Starting phenix.real_space_refine on Fri Mar 6 09:19:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vxm_32184/03_2026/7vxm_32184.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vxm_32184/03_2026/7vxm_32184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vxm_32184/03_2026/7vxm_32184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vxm_32184/03_2026/7vxm_32184.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vxm_32184/03_2026/7vxm_32184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vxm_32184/03_2026/7vxm_32184.map" } resolution = 3.6 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= -0.001 sd= 0.151 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 142 5.16 5 C 19101 2.51 5 N 4984 2.21 5 O 5674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 29901 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: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 567} Chain breaks: 1 Chain: "D" Number of atoms: 8301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8301 Classifications: {'peptide': 1059} Link IDs: {'CIS': 1, 'PTRANS': 51, 'TRANS': 1006} Chain breaks: 6 Chain: "B" Number of atoms: 8301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8301 Classifications: {'peptide': 1059} Link IDs: {'CIS': 1, 'PTRANS': 51, 'TRANS': 1006} Chain breaks: 6 Time building chain proxies: 6.09, per 1000 atoms: 0.20 Number of scatterers: 29901 At special positions: 0 Unit cell: (161.764, 151.927, 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 142 16.00 O 5674 8.00 N 4984 7.00 C 19101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " 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 379 " - pdb=" SG CYS B 432 " 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: 2.34 Conformation dependent library (CDL) restraints added in 1.4 seconds 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 47 sheets defined 31.7% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.582A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.939A 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: 3.743A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.744A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.529A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.557A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.540A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.233A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.703A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.661A 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: 3.940A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.649A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.538A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1152 removed outlier: 4.005A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1161 removed outlier: 3.921A pdb=" N HIS A1159 " --> pdb=" O TYR A1155 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A1160 " --> pdb=" O PHE A1156 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 53 removed outlier: 4.055A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.746A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.935A pdb=" N GLU C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.534A 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: 4.040A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.946A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 removed outlier: 3.832A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 removed outlier: 3.790A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.604A pdb=" N ARG C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 194 removed outlier: 3.650A pdb=" N MET C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.809A pdb=" N TRP C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 250 removed outlier: 3.960A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.822A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 293 through 301 removed outlier: 3.754A pdb=" N ASP C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 removed outlier: 4.030A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.618A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.686A pdb=" N PHE C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 370 " --> pdb=" O MET C 366 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) removed outlier: 4.350A 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: 3.564A pdb=" N VAL C 404 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.772A pdb=" N ILE C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.626A pdb=" N ASN C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 466 removed outlier: 4.008A 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: 3.891A pdb=" N GLU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 removed outlier: 4.109A pdb=" N SER C 502 " --> pdb=" O CYS C 498 " (cutoff:3.500A) removed outlier: 3.827A 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: 3.534A pdb=" N THR C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS C 530 " --> pdb=" O GLN C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.630A pdb=" N GLN C 552 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C 556 " --> pdb=" O GLN C 552 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 removed outlier: 3.541A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.594A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.672A pdb=" N TRP C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 3.680A 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 365 through 371 removed outlier: 3.533A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.213A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 782 removed outlier: 3.967A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 removed outlier: 4.025A 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 884 Processing helix chain 'D' and resid 886 through 891 removed outlier: 4.112A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.632A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 3.724A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.869A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (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 