 - 0.087: 709 0.087 - 0.131: 326 0.131 - 0.174: 7 0.174 - 0.218: 3 Chirality restraints: 4671 Sorted by residual: chirality pdb=" CA ALA A 292 " pdb=" N ALA A 292 " pdb=" C ALA A 292 " pdb=" CB ALA A 292 " both_signs ideal model delta sigma weight residual False 2.48 2.70 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA CYS A 291 " pdb=" N CYS A 291 " pdb=" C CYS A 291 " pdb=" CB CYS A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CB ILE B 243 " pdb=" CA ILE B 243 " pdb=" CG1 ILE B 243 " pdb=" CG2 ILE B 243 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 4668 not shown) Planarity restraints: 5431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 290 " -0.017 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ASP A 290 " 0.061 2.00e-02 2.50e+03 pdb=" O ASP A 290 " -0.024 2.00e-02 2.50e+03 pdb=" N CYS A 291 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 24 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C LEU B 24 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU B 24 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO B 25 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 295 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.032 5.00e-02 4.00e+02 ... (remaining 5428 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5026 2.77 - 3.30: 27550 3.30 - 3.83: 48173 3.83 - 4.37: 56600 4.37 - 4.90: 98506 Nonbonded interactions: 235855 Sorted by model distance: nonbonded pdb=" O GLN A 755 " pdb=" OG SER B 968 " model vdw 2.235 3.040 nonbonded pdb=" N GLY B 142 " pdb=" O GLU B 156 " model vdw 2.244 3.120 nonbonded pdb=" OG1 THR A 912 " pdb=" NE2 GLN A1106 " model vdw 2.249 3.120 nonbonded pdb=" OH TYR D 756 " pdb=" OD1 ASP D 994 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR D 33 " pdb=" O GLY D 219 " model vdw 2.265 3.040 ... (remaining 235850 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 470 or resid 491 through 1161)) selection = chain 'B' selection = (chain 'D' and (resid 14 through 470 or resid 491 through 1161)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.180 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 30843 Z= 0.108 Angle : 0.509 11.099 41967 Z= 0.300 Chirality : 0.041 0.218 4671 Planarity : 0.003 0.057 5431 Dihedral : 7.671 79.957 11044 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.84 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % 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: -2.36 (0.11), residues: 3774 helix: -3.22 (0.10), residues: 1002 sheet: -0.26 (0.17), residues: 649 loop : -1.08 (0.12), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 905 TYR 0.017 0.001 TYR D 501 PHE 0.016 0.001 PHE D 133 TRP 0.020 0.001 TRP A 436 HIS 0.005 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00183 (30804) covalent geometry : angle 0.50444 (41889) SS BOND : bond 0.00573 ( 39) SS BOND : angle 1.65621 ( 78) hydrogen bonds : bond 0.28698 ( 1132) hydrogen bonds : angle 9.75358 ( 3198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 948 time to evaluate : 1.070 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 955 ASN cc_start: 0.6885 (m-40) cc_final: 0.6428 (m-40) REVERT: C 159 ASN cc_start: 0.7226 (m-40) cc_final: 0.6823 (p0) REVERT: C 432 ASN cc_start: 0.3267 (m-40) cc_final: 0.2064 (t0) REVERT: C 462 MET cc_start: 0.3544 (mtp) cc_final: 0.3106 (ptp) REVERT: C 558 LEU cc_start: 0.0689 (mt) cc_final: 0.0181 (mt) REVERT: D 976 VAL cc_start: 0.8024 (t) cc_final: 0.7766 (t) REVERT: D 1033 VAL cc_start: 0.8188 (t) cc_final: 0.7878 (t) REVERT: B 130 VAL cc_start: 0.5815 (t) cc_final: 0.5611 (t) REVERT: B 398 ASP cc_start: 0.2464 (m-30) cc_final: -0.0777 (m-30) REVERT: B 509 ARG cc_start: 0.4103 (mtt180) cc_final: 0.1998 (ptt180) REVERT: B 549 THR cc_start: 0.6546 (m) cc_final: 0.6313 (p) REVERT: B 693 ILE cc_start: 0.8519 (pt) cc_final: 0.7423 (pt) REVERT: B 962 LEU cc_start: 0.7463 (tp) cc_final: 0.6892 (tt) outliers start: 0 outliers final: 0 residues processed: 948 average time/residue: 0.1936 time to fit residues: 290.5118 Evaluate side-chains 441 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 394 ASN A 414 GLN A 544 ASN A 563 GLN A 787 GLN A 914 ASN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1106 GLN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 HIS C 378 HIS C 493 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 334 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 655 HIS D 774 GLN ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN D 895 GLN D1002 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN B 188 ASN B 644 GLN B 655 HIS B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 926 GLN B 953 ASN B 955 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.137478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.105209 restraints weight = 109160.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.107802 restraints weight = 52326.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.109795 restraints weight = 27953.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.109718 restraints weight = 19317.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.109658 restraints weight = 18376.682| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 30843 Z= 0.348 Angle : 0.876 13.846 41967 Z= 0.465 Chirality : 0.053 0.233 4671 Planarity : 0.006 0.096 5431 Dihedral : 5.195 27.286 4087 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.38 % Rotamer: Outliers : 3.44 % Allowed : 9.24 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % 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: -1.30 (0.12), residues: 3774 helix: -1.03 (0.14), residues: 1064 sheet: -0.02 (0.18), residues: 692 loop : -1.02 (0.12), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 102 TYR 0.043 0.003 TYR B 265 PHE 0.036 0.004 PHE B1121 TRP 0.033 0.002 TRP B 886 HIS 0.014 0.003 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00774 (30804) covalent geometry : angle 0.87232 (41889) SS BOND : bond 0.00786 ( 39) SS BOND : angle 2.00011 ( 78) hydrogen bonds : bond 0.05694 ( 1132) hydrogen bonds : angle 6.14289 ( 3198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 438 time to evaluate : 0.999 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: A 455 LEU cc_start: 0.5599 (tp) cc_final: 0.4888 (tp) REVERT: A 866 THR cc_start: 0.9165 (p) cc_final: 0.8927 (t) REVERT: A 900 MET cc_start: 0.8373 (mmm) cc_final: 0.7937 (mpp) REVERT: A 969 ASN cc_start: 0.7943 (m-40) cc_final: 0.7735 (m-40) REVERT: C 19 SER cc_start: 0.6224 (t) cc_final: 0.6023 (p) REVERT: C 159 ASN cc_start: 0.7557 (m-40) cc_final: 0.7059 (p0) REVERT: C 249 MET cc_start: 0.0776 (ptt) cc_final: -0.0582 (mmt) REVERT: C 274 PHE cc_start: 0.5909 (m-10) cc_final: 0.5451 (p90) REVERT: C 474 MET cc_start: 0.2443 (mmm) cc_final: 0.2124 (tpp) REVERT: C 558 LEU cc_start: -0.0444 (mt) cc_final: -0.0771 (mt) REVERT: D 88 ASP cc_start: 0.6926 (p0) cc_final: 0.6434 (p0) REVERT: D 177 MET cc_start: 0.1867 (mtp) cc_final: 0.0974 (mtp) REVERT: D 229 LEU cc_start: 0.7734 (mt) cc_final: 0.7345 (mp) REVERT: D 270 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.7765 (mm) REVERT: D 516 GLU cc_start: 0.7941 (tt0) cc_final: 0.7534 (tm-30) REVERT: D 732 THR cc_start: 0.9341 (m) cc_final: 0.9119 (p) REVERT: D 867 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7910 (t70) REVERT: D 882 ILE cc_start: 0.9320 (pt) cc_final: 0.9118 (mt) REVERT: D 976 VAL cc_start: 0.8157 (t) cc_final: 0.7875 (m) REVERT: D 979 ASP cc_start: 0.9039 (m-30) cc_final: 0.8798 (m-30) REVERT: D 1031 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7659 (mp0) REVERT: D 1041 ASP cc_start: 0.7365 (t70) cc_final: 0.6960 (t0) REVERT: B 55 PHE cc_start: 0.8343 (m-10) cc_final: 0.7742 (m-10) REVERT: B 104 TRP cc_start: 0.6679 (m100) cc_final: 0.6420 (m100) REVERT: B 192 PHE cc_start: 0.8386 (m-10) cc_final: 0.8080 (m-10) REVERT: B 509 ARG cc_start: 0.3545 (mtt180) cc_final: 0.1207 (ptt180) REVERT: B 737 ASP cc_start: 0.7539 (t0) cc_final: 0.7234 (t70) REVERT: B 754 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8987 (mm) REVERT: B 811 LYS cc_start: 0.6186 (OUTLIER) cc_final: 0.5977 (ptmt) REVERT: B 820 ASP cc_start: 0.8173 (t0) cc_final: 0.7875 (t0) REVERT: B 1149 LYS cc_start: 0.5921 (mttt) cc_final: 0.4822 (tptt) outliers start: 115 outliers final: 59 residues processed: 529 average time/residue: 0.1816 time to fit residues: 156.2454 Evaluate side-chains 391 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 328 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 711 SER Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 961 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1117 THR Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 984 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 305 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 297 optimal weight: 0.9980 chunk 294 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 314 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 751 ASN C 34 HIS C 63 ASN C 401 HIS D 394 ASN D 448 ASN D 450 ASN D 544 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN D1071 GLN D1088 HIS B 394 ASN B 498 GLN B 563 GLN B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.138275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.105557 restraints weight = 107990.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.107975 restraints weight = 53974.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.108902 restraints weight = 29229.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.109265 restraints weight = 22842.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.109276 restraints weight = 22053.129| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30843 Z= 0.144 Angle : 0.584 10.108 41967 Z= 0.303 Chirality : 0.044 0.211 4671 Planarity : 0.004 0.049 5431 Dihedral : 4.448 23.633 4087 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 2.36 % Allowed : 12.32 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % 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: -0.65 (0.13), residues: 3774 helix: 0.18 (0.15), residues: 1042 sheet: 0.02 (0.18), residues: 690 loop : -0.87 (0.12), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 328 TYR 0.026 0.001 TYR D 501 PHE 0.025 0.002 PHE C 230 TRP 0.019 0.001 TRP B 886 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00318 (30804) covalent geometry : angle 0.58125 (41889) SS BOND : bond 0.00559 ( 39) SS BOND : angle 1.44263 ( 78) hydrogen bonds : bond 0.04544 ( 1132) hydrogen bonds : angle 5.52018 ( 3198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 371 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 LEU cc_start: 0.5033 (tp) cc_final: 0.4721 (tp) REVERT: A 900 MET cc_start: 0.8453 (mmm) cc_final: 0.7852 (mpp) REVERT: A 955 ASN cc_start: 0.7997 (m-40) cc_final: 0.7556 (m-40) REVERT: A 960 ASN cc_start: 0.8749 (t0) cc_final: 0.8390 (m-40) REVERT: A 968 SER cc_start: 0.9410 (m) cc_final: 0.9094 (p) REVERT: A 969 ASN cc_start: 0.8104 (m-40) cc_final: 0.7847 (t0) REVERT: C 67 ASP cc_start: 0.5062 (OUTLIER) cc_final: 0.4729 (p0) REVERT: C 159 ASN cc_start: 0.7552 (m-40) cc_final: 0.7130 (p0) REVERT: C 249 MET cc_start: 0.0676 (ptt) cc_final: -0.0542 (mmt) REVERT: C 274 PHE cc_start: 0.5932 (m-10) cc_final: 0.5522 (p90) REVERT: C 474 MET cc_start: 0.2556 (mmm) cc_final: 0.2325 (tpt) REVERT: C 579 MET cc_start: 0.0675 (mmm) cc_final: 0.0393 (mmm) REVERT: D 516 GLU cc_start: 0.8097 (tt0) cc_final: 0.7550 (tm-30) REVERT: D 732 THR cc_start: 0.9338 (m) cc_final: 0.9119 (p) REVERT: D 867 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7693 (t70) REVERT: D 1041 ASP cc_start: 0.7348 (t70) cc_final: 0.6784 (t0) REVERT: D 1106 GLN cc_start: 0.7965 (mp10) cc_final: 0.7202 (mp10) REVERT: B 55 PHE cc_start: 0.8129 (m-10) cc_final: 0.7541 (m-10) REVERT: B 104 TRP cc_start: 0.6667 (m100) cc_final: 0.6420 (m100) REVERT: B 313 TYR cc_start: 0.8483 (m-80) cc_final: 0.7826 (m-80) REVERT: B 509 ARG cc_start: 0.3546 (mtt180) cc_final: 0.1275 (ptt180) REVERT: B 823 PHE cc_start: 0.8470 (t80) cc_final: 0.8112 (t80) REVERT: B 955 ASN cc_start: 0.8659 (m-40) cc_final: 0.8200 (t0) outliers start: 79 outliers final: 51 residues processed: 429 average time/residue: 0.1634 time to fit residues: 119.2391 Evaluate side-chains 355 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 302 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 535 HIS Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 743 CYS Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR 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 546 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 996 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 371 optimal weight: 5.9990 chunk 24 optimal weight: 0.2980 chunk 178 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 319 optimal weight: 9.9990 chunk 334 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 155 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 526 GLN C 540 HIS C 556 ASN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN D 450 ASN ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN D 955 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.136261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.105450 restraints weight = 110374.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.106301 restraints weight = 70621.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.107016 restraints weight = 39004.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.107090 restraints weight = 33886.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.107283 restraints weight = 31449.453| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30843 Z= 0.219 Angle : 0.645 11.887 41967 Z= 0.332 Chirality : 0.045 0.216 4671 Planarity : 0.004 0.052 5431 Dihedral : 4.596 22.942 4087 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 3.20 % Allowed : 12.77 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % 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: -0.59 (0.13), residues: 3774 helix: 0.42 (0.16), residues: 1042 sheet: -0.08 (0.18), residues: 703 loop : -0.92 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 102 TYR 0.029 0.002 TYR A 160 PHE 0.034 0.002 PHE B 92 TRP 0.017 0.002 TRP B 104 HIS 0.007 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00499 (30804) covalent geometry : angle 0.64238 (41889) SS BOND : bond 0.00541 ( 39) SS BOND : angle 1.54150 ( 78) hydrogen bonds : bond 0.04424 ( 1132) hydrogen bonds : angle 5.45183 ( 3198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 305 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 LEU cc_start: 0.5019 (tp) cc_final: 0.4702 (tp) REVERT: A 900 MET cc_start: 0.8478 (mmm) cc_final: 0.8053 (mpp) REVERT: A 960 ASN cc_start: 0.8784 (t0) cc_final: 0.8547 (m-40) REVERT: A 968 SER cc_start: 0.9444 (m) cc_final: 0.9242 (p) REVERT: A 1005 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 159 ASN cc_start: 0.7505 (m-40) cc_final: 0.6976 (t0) REVERT: C 249 MET cc_start: 0.1021 (ptt) cc_final: -0.0394 (mmt) REVERT: C 474 MET cc_start: 0.2298 (mmm) cc_final: 0.2080 (tpt) REVERT: C 579 MET cc_start: 0.0633 (mmm) cc_final: 0.0337 (mmm) REVERT: D 227 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8430 (t) REVERT: D 298 GLU cc_start: 0.8916 (tp30) cc_final: 0.8660 (tp30) REVERT: D 516 GLU cc_start: 0.8158 (tt0) cc_final: 0.7688 (tm-30) REVERT: D 867 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7928 (t70) REVERT: D 976 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8150 (m) REVERT: D 1041 ASP cc_start: 0.7416 (t70) cc_final: 