removed outlier: 3.776A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.109A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D1030 " --> pdb=" O ALA D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1161 removed outlier: 3.860A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS D1154 " --> pdb=" O GLU D1150 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR D1155 " --> pdb=" O GLU D1151 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE D1156 " --> pdb=" O LEU D1152 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS D1157 " --> pdb=" O ASP D1153 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN D1158 " --> pdb=" O LYS D1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.520A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.295A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.575A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.622A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.653A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.973A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (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 780 removed outlier: 3.854A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 removed outlier: 4.379A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 854 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.510A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.091A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 4.169A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.518A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.955A 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 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.234A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 3.697A pdb=" N VAL B1128 " --> pdb=" O ASN B1125 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B1129 " --> pdb=" O CYS B1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1125 through 1129' Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 4.286A 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: 3.784A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.794A 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: 3.964A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.237A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.532A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.910A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.501A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.604A 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: 3.998A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.796A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (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: 5.624A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 672 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 3.991A 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: 3.612A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.690A 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: 3.627A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.741A 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 788 through 789 removed outlier: 6.320A pdb=" N ILE A 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.554A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.573A pdb=" N LEU C 142 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.046A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.538A pdb=" N THR C 347 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 27 through 31 removed outlier: 3.798A pdb=" N ALA D 27 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 31 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE D 194 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS D 187 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 48 through 55 removed outlier: 4.133A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.531A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP D 104 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLN D 134 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N ASN D 164 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 311 through 318 removed outlier: 5.277A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 325 through 328 removed outlier: 3.795A pdb=" N ASN D 542 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 328 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU D 585 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 576 " --> pdb=" O LEU D 585 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 354 through 358 removed outlier: 4.291A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (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 655 removed outlier: 5.976A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.560A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.606A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.314A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 787 through 788 Processing sheet with id=AD5, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.823A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.740A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.682A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B 101 " --> pdb=" O ILE B 243 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.682A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.585A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.476A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AE4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.872A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 removed outlier: 8.119A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.043A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.511A 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 removed outlier: 3.575A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.677A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.829A 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: 4.284A 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 1078 hydrogen bonds defined for protein. 