0.7048 (t0) REVERT: D 1142 GLN cc_start: 0.8157 (tp-100) cc_final: 0.7929 (tp-100) REVERT: B 55 PHE cc_start: 0.8050 (m-80) cc_final: 0.7665 (m-10) REVERT: B 509 ARG cc_start: 0.3320 (mtt180) cc_final: 0.1077 (ptt180) REVERT: B 823 PHE cc_start: 0.8473 (t80) cc_final: 0.8085 (t80) REVERT: B 955 ASN cc_start: 0.8828 (m-40) cc_final: 0.8447 (t0) REVERT: B 984 LEU cc_start: 0.8708 (mt) cc_final: 0.8491 (tp) REVERT: B 1019 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7736 (ttp80) REVERT: B 1149 LYS cc_start: 0.5901 (mttt) cc_final: 0.4762 (tptt) outliers start: 107 outliers final: 73 residues processed: 392 average time/residue: 0.1611 time to fit residues: 107.5226 Evaluate side-chains 352 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 276 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 961 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 967 SER Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1117 THR Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 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 494 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 996 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 141 optimal weight: 20.0000 chunk 355 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 312 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 250 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A1002 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 787 GLN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 563 GLN B 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** 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 = 0.4252 r_free = 0.4252 target = 0.130876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.100291 restraints weight = 106461.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.102445 restraints weight = 60973.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.103285 restraints weight = 34649.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.103291 restraints weight = 29187.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.103604 restraints weight = 27698.190| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.7639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 30843 Z= 0.284 Angle : 0.722 11.848 41967 Z= 0.376 Chirality : 0.047 0.236 4671 Planarity : 0.005 0.059 5431 Dihedral : 5.145 26.310 4087 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 4.28 % Allowed : 12.77 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % 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: -0.89 (0.13), residues: 3774 helix: 0.21 (0.15), residues: 1064 sheet: -0.37 (0.18), residues: 720 loop : -1.09 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 102 TYR 0.032 0.002 TYR B 495 PHE 0.038 0.003 PHE B 92 TRP 0.024 0.002 TRP B 104 HIS 0.009 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00651 (30804) covalent geometry : angle 0.71840 (41889) SS BOND : bond 0.00476 ( 39) SS BOND : angle 1.83518 ( 78) hydrogen bonds : bond 0.04834 ( 1132) hydrogen bonds : angle 5.64787 ( 3198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 295 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 LEU cc_start: 0.5235 (tp) cc_final: 0.4884 (tp) REVERT: A 565 PHE cc_start: 0.7525 (m-10) cc_final: 0.7265 (m-10) REVERT: A 900 MET cc_start: 0.8640 (mmm) cc_final: 0.8315 (mpp) REVERT: A 957 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7658 (tm-30) REVERT: A 1005 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8306 (tm-30) REVERT: C 159 ASN cc_start: 0.7217 (m-40) cc_final: 0.6679 (t0) REVERT: C 474 MET cc_start: 0.2297 (mmm) cc_final: 0.2050 (tpp) REVERT: D 516 GLU cc_start: 0.8425 (tt0) cc_final: 0.7880 (tm-30) REVERT: D 867 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.8020 (t70) REVERT: D 976 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7914 (m) REVERT: D 1010 GLN cc_start: 0.8777 (mt0) cc_final: 0.8569 (mm-40) REVERT: D 1041 ASP cc_start: 0.7498 (t70) cc_final: 0.7199 (t0) REVERT: B 55 PHE cc_start: 0.7987 (m-80) cc_final: 0.7617 (m-80) REVERT: B 119 ILE cc_start: 0.9098 (mp) cc_final: 0.8843 (pt) REVERT: B 233 ILE cc_start: 0.7705 (pt) cc_final: 0.7288 (mt) REVERT: B 313 TYR cc_start: 0.8748 (m-80) cc_final: 0.8365 (m-80) REVERT: B 582 LEU cc_start: 0.8353 (mt) cc_final: 0.8117 (pt) REVERT: B 955 ASN cc_start: 0.8846 (m-40) cc_final: 0.8432 (t0) REVERT: B 1019 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7665 (ttp80) REVERT: B 1149 LYS cc_start: 0.5418 (mttt) cc_final: 0.4456 (tptt) outliers start: 143 outliers final: 99 residues processed: 412 average time/residue: 0.1586 time to fit residues: 111.6989 Evaluate side-chains 361 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 260 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 535 HIS Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 711 SER Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 961 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 967 SER Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1117 THR Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1096 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 94 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 301 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN C 599 ASN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN D 450 ASN ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1142 GLN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.131876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.102032 restraints weight = 105208.