3066 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: 6.24 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9649 1.34 - 1.46: 7530 1.46 - 1.58: 13246 1.58 - 1.70: 0 1.70 - 1.83: 193 Bond restraints: 30618 Sorted by residual: bond pdb=" C PRO B 25 " pdb=" N PRO B 26 " ideal model delta sigma weight residual 1.334 1.437 -0.103 2.34e-02 1.83e+03 1.95e+01 bond pdb=" C PRO D 25 " pdb=" N PRO D 26 " ideal model delta sigma weight residual 1.334 1.426 -0.092 2.34e-02 1.83e+03 1.54e+01 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.80e+00 bond pdb=" C PRO A 25 " pdb=" N PRO A 26 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.50e+00 bond pdb=" C LEU D 229 " pdb=" N PRO D 230 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.19e+00 ... (remaining 30613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 41353 2.37 - 4.74: 253 4.74 - 7.10: 20 7.10 - 9.47: 5 9.47 - 11.84: 1 Bond angle restraints: 41632 Sorted by residual: angle pdb=" N ALA A 292 " pdb=" CA ALA A 292 " pdb=" C ALA A 292 " ideal model delta sigma weight residual 110.80 98.96 11.84 2.13e+00 2.20e-01 3.09e+01 angle pdb=" N CYS D 291 " pdb=" CA CYS D 291 " pdb=" C CYS D 291 " ideal model delta sigma weight residual 108.73 117.23 -8.50 1.63e+00 3.76e-01 2.72e+01 angle pdb=" N CYS A 291 " pdb=" CA CYS A 291 " pdb=" C CYS A 291 " ideal model delta sigma weight residual 108.73 116.32 -7.59 1.63e+00 3.76e-01 2.17e+01 angle pdb=" CA LEU B 492 " pdb=" C LEU B 492 " pdb=" N GLN B 493 " ideal model delta sigma weight residual 114.17 120.92 -6.75 1.45e+00 4.76e-01 2.17e+01 angle pdb=" N ALA D 292 " pdb=" CA ALA D 292 " pdb=" C ALA D 292 " ideal model delta sigma weight residual 110.80 101.51 9.29 2.13e+00 2.20e-01 1.90e+01 ... (remaining 41627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 17759 16.09 - 32.19: 309 32.19 - 48.28: 109 48.28 - 64.38: 21 64.38 - 80.47: 8 Dihedral angle restraints: 18206 sinusoidal: 7153 harmonic: 11053 Sorted by residual: dihedral pdb=" CA GLY B 142 " pdb=" C GLY B 142 " pdb=" N VAL B 143 " pdb=" CA VAL B 143 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 55.59 37.41 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -123.03 37.03 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 18203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4053 0.060 - 0.119: 566 0.119 - 0.179: 25 0.179 - 0.239: 2 0.239 - 0.298: 2 Chirality restraints: 4648 Sorted by residual: chirality pdb=" CA CYS D 291 " pdb=" N CYS D 291 " pdb=" C CYS D 291 " pdb=" CB CYS D 291 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+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 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 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 2.72 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4645 not shown) Planarity restraints: 5393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 290 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C ASP A 290 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP A 290 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS A 291 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 290 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C ASP D 290 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP D 290 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS D 291 " -0.014 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 5.57e-02 4.97e+00 pdb=" N PRO A 295 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.031 5.00e-02 4.00e+02 ... (remaining 5390 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 711 2.71 - 3.26: 28521 3.26 - 3.80: 44723 3.80 - 4.35: 59366 4.35 - 4.90: 98480 Nonbonded interactions: 231801 Sorted by model distance: nonbonded pdb=" OG1 THR D 108 " pdb=" O ASN D 234 " model vdw 2.159 3.040 nonbonded pdb=" CZ PHE B 140 " pdb=" CB SER B 244 " model vdw 2.214 3.740 nonbonded pdb=" NE ARG B 102 " pdb=" CG1 ILE B 243 " model vdw 2.215 3.520 nonbonded pdb=" O GLN A 755 " pdb=" OG SER D 968 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR A 912 " pdb=" NE2 GLN A1106 " model vdw 2.256 3.120 ... (remaining 231796 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' } 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: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.720 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5263 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 0.103 30656 Z= 0.115 Angle : 0.509 11.839 41708 Z= 0.304 Chirality : 0.041 0.298 4648 Planarity : 0.004 0.056 5393 Dihedral : 7.685 80.472 10976 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -2.41 (0.11), residues: 3747 helix: -3.35 (0.09), residues: 975 sheet: -0.40 (0.17), residues: 654 loop : -1.05 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 346 TYR 0.016 0.001 TYR A 495 PHE 0.015 0.001 PHE A 32 TRP 0.018 0.001 TRP A 436 HIS 0.006 0.000 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00201 (30618) covalent geometry : angle 0.50830 (41632) SS BOND : bond 0.00238 ( 38) SS BOND : angle 0.86701 ( 76) hydrogen bonds : bond 0.29517 ( 1077) hydrogen bonds : angle 9.92442 ( 3066) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 881 time to evaluate : 1.220 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: A 1029 MET cc_start: 0.7833 (tpp) cc_final: 0.7382 (tpt) REVERT: A 1037 SER cc_start: 0.8775 (t) cc_final: 0.8433 (p) REVERT: C 303 ASP cc_start: 0.5418 (p0) cc_final: 0.4960 (t0) REVERT: C 535 HIS cc_start: 0.2760 (m-70) cc_final: 0.2354 (t70) REVERT: D 177 MET cc_start: 0.1932 (ttm) cc_final: -0.0503 (mtp) REVERT: D 858 LEU cc_start: 0.6847 (mp) cc_final: 0.6552 (mp) REVERT: D 929 SER cc_start: 0.7551 (m) cc_final: 0.7322 (t) REVERT: B 695 TYR cc_start: 0.6318 (p90) cc_final: 0.5949 (p90) outliers start: 0 outliers final: 0 residues processed: 881 average time/residue: 0.1882 time to fit residues: 263.0349 Evaluate side-chains 420 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 920 GLN A 935 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1159 HIS C 34 HIS C 325 GLN C 417 HIS D 69 HIS D 394 ASN D 655 HIS ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN D 907 ASN D 913 GLN D 920 GLN D 949 GLN D1048 HIS D1106 GLN B 66 HIS B 146 HIS B 148 ASN B 239 GLN B1101 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.154255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.118787 restraints weight = 97345.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.119278 restraints weight = 68428.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.119662 restraints weight = 45422.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120051 restraints weight = 37189.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.120413 restraints weight = 33886.199| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 30656 Z= 0.312 Angle : 0.848 14.680 41708 Z= 0.443 Chirality : 0.051 0.217 4648 Planarity : 0.006 0.079 5393 Dihedral : 4.964 21.236 4060 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.09 % Allowed : 8.84 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -1.21 (0.12), residues: 3747 helix: -0.88 (0.14), residues: 1003 sheet: -0.07 (0.18), residues: 625 loop : -0.95 (0.12), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1107 TYR 0.030 0.003 TYR D 789 PHE 0.030 0.003 PHE D 888 TRP 0.019 0.002 TRP C 473 HIS 0.012 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00719 (30618) covalent geometry : angle 0.84056 (41632) SS BOND : bond 0.00770 ( 38) SS BOND : angle 2.73877 ( 76) hydrogen bonds : bond 0.05614 ( 1077) hydrogen bonds : angle 6.23988 ( 3066) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 432 time to evaluate : 1.179 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: A 106 PHE cc_start: 0.4956 (m-10) cc_final: 0.4721 (m-10) REVERT: A 117 LEU cc_start: 0.8102 (tp) cc_final: 0.7766 (tt) REVERT: A 153 MET cc_start: 0.1698 (mtt) cc_final: 0.0654 (pmm) REVERT: A 177 MET cc_start: -0.0161 (ttm) cc_final: -0.0512 (ttp) REVERT: A 318 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7036 (p90) REVERT: A 396 TYR cc_start: 0.7840 (m-80) cc_final: 0.7568 (m-80) REVERT: A 490 PHE cc_start: 0.3389 (t80) cc_final: 0.3034 (t80) REVERT: A 900 MET cc_start: 0.7997 (mmm) cc_final: 0.7364 (mpp) REVERT: A 962 LEU cc_start: 0.8837 (tp) cc_final: 0.8536 (tt) REVERT: A 1001 LEU cc_start: 0.9159 (mt) cc_final: 0.8956 (mt) REVERT: A 1037 SER cc_start: 0.9295 (t) cc_final: 0.8847 (p) REVERT: A 1083 HIS cc_start: 0.7721 (OUTLIER) cc_final: 0.7204 (t70) REVERT: A 1125 ASN cc_start: 0.8433 (p0) cc_final: 0.7983 (m-40) REVERT: C 323 MET cc_start: 0.3482 (mmm) cc_final: 0.1960 (mtm) REVERT: C 535 HIS cc_start: 0.3193 (m-70) cc_final: 0.1997 (t-170) REVERT: D 705 VAL cc_start: 0.5044 (t) cc_final: 0.4716 (t) REVERT: D 900 MET cc_start: 0.8184 (mtt) cc_final: 0.7939 (mtp) REVERT: D 957 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8266 (tm-30) REVERT: D 966 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8707 (mm) REVERT: D 979 ASP cc_start: 0.8141 (m-30) cc_final: 0.7584 (t0) REVERT: D 1037 SER cc_start: 0.9156 (t) cc_final: 0.8814 (p) REVERT: D 1050 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7499 (ptm) REVERT: D 1139 ASP cc_start: 0.7454 (t0) cc_final: 0.7189 (t0) REVERT: B 379 CYS cc_start: 0.2873 (OUTLIER) cc_final: 0.1892 (p) REVERT: B 985 ASP cc_start: 0.7134 (p0) cc_final: 0.5407 (p0) outliers start: 136 outliers final: 83 residues processed: 538 average time/residue: 0.1735 time to fit residues: 154.2417 Evaluate side-chains 402 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 314 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 920 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 698 SER Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 805 ILE Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain D residue 1146 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 38 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 201 optimal weight: 7.9990 chunk 237 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 338 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 323 optimal weight: 9.9990 chunk 260 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 755 GLN A1054 GLN A1088 HIS A1106 GLN C 508 ASN C 580 ASN D 239 GLN D 901 GLN B 926 GLN B1002 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.154391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.118534 restraints weight = 95782.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.119610 restraints weight = 53925.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.120179 restraints weight = 35946.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.120857 restraints weight = 27880.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.120976 restraints weight = 27375.186| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30656 Z= 0.141 Angle : 0.571 10.818 41708 Z= 0.296 Chirality : 0.043 0.184 4648 Planarity : 0.004 0.051 5393 Dihedral : 4.287 22.542 4060 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.59 % Allowed : 11.88 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.53 (0.13), residues: 3747 helix: 0.30 (0.16), residues: 1015 sheet: 0.02 (0.18), residues: 637 loop : -0.77 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1019 TYR 0.019 0.001 TYR D 145 PHE 0.024 0.002 PHE D 562 TRP 0.025 0.001 TRP A 104 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00314 (30618) covalent geometry : angle 0.56769 (41632) SS BOND : bond 0.00799 ( 38) SS BOND : angle 1.56112 ( 76) hydrogen bonds : bond 0.04556 ( 1077) hydrogen bonds : angle 5.63912 ( 3066) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 329 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7671 (tp) cc_final: 0.7311 (tt) REVERT: A 153 MET cc_start: 0.1684 (mtt) cc_final: 0.0645 (ppp) REVERT: A 177 MET cc_start: -0.1703 (ttm) cc_final: -0.1906 (tmm) REVERT: A 291 CYS cc_start: 0.4588 (OUTLIER) cc_final: 0.4167 (m) REVERT: A 318 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7099 (p90) REVERT: A 396 TYR cc_start: 0.7968 (m-80) cc_final: 0.7607 (m-80) REVERT: A 900 MET cc_start: 0.7938 (mmm) cc_final: 0.7304 (mpp) REVERT: A 1037 SER cc_start: 0.9188 (t) cc_final: 0.8701 (p) REVERT: A 1125 ASN cc_start: 0.8289 (p0) cc_final: 0.8060 (m-40) REVERT: A 1128 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.9033 (p) REVERT: A 1148 PHE cc_start: 0.3010 (t80) cc_final: 0.2531 (t80) REVERT: A 1149 LYS cc_start: 0.3779 (mmtm) cc_final: 0.2520 (ptpt) REVERT: C 383 MET cc_start: 0.5411 (ptm) cc_final: 0.4747 (ppp) REVERT: C 535 HIS cc_start: 0.3040 (m-70) cc_final: 0.2084 (t-170) REVERT: D 699 LEU cc_start: 0.7837 (mt) cc_final: 0.7439 (mt) REVERT: D 855 PHE cc_start: 0.6554 (m-80) cc_final: 0.6213 (m-80) REVERT: D 957 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8219 (tm-30) REVERT: D 966 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8662 (mm) REVERT: D 1037 SER cc_start: 0.9028 (t) cc_final: 0.8764 (p) REVERT: D 1071 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: D 1139 ASP cc_start: 0.7448 (t0) cc_final: 0.7106 (t0) REVERT: B 177 MET cc_start: 0.1113 (tmm) cc_final: 0.0588 (tmm) REVERT: B 296 LEU cc_start: 0.8742 (tp) cc_final: 0.8227 (tt) REVERT: B 1045 LYS cc_start: 0.7727 (mttm) cc_final: 0.7447 (ttmt) outliers start: 86 outliers final: 41 residues processed: 394 average time/residue: 0.1671 time to fit residues: 110.8345 Evaluate side-chains 322 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 698 SER Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1071 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 364 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 338 optimal weight: 0.9980 chunk 280 optimal weight: 8.9990 chunk 189 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 310 optimal weight: 10.0000 chunk 283 optimal weight: 8.9990 chunk 263 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN C 90 ASN C 300 GLN B 926 GLN B1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.150317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.115393 restraints weight = 93976.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.116296 restraints weight = 60039.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.116439 restraints weight = 38464.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.116578 restraints weight = 36855.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.116883 restraints weight = 32871.424| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 30656 Z= 0.216 Angle : 0.635 10.652 41708 Z= 0.328 Chirality : 0.045 0.176 4648 Planarity : 0.005 0.055 5393 Dihedral : 4.479 20.492 4060 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.10 % Allowed : 12.27 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.42 (0.13), residues: 3747 helix: 0.64 (0.16), residues: 1022 sheet: -0.10 (0.18), residues: 675 loop : -0.78 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1019 TYR 0.021 0.002 TYR C 243 PHE 0.036 0.002 PHE A 275 TRP 0.030 0.002 TRP B 353 HIS 0.006 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00498 (30618) covalent geometry : angle 0.63088 (41632) SS BOND : bond 0.00462 ( 38) SS BOND : angle 1.73161 ( 76) hydrogen bonds : bond 0.04427 ( 1077) hydrogen bonds : angle 5.54599 ( 3066) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 294 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: A 119 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6502 (mp) REVERT: A 153 MET cc_start: 0.1825 (mtt) cc_final: 0.0879 (pmm) REVERT: A 318 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.6851 (p90) REVERT: A 368 LEU cc_start: 0.7388 (mt) cc_final: 0.7083 (pp) REVERT: A 396 TYR cc_start: 0.7910 (m-80) cc_final: 0.7475 (m-80) REVERT: A 598 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8199 (mp) REVERT: A 1037 SER cc_start: 0.9319 (t) cc_final: 0.8822 (p) REVERT: A 1125 ASN cc_start: 0.8507 (p0) cc_final: 0.8187 (m-40) REVERT: C 163 TRP cc_start: 0.2128 (m-10) cc_final: 0.1420 (t60) REVERT: D 747 THR cc_start: 0.8843 (p) cc_final: 0.8557 (t) REVERT: D 855 PHE cc_start: 0.6623 (m-80) cc_final: 0.6340 (m-80) REVERT: D 900 MET cc_start: 0.7920 (mtt) cc_final: 0.7664 (mtp) REVERT: D 957 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8245 (tm-30) REVERT: D 1037 SER cc_start: 0.9103 (t) cc_final: 0.8833 (p) REVERT: D 1139 ASP cc_start: 0.7539 (t0) cc_final: 0.7181 (t0) REVERT: B 177 MET cc_start: 0.1165 (tmm) cc_final: 0.0928 (tmm) REVERT: B 379 CYS cc_start: 0.3046 (OUTLIER) cc_final: 0.1607 (p) REVERT: B 1045 LYS cc_start: 0.7982 (mttm) cc_final: 0.7637 (ttmt) outliers start: 103 outliers final: 69 residues processed: 375 average time/residue: 0.1656 time to fit residues: 104.3385 Evaluate side-chains 325 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 252 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 698 SER Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1146 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 106 optimal weight: 6.9990 chunk 352 optimal weight: 0.9990 chunk 133 optimal weight: 0.0980 chunk 204 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 374 optimal weight: 7.9990 chunk 294 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 257 optimal weight: 0.9980 chunk 187 optimal weight: 0.0570 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN C 373 HIS C 540 HIS D 784 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.151861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.116677 restraints weight = 95288.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.117101 restraints weight = 67635.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.117797 restraints weight = 38655.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.117927 restraints weight = 33220.