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.103622 restraints weight = 59242.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.104072 restraints weight = 35248.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.104271 restraints weight = 30316.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.104387 restraints weight = 29124.411| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.7860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30843 Z= 0.184 Angle : 0.618 11.603 41967 Z= 0.319 Chirality : 0.044 0.228 4671 Planarity : 0.004 0.052 5431 Dihedral : 4.795 24.912 4087 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 3.38 % Allowed : 14.39 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % 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: 3774 helix: 0.52 (0.16), residues: 1057 sheet: -0.24 (0.18), residues: 723 loop : -1.06 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 995 TYR 0.024 0.002 TYR B 495 PHE 0.027 0.002 PHE A 275 TRP 0.018 0.002 TRP D 436 HIS 0.005 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00421 (30804) covalent geometry : angle 0.61506 (41889) SS BOND : bond 0.00425 ( 39) SS BOND : angle 1.59242 ( 78) hydrogen bonds : bond 0.04267 ( 1132) hydrogen bonds : angle 5.40309 ( 3198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 297 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.6924 (mm-40) cc_final: 0.6101 (pp30) REVERT: A 455 LEU cc_start: 0.5459 (tp) cc_final: 0.5142 (tp) REVERT: A 804 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7569 (mm-40) REVERT: A 900 MET cc_start: 0.8619 (mmm) cc_final: 0.8316 (mpp) REVERT: A 960 ASN cc_start: 0.8780 (t0) cc_final: 0.8541 (m-40) REVERT: A 969 ASN cc_start: 0.8748 (t0) cc_final: 0.8519 (t0) REVERT: A 1005 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8295 (tm-30) REVERT: C 159 ASN cc_start: 0.7260 (m-40) cc_final: 0.6724 (t0) REVERT: C 376 MET cc_start: -0.0039 (mmm) cc_final: -0.0266 (mmm) REVERT: C 510 TYR cc_start: 0.3108 (OUTLIER) cc_final: 0.2365 (m-80) REVERT: D 177 MET cc_start: 0.2265 (mtt) cc_final: 0.1931 (mtt) REVERT: D 460 ASN cc_start: 0.6922 (m-40) cc_final: 0.6698 (p0) REVERT: D 516 GLU cc_start: 0.8451 (tt0) cc_final: 0.7890 (tm-30) REVERT: D 867 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7914 (t70) REVERT: D 976 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7839 (m) REVERT: D 980 ILE cc_start: 0.8836 (mm) cc_final: 0.8625 (mp) REVERT: D 1041 ASP cc_start: 0.7536 (t70) cc_final: 0.7209 (t0) REVERT: B 55 PHE cc_start: 0.7937 (m-80) cc_final: 0.7549 (m-10) REVERT: B 233 ILE cc_start: 0.7697 (pt) cc_final: 0.7297 (mt) REVERT: B 313 TYR cc_start: 0.8666 (m-80) cc_final: 0.8314 (m-80) REVERT: B 509 ARG cc_start: 0.3650 (mtt180) cc_final: 0.1244 (ptt180) REVERT: B 582 LEU cc_start: 0.8522 (mt) cc_final: 0.8319 (pt) REVERT: B 789 TYR cc_start: 0.8621 (m-80) cc_final: 0.8419 (m-80) REVERT: B 955 ASN cc_start: 0.8813 (m-40) cc_final: 0.8507 (t0) REVERT: B 984 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8218 (tp) REVERT: B 1019 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7538 (ttm-80) REVERT: B 1149 LYS cc_start: 0.5630 (mttt) cc_final: 0.4708 (tptt) outliers start: 113 outliers final: 85 residues processed: 386 average time/residue: 0.1614 time to fit residues: 106.6103 Evaluate side-chains 365 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 276 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 535 HIS Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 894 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 967 SER Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1117 THR Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 255 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 343 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 320 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 367 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1142 GLN B 49 HIS B 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.133106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.102879 restraints weight = 104291.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.104601 restraints weight = 55983.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.105619 restraints weight = 31611.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.105735 restraints weight = 27964.