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.118133 restraints weight = 31542.740| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30656 Z= 0.117 Angle : 0.530 9.222 41708 Z= 0.274 Chirality : 0.042 0.177 4648 Planarity : 0.004 0.054 5393 Dihedral : 4.156 19.130 4060 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.32 % Allowed : 13.57 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.20 (0.13), residues: 3747 helix: 0.97 (0.16), residues: 1028 sheet: -0.08 (0.18), residues: 698 loop : -0.70 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.017 0.001 TYR D 904 PHE 0.023 0.001 PHE B 823 TRP 0.026 0.001 TRP A 104 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00258 (30618) covalent geometry : angle 0.52738 (41632) SS BOND : bond 0.00551 ( 38) SS BOND : angle 1.32749 ( 76) hydrogen bonds : bond 0.03861 ( 1077) hydrogen bonds : angle 5.22709 ( 3066) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 282 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6816 (mp) REVERT: A 153 MET cc_start: 0.1446 (mtt) cc_final: 0.0570 (pmm) REVERT: A 318 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.6509 (p90) REVERT: A 368 LEU cc_start: 0.7131 (mt) cc_final: 0.6900 (pp) REVERT: A 392 PHE cc_start: 0.2466 (OUTLIER) cc_final: 0.1482 (m-80) REVERT: A 900 MET cc_start: 0.7924 (mmm) cc_final: 0.7331 (mpp) REVERT: A 1041 ASP cc_start: 0.7934 (m-30) cc_final: 0.7662 (t0) REVERT: A 1125 ASN cc_start: 0.8408 (p0) cc_final: 0.8056 (m-40) REVERT: C 135 PRO cc_start: 0.0620 (Cg_exo) cc_final: -0.0001 (Cg_endo) REVERT: C 163 TRP cc_start: 0.2126 (m-10) cc_final: 0.1497 (t60) REVERT: D 747 THR cc_start: 0.8715 (p) cc_final: 0.8508 (t) REVERT: D 823 PHE cc_start: 0.8149 (t80) cc_final: 0.7941 (t80) REVERT: D 855 PHE cc_start: 0.6666 (m-80) cc_final: 0.6347 (m-80) REVERT: D 900 MET cc_start: 0.7745 (mtt) cc_final: 0.7520 (mtp) REVERT: D 957 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8135 (tm-30) REVERT: D 1030 SER cc_start: 0.9101 (m) cc_final: 0.8870 (t) REVERT: D 1037 SER cc_start: 0.8991 (t) cc_final: 0.8741 (p) REVERT: D 1071 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7281 (mp10) REVERT: D 1139 ASP cc_start: 0.7502 (t0) cc_final: 0.7181 (t0) REVERT: B 177 MET cc_start: 0.1323 (tmm) cc_final: 0.1051 (tmm) REVERT: B 379 CYS cc_start: 0.2830 (OUTLIER) cc_final: 0.1729 (p) REVERT: B 1045 LYS cc_start: 0.7825 (mttm) cc_final: 0.7561 (ttmt) outliers start: 77 outliers final: 47 residues processed: 343 average time/residue: 0.1591 time to fit residues: 92.8345 Evaluate side-chains 303 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1071 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1037 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 149 optimal weight: 7.9990 chunk 309 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 293 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 954 GLN C 572 ASN D 498 GLN B 321 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 914 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.145637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.111328 restraints weight = 93848.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.111488 restraints weight = 63379.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.111930 restraints weight = 38127.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.112092 restraints weight = 35040.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.112281 restraints weight = 31972.199| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.7630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 30656 Z= 0.270 Angle : 0.692 11.763 41708 Z= 0.359 Chirality : 0.047 0.175 4648 Planarity : 0.005 0.075 5393 Dihedral : 4.864 21.603 4060 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.95 % Allowed : 14.23 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.13), residues: 3747 helix: 0.69 (0.16), residues: 1022 sheet: -0.19 (0.18), residues: 713 loop : -0.93 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 815 TYR 0.036 0.002 TYR B 660 PHE 0.035 0.002 PHE D 86 TRP 0.032 0.002 TRP B 353 HIS 0.009 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00621 (30618) covalent geometry : angle 0.68753 (41632) SS BOND : bond 0.00508 ( 38) SS BOND : angle 2.00382 ( 76) hydrogen bonds : bond 0.04574 ( 1077) hydrogen bonds : angle 5.62326 ( 3066) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 276 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2308 (mtt) cc_final: 0.1341 (pmm) REVERT: A 318 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.6939 (p90) REVERT: A 392 PHE cc_start: 0.3015 (OUTLIER) cc_final: 0.2072 (m-80) REVERT: A 541 PHE cc_start: 0.8439 (p90) cc_final: 0.7905 (p90) REVERT: A 701 VAL cc_start: 0.9097 (p) cc_final: 0.8896 (m) REVERT: A 868 GLU cc_start: 0.8095 (tp30) cc_final: 0.7865 (tm-30) REVERT: A 1125 ASN cc_start: 0.8590 (p0) cc_final: 0.8199 (m-40) REVERT: C 135 PRO cc_start: 0.0851 (Cg_exo) cc_final: 0.0312 (Cg_endo) REVERT: C 163 TRP cc_start: 0.2425 (m-10) cc_final: 0.1356 (t60) REVERT: D 740 MET cc_start: 0.8043 (mmm) cc_final: 0.7826 (tpt) REVERT: D 747 THR cc_start: 0.8888 (p) cc_final: 0.8666 (t) REVERT: D 855 PHE cc_start: 0.6669 (m-80) cc_final: 0.6328 (m-80) REVERT: D 900 MET cc_start: 0.7842 (mtt) cc_final: 0.7554 (mtp) REVERT: D 957 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8239 (tm-30) REVERT: D 1030 SER cc_start: 0.9198 (m) cc_final: 0.8837 (t) REVERT: D 1037 SER cc_start: 0.9148 (t) cc_final: 0.8847 (p) REVERT: D 1139 ASP cc_start: 0.7634 (t0) cc_final: 0.7325 (t0) REVERT: B 379 CYS cc_start: 0.3014 (OUTLIER) cc_final: 0.1826 (p) REVERT: B 774 GLN cc_start: 0.8487 (mm110) cc_final: 0.8283 (mm110) REVERT: B 902 MET cc_start: 0.8784 (mmm) cc_final: 0.7896 (mmt) REVERT: B 1045 LYS cc_start: 0.8035 (mttm) cc_final: 0.7720 (ttmt) outliers start: 98 outliers final: 69 residues processed: 351 average time/residue: 0.1625 time to fit residues: 96.4913 Evaluate side-chains 309 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 237 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1146 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 336 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 263 optimal weight: 0.9990 chunk 162 optimal weight: 0.3980 chunk 304 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 364 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 133 optimal weight: 0.0570 chunk 136 optimal weight: 9.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A1011 GLN C 572 ASN D 99 ASN D 856 ASN D 955 ASN D1011 GLN B 774 GLN B 787 GLN B 957 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.149587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.115092 restraints weight = 93893.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.115290 restraints weight = 63102.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.115503 restraints weight = 39519.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.115891 restraints weight = 37683.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.116134 restraints weight = 31039.797| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.7568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30656 Z= 0.108 Angle : 0.548 10.149 41708 Z= 0.283 Chirality : 0.043 0.161 4648 Planarity : 0.004 0.066 5393 Dihedral : 4.340 18.964 4060 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.77 % Allowed : 15.85 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.20 (0.13), residues: 3747 helix: 0.99 (0.16), residues: 1040 sheet: -0.05 (0.19), residues: 687 loop : -0.74 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.018 0.001 TYR D 170 PHE 0.023 0.001 PHE D 168 TRP 0.047 0.002 TRP B 353 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00232 (30618) covalent geometry : angle 0.54560 (41632) SS BOND : bond 0.00314 ( 38) SS BOND : angle 1.37614 ( 76) hydrogen bonds : bond 0.03771 ( 1077) hydrogen bonds : angle 5.16883 ( 3066) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 276 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1338 (mtt) cc_final: 0.0881 (pmm) REVERT: A 318 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7047 (p90) REVERT: A 368 LEU cc_start: 0.6977 (mt) cc_final: 0.6517 (pp) REVERT: A 369 TYR cc_start: 0.1516 (OUTLIER) cc_final: -0.0135 (t80) REVERT: A 392 PHE cc_start: 0.2927 (OUTLIER) cc_final: 0.1971 (m-80) REVERT: A 701 VAL cc_start: 0.9124 (p) cc_final: 0.8918 (m) REVERT: A 990 GLU cc_start: 0.8267 (pm20) cc_final: 0.7976 (pm20) REVERT: A 1125 ASN cc_start: 0.8504 (p0) cc_final: 0.8230 (m-40) REVERT: D 740 MET cc_start: 0.7865 (mmm) cc_final: 0.7619 (tpt) REVERT: D 747 THR cc_start: 0.8741 (p) cc_final: 0.8496 (t) REVERT: D 855 PHE cc_start: 0.6745 (m-80) cc_final: 0.6481 (m-80) REVERT: D 900 MET cc_start: 0.7902 (mtt) cc_final: 0.7568 (mtp) REVERT: D 957 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8102 (tm-30) REVERT: D 1030 SER cc_start: 0.9098 (m) cc_final: 0.8806 (t) REVERT: D 1037 SER cc_start: 0.9046 (t) cc_final: 0.8823 (p) REVERT: D 1050 MET cc_start: 0.8010 (ptm) cc_final: 0.7750 (ptm) REVERT: D 1139 ASP cc_start: 0.7544 (t0) cc_final: 0.7229 (t0) REVERT: B 177 MET cc_start: 0.1721 (tmm) cc_final: 0.1355 (tmm) REVERT: B 379 CYS cc_start: 0.2637 (OUTLIER) cc_final: 0.1840 (p) REVERT: B 902 MET cc_start: 0.8582 (mmm) cc_final: 0.8275 (mmt) REVERT: B 918 GLU cc_start: 0.8006 (mp0) cc_final: 0.7639 (mp0) outliers start: 59 outliers final: 44 residues processed: 319 average time/residue: 0.1727 time to fit residues: 90.7698 Evaluate side-chains 290 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1017 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 283 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 315 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 338 optimal weight: 0.0870 chunk 310 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 346 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 overall best weight: 3.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 992 GLN ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.145917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.109407 restraints weight = 94003.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111286 restraints weight = 56421.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.111356 restraints weight = 31353.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.111616 restraints weight = 29855.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.111796 restraints weight = 25729.041| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.7984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30656 Z= 0.209 Angle : 0.624 11.064 41708 Z= 0.323 Chirality : 0.044 0.155 4648 Planarity : 0.004 0.057 5393 Dihedral : 4.598 26.945 4060 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.41 % Allowed : 15.43 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.35 (0.13), residues: 3747 helix: 0.94 (0.16), residues: 1043 sheet: -0.19 (0.18), residues: 698 loop : -0.85 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 995 TYR 0.018 0.002 TYR A 421 PHE 0.033 0.002 PHE D 86 TRP 0.047 0.002 TRP C 163 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00477 (30618) covalent geometry : angle 0.61999 (41632) SS BOND : bond 0.00439 ( 38) SS BOND : angle 1.84615 ( 76) hydrogen bonds : bond 0.04081 ( 1077) hydrogen bonds : angle 5.30706 ( 3066) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 250 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0005 (tmm) cc_final: -0.2790 (tpt) REVERT: A 318 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7167 (p90) REVERT: A 369 TYR cc_start: 0.1564 (OUTLIER) cc_final: -0.0176 (t80) REVERT: A 392 PHE cc_start: 0.3113 (OUTLIER) cc_final: 0.2342 (m-80) REVERT: A 1125 ASN cc_start: 0.8704 (p0) cc_final: 0.8172 (m-40) REVERT: C 332 MET cc_start: -0.1988 (tmm) cc_final: -0.2290 (tmm) REVERT: D 740 MET cc_start: 0.8401 (mmm) cc_final: 0.8169 (tpt) REVERT: D 747 THR cc_start: 0.9041 (p) cc_final: 0.8737 (t) REVERT: D 855 PHE cc_start: 0.6817 (m-80) cc_final: 0.6421 (m-80) REVERT: D 900 MET cc_start: 0.8153 (mtt) cc_final: 0.7849 (mtp) REVERT: D 950 ASP cc_start: 0.8141 (t70) cc_final: 0.7769 (t0) REVERT: D 957 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8233 (tm-30) REVERT: D 1030 SER cc_start: 0.9257 (m) cc_final: 0.8916 (t) REVERT: D 1037 SER cc_start: 0.9239 (t) cc_final: 0.8955 (p) REVERT: D 1050 MET cc_start: 0.8411 (ptm) cc_final: 0.8131 (ptm) REVERT: D 1092 GLU cc_start: 0.7998 (tt0) cc_final: 0.7114 (pp20) REVERT: D 1139 ASP cc_start: 0.7461 (t0) cc_final: 0.7107 (t0) REVERT: B 64 TRP cc_start: 0.7227 (OUTLIER) cc_final: 0.6543 (m-10) REVERT: B 118 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8107 (tp) REVERT: B 379 CYS cc_start: 0.2746 (OUTLIER) cc_final: 0.1590 (p) REVERT: B 902 MET cc_start: 0.8689 (mmm) cc_final: 0.8140 (mmt) outliers start: 80 outliers final: 59 residues processed: 309 average time/residue: 0.1533 time to fit residues: 79.6679 Evaluate side-chains 302 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 237 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1146 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 276 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 298 optimal weight: 0.7980 chunk 277 optimal weight: 6.9990 chunk 322 optimal weight: 0.0980 chunk 34 optimal weight: 0.0050 chunk 51 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 chunk 372 optimal weight: 3.