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.105822 restraints weight = 27503.247| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.7920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30843 Z= 0.125 Angle : 0.570 10.883 41967 Z= 0.290 Chirality : 0.044 0.452 4671 Planarity : 0.004 0.053 5431 Dihedral : 4.457 23.743 4087 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 2.48 % Allowed : 15.35 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % 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: -0.41 (0.13), residues: 3774 helix: 0.83 (0.16), residues: 1040 sheet: -0.08 (0.18), residues: 720 loop : -0.91 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 190 TYR 0.022 0.001 TYR A1138 PHE 0.024 0.002 PHE D1109 TRP 0.019 0.001 TRP D 436 HIS 0.005 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00281 (30804) covalent geometry : angle 0.56749 (41889) SS BOND : bond 0.00272 ( 39) SS BOND : angle 1.26308 ( 78) hydrogen bonds : bond 0.03865 ( 1132) hydrogen bonds : angle 5.14067 ( 3198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 299 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.6688 (mm-40) cc_final: 0.6007 (pp30) REVERT: A 455 LEU cc_start: 0.5488 (tp) cc_final: 0.5071 (tp) REVERT: A 900 MET cc_start: 0.8550 (mmm) cc_final: 0.8234 (mpp) REVERT: A 954 GLN cc_start: 0.8320 (mm110) cc_final: 0.8089 (mt0) REVERT: A 969 ASN cc_start: 0.8709 (t0) cc_final: 0.7755 (t0) REVERT: C 159 ASN cc_start: 0.7423 (m-40) cc_final: 0.6903 (t0) REVERT: C 510 TYR cc_start: 0.3191 (OUTLIER) cc_final: 0.2482 (m-80) REVERT: D 177 MET cc_start: 0.2015 (mtt) cc_final: 0.1461 (mtt) REVERT: D 516 GLU cc_start: 0.8451 (tt0) cc_final: 0.7886 (tm-30) REVERT: D 974 SER cc_start: 0.9093 (t) cc_final: 0.8862 (p) REVERT: D 1041 ASP cc_start: 0.7591 (t70) cc_final: 0.7246 (t0) REVERT: B 55 PHE cc_start: 0.7893 (m-80) cc_final: 0.7438 (m-10) REVERT: B 233 ILE cc_start: 0.7703 (pt) cc_final: 0.7275 (mt) REVERT: B 697 MET cc_start: 0.8590 (tpp) cc_final: 0.8295 (tpt) REVERT: B 789 TYR cc_start: 0.8615 (m-80) cc_final: 0.8414 (m-80) REVERT: B 823 PHE cc_start: 0.8224 (t80) cc_final: 0.7739 (t80) REVERT: B 955 ASN cc_start: 0.8750 (m-40) cc_final: 0.8446 (t0) REVERT: B 984 LEU cc_start: 0.8558 (tp) cc_final: 0.8291 (tp) REVERT: B 1106 GLN cc_start: 0.7830 (mp10) cc_final: 0.7446 (mp10) REVERT: B 1149 LYS cc_start: 0.5633 (mttt) cc_final: 0.4679 (tptt) outliers start: 83 outliers final: 69 residues processed: 359 average time/residue: 0.1662 time to fit residues: 101.0616 Evaluate side-chains 339 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 269 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 535 HIS Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 894 LEU Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1117 THR Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 293 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 320 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 128 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 291 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 319 optimal weight: 8.9990 chunk 237 optimal weight: 4.9990 chunk 364 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 264 optimal weight: 0.9980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A1005 GLN A1048 HIS ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN D 450 ASN ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 926 GLN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN B 99 ASN B 675 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.129785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.099628 restraints weight = 105982.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.101422 restraints weight = 58383.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.101741 restraints weight = 34883.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.102495 restraints weight = 29477.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.102512 restraints weight = 28935.814| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.8324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 30843 Z= 0.222 Angle : 0.654 16.235 41967 Z= 0.335 Chirality : 0.045 0.315 4671 Planarity : 0.004 0.053 5431 Dihedral : 4.710 24.608 4087 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.72 % Favored : 95.26 % Rotamer: Outliers : 3.50 % Allowed : 14.87 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % 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: 3774 helix: 0.68 (0.16), residues: 1054 sheet: -0.23 (0.18), residues: 724 loop : -0.99 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 765 TYR 0.030 0.002 TYR D 160 PHE 0.028 0.002 PHE D 192 TRP 0.019 0.002 TRP C 69 HIS 0.006 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00508 (30804) covalent geometry : angle 0.64972 (41889) SS BOND : bond 0.00649 ( 39) SS BOND : angle 1.80926 ( 78) hydrogen bonds : bond 0.04317 ( 1132) hydrogen bonds : angle 5.36518 ( 3198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 280 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 LEU cc_start: 0.5379 (tp) cc_final: 0.5003 (tp) REVERT: A 900 MET cc_start: 0.8694 (mmm) cc_final: 0.8390 (mpp) REVERT: A 969 ASN cc_start: 0.8820 (t0) cc_final: 0.7956 (t0) REVERT: A 1005 GLN cc_start: 0.8594 (tm130) cc_final: 0.7968 (tm-30) REVERT: C 159 ASN cc_start: 0.7347 (m-40) cc_final: 0.6867 (t0) REVERT: C 510 TYR cc_start: 0.3432 (OUTLIER) cc_final: 0.2698 (m-80) REVERT: D 177 MET cc_start: 0.2126 (OUTLIER) cc_final: 0.1684 (mtt) REVERT: D 516 GLU cc_start: 0.8509 (tt0) cc_final: 0.7965 (tm-30) REVERT: D 867 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7996 (t70) REVERT: D 976 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7903 (m) REVERT: D 980 ILE cc_start: 0.9000 (mm) cc_final: 0.8788 (mp) REVERT: D 1041 ASP cc_start: 0.7591 (t70) cc_final: 0.7278 (t0) REVERT: D 1111 GLU cc_start: 0.7911 (pp20) cc_final: 0.7392 (pp20) REVERT: B 55 PHE cc_start: 0.7934 (m-80) cc_final: 0.7625 (m-10) REVERT: B 141 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8026 (tp) REVERT: B 153 MET cc_start: 0.3780 (ppp) cc_final: 0.3111 (ppp) REVERT: B 233 ILE cc_start: 0.7799 (pt) cc_final: 0.7413 (mt) REVERT: B 752 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9265 (mp) REVERT: B 823 PHE cc_start: 0.8274 (t80) cc_final: 0.7828 (t80) REVERT: B 955 ASN cc_start: 0.8815 (m-40) cc_final: 0.8552 (t0) REVERT: B 1149 LYS cc_start: 0.5600 (mttt) cc_final: 0.4608 (tptt) outliers start: 117 outliers final: 89 residues processed: 371 average time/residue: 0.1615 time to fit residues: 104.1848 Evaluate side-chains 354 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 259 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 535 HIS Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 894 LEU Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1117 THR Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 342 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 chunk 374 optimal weight: 1.9990 chunk 325 optimal weight: 7.9990 chunk 266 optimal weight: 0.7980 chunk 259 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN D 450 ASN ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 774 GLN D 895 GLN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1142 GLN B 14 GLN B 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.131860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.102099 restraints weight = 103975.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.104204 restraints weight = 57259.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.104498 restraints weight = 30863.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.104640 restraints weight = 29369.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.104839 restraints weight = 27291.364| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.8389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30843 Z= 0.137 Angle : 0.592 14.793 41967 Z= 0.302 Chirality : 0.044 0.275 4671 Planarity : 0.004 0.051 5431 Dihedral : 4.484 23.547 4087 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 2.21 % Allowed : 16.60 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % 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: -0.45 (0.13), residues: 3774 helix: 0.79 (0.16), residues: 1047 sheet: -0.19 (0.18), residues: 724 loop : -0.90 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 582 TYR 0.028 0.001 TYR D 160 PHE 0.027 0.002 PHE D 192 TRP 0.019 0.001 TRP C 69 HIS 0.004 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00312 (30804) covalent geometry : angle 0.58813 (41889) SS BOND : bond 0.00420 ( 39) SS BOND : angle 1.69128 ( 78) hydrogen bonds : bond 0.03862 ( 1132) hydrogen bonds : angle 5.17812 ( 3198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 283 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 LEU cc_start: 0.5574 (tp) cc_final: 0.5228 (tp) REVERT: A 869 MET cc_start: 0.8277 (mtp) cc_final: 0.8065 (mtm) REVERT: A 900 MET cc_start: 0.8614 (mmm) cc_final: 0.8286 (mpp) REVERT: A 969 ASN cc_start: 0.8820 (t0) cc_final: 0.8080 (t0) REVERT: C 159 ASN cc_start: 0.7390 (m-40) cc_final: 0.6947 (t0) REVERT: C 510 TYR cc_start: 0.3535 (OUTLIER) cc_final: 0.2826 (m-80) REVERT: D 177 MET cc_start: 0.2272 (OUTLIER) cc_final: 0.1821 (mtt) REVERT: D 430 THR cc_start: 0.8432 (p) cc_final: 0.8212 (p) REVERT: D 516 GLU cc_start: 0.8533 (tt0) cc_final: 0.8034 (tm-30) REVERT: D 974 SER cc_start: 0.9154 (t) cc_final: 0.8925 (p) REVERT: D 1005 GLN cc_start: 0.8551 (tp40) cc_final: 0.8351 (tp40) REVERT: D 1041 ASP cc_start: 0.7650 (t70) cc_final: 0.7311 (t0) REVERT: B 55 PHE cc_start: 0.7893 (m-80) cc_final: 0.7573 (m-10) REVERT: B 153 MET cc_start: 0.3925 (ppp) cc_final: 0.3132 (ppp) REVERT: B 233 ILE cc_start: 0.7751 (pt) cc_final: 0.7383 (mt) REVERT: B 509 ARG cc_start: 0.3341 (mtt180) cc_final: 0.1299 (ptt180) REVERT: B 751 ASN cc_start: 0.9240 (m-40) cc_final: 0.8967 (m-40) REVERT: B 823 PHE cc_start: 0.8195 (t80) cc_final: 0.7702 (t80) REVERT: B 955 ASN cc_start: 0.8779 (m-40) cc_final: 0.8529 (t0) REVERT: B 984 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8332 (tp) REVERT: B 1149 LYS cc_start: 0.5556 (mttt) cc_final: 0.4635 (tptt) outliers start: 74 outliers final: 59 residues processed: 340 average time/residue: 0.1622 time to fit residues: 94.1280 Evaluate side-chains 332 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 270 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 894 LEU Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1117 THR Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1159 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 330 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 337 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN D 580 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.131937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.102220 restraints weight = 103183.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.103770 restraints weight = 52939.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.104340 restraints weight = 31768.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.104383 restraints weight = 28145.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.105074 restraints weight = 27856.875| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.8476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30843 Z= 0.139 Angle : 0.596 13.945 41967 Z= 0.305 Chirality : 0.044 0.245 4671 Planarity : 0.004 0.052 5431 Dihedral : 4.430 26.494 4087 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 2.42 % Allowed : 16.36 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % 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: -0.44 (0.13), residues: 3774 helix: 0.85 (0.16), residues: 1044 sheet: -0.24 (0.18), residues: 742 loop : -0.91 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 559 TYR 0.055 0.001 TYR D 160 PHE 0.031 0.002 PHE D 192 TRP 0.017 0.001 TRP C 69 HIS 0.011 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00315 (30804) covalent geometry : angle 0.59241 (41889) SS BOND : bond 0.00412 ( 39) SS BOND : angle 1.61654 ( 78) hydrogen bonds : bond 0.03849 ( 1132) hydrogen bonds : angle 5.14681 ( 3198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 283 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 LEU cc_start: 0.5382 (tp) cc_final: 0.4989 (tp) REVERT: A 900 MET cc_start: 0.8597 (mmm) cc_final: 0.8289 (mpp) REVERT: A 969 ASN cc_start: 0.8846 (t0) cc_final: 0.8007 (t0) REVERT: C 159 ASN cc_start: 0.7374 (m-40) cc_final: 0.6909 (t0) REVERT: C 510 TYR cc_start: 0.3575 (OUTLIER) cc_final: 0.2837 (m-80) REVERT: C 559 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5340 (ptm-80) REVERT: D 177 MET cc_start: 0.2089 (OUTLIER) cc_final: 0.1663 (mtt) REVERT: D 430 THR cc_start: 0.8376 (p) cc_final: 0.8144 (p) REVERT: D 516 GLU cc_start: 0.8502 (tt0) cc_final: 0.8088 (tm-30) REVERT: D 823 PHE cc_start: 0.8813 (t80) cc_final: 0.8593 (t80) REVERT: D 867 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7770 (t70) REVERT: D 974 SER cc_start: 0.9195 (t) cc_final: 0.8994 (p) REVERT: D 1041 ASP cc_start: 0.7594 (t70) cc_final: 0.7276 (t0) REVERT: D 1111 GLU cc_start: 0.7849 (pp20) cc_final: 0.7382 (pp20) REVERT: B 55 PHE cc_start: 0.7781 (m-80) cc_final: 0.7467 (m-10) REVERT: B 153 MET cc_start: 0.3813 (ppp) cc_final: 0.2926 (ppp) REVERT: B 233 ILE cc_start: 0.7786 (pt) cc_final: 0.7403 (mt) REVERT: B 509 ARG cc_start: 0.3371 (mtt180) cc_final: 0.1314 (ptt180) REVERT: B 751 ASN cc_start: 0.9192 (m-40) cc_final: 0.8927 (m-40) REVERT: B 823 PHE cc_start: 0.8211 (t80) cc_final: 0.7754 (t80) REVERT: B 955 ASN cc_start: 0.8723 (m-40) cc_final: 0.8504 (t0) REVERT: B 984 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8358 (tp) REVERT: B 1149 LYS cc_start: 0.5729 (mttt) cc_final: 0.4775 (tptt) outliers start: 81 outliers final: 64 residues processed: 349 average time/residue: 0.1582 time to fit residues: 94.4800 Evaluate side-chains 342 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 559 ARG Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 894 LEU Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1117 THR Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1159 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 311 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 331 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN D 774 GLN ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN B 14 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.130708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.101072 restraints weight = 104289.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.102683 restraints weight = 59062.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.102747 restraints weight = 33013.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.103002 restraints weight = 31374.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.103085 restraints weight = 30793.597| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.8634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30843 Z= 0.167 Angle : 0.616 13.609 41967 Z= 0.315 Chirality : 0.044 0.224 4671 Planarity : 0.004 0.051 5431 Dihedral : 4.503 26.478 4087 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 2.36 % Allowed : 16.63 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % 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: -0.45 (0.13), residues: 3774 helix: 0.84 (0.16), residues: 1039 sheet: -0.20 (0.18), residues: 732 loop : -0.92 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 328 TYR 0.030 0.002 TYR A 145 PHE 0.033 0.002 PHE D 192 TRP 0.020 0.001 TRP C 69 HIS 0.022 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00383 (30804) covalent geometry : angle 0.61259 (41889) SS BOND : bond 0.00381 ( 39) SS BOND : angle 1.69607 ( 78) hydrogen bonds : bond 0.03927 ( 1132) hydrogen bonds : angle 5.18567 ( 3198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5521.01 seconds wall clock time: 96 minutes 6.53 seconds (5766.53 seconds total)