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.149869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.112893 restraints weight = 93735.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.115162 restraints weight = 47553.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.115339 restraints weight = 27063.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.115804 restraints weight = 24099.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.116445 restraints weight = 21430.642| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.7914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30656 Z= 0.103 Angle : 0.543 9.857 41708 Z= 0.279 Chirality : 0.042 0.166 4648 Planarity : 0.004 0.050 5393 Dihedral : 4.200 28.946 4060 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.65 % Allowed : 16.13 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.11 (0.13), residues: 3747 helix: 1.14 (0.16), residues: 1058 sheet: -0.07 (0.19), residues: 684 loop : -0.70 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.024 0.001 TYR C 50 PHE 0.021 0.001 PHE A 55 TRP 0.049 0.002 TRP B 353 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00225 (30618) covalent geometry : angle 0.54074 (41632) SS BOND : bond 0.00293 ( 38) SS BOND : angle 1.31468 ( 76) hydrogen bonds : bond 0.03523 ( 1077) hydrogen bonds : angle 4.98877 ( 3066) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 277 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7348 (mmm160) cc_final: 0.6997 (mmp-170) REVERT: A 177 MET cc_start: -0.0621 (tmm) cc_final: -0.3415 (tpt) REVERT: A 318 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7071 (p90) REVERT: A 368 LEU cc_start: 0.6985 (mt) cc_final: 0.6528 (pp) REVERT: A 392 PHE cc_start: 0.2985 (OUTLIER) cc_final: 0.2186 (m-80) REVERT: A 900 MET cc_start: 0.8224 (mtp) cc_final: 0.7991 (mtm) REVERT: A 990 GLU cc_start: 0.8298 (pm20) cc_final: 0.7929 (pm20) REVERT: A 1125 ASN cc_start: 0.8583 (p0) cc_final: 0.8152 (m-40) REVERT: C 323 MET cc_start: 0.4332 (tpp) cc_final: 0.4094 (tpt) REVERT: C 332 MET cc_start: -0.2437 (tmm) cc_final: -0.2691 (tmm) REVERT: D 747 THR cc_start: 0.8877 (p) cc_final: 0.8572 (t) REVERT: D 855 PHE cc_start: 0.6967 (m-80) cc_final: 0.6601 (m-80) REVERT: D 957 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8129 (tm-30) REVERT: D 1030 SER cc_start: 0.9169 (m) cc_final: 0.8855 (t) REVERT: D 1037 SER cc_start: 0.9193 (t) cc_final: 0.8978 (m) REVERT: D 1050 MET cc_start: 0.8215 (ptm) cc_final: 0.8001 (ptm) REVERT: D 1139 ASP cc_start: 0.7279 (t0) cc_final: 0.6951 (t0) REVERT: B 118 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8365 (tp) REVERT: B 177 MET cc_start: 0.1807 (tmm) cc_final: 0.1399 (tmm) REVERT: B 379 CYS cc_start: 0.2230 (OUTLIER) cc_final: 0.1605 (p) REVERT: B 671 CYS cc_start: 0.6112 (OUTLIER) cc_final: 0.5892 (t) REVERT: B 918 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: B 968 SER cc_start: 0.9038 (m) cc_final: 0.8735 (p) REVERT: B 1002 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7788 (tp-100) outliers start: 55 outliers final: 39 residues processed: 313 average time/residue: 0.1687 time to fit residues: 88.5794 Evaluate side-chains 291 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 279 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 339 optimal weight: 0.7980 chunk 252 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 323 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 955 ASN C 580 ASN D1005 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.145974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.109662 restraints weight = 93610.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.111149 restraints weight = 58806.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.111296 restraints weight = 32283.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.111634 restraints weight = 28198.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.111769 restraints weight = 26065.876| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.8250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30656 Z= 0.187 Angle : 0.613 11.008 41708 Z= 0.316 Chirality : 0.044 0.160 4648 Planarity : 0.004 0.048 5393 Dihedral : 4.504 34.605 4060 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.56 % Allowed : 16.40 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.25 (0.13), residues: 3747 helix: 1.04 (0.16), residues: 1059 sheet: -0.14 (0.19), residues: 702 loop : -0.82 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 815 TYR 0.026 0.002 TYR D 904 PHE 0.032 0.002 PHE D 86 TRP 0.054 0.002 TRP B 353 HIS 0.007 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00429 (30618) covalent geometry : angle 0.60854 (41632) SS BOND : bond 0.00399 ( 38) SS BOND : angle 1.75873 ( 76) hydrogen bonds : bond 0.03952 ( 1077) hydrogen bonds : angle 5.23189 ( 3066) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0460 (tmm) cc_final: -0.3336 (tpp) REVERT: A 318 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7302 (p90) REVERT: A 392 PHE cc_start: 0.3364 (OUTLIER) cc_final: 0.2678 (m-80) REVERT: A 1125 ASN cc_start: 0.8662 (p0) cc_final: 0.8234 (m-40) REVERT: C 152 MET cc_start: -0.2620 (mmt) cc_final: -0.2984 (mtt) REVERT: C 474 MET cc_start: 0.0471 (ttm) cc_final: -0.0356 (ttm) REVERT: D 275 PHE cc_start: 0.7577 (m-10) cc_final: 0.7042 (m-10) REVERT: D 740 MET cc_start: 0.8290 (mmm) cc_final: 0.8019 (tpt) REVERT: D 747 THR cc_start: 0.9019 (p) cc_final: 0.8705 (t) REVERT: D 855 PHE cc_start: 0.7113 (m-80) cc_final: 0.6687 (m-80) REVERT: D 950 ASP cc_start: 0.8120 (t70) cc_final: 0.7758 (t0) REVERT: D 957 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8205 (tm-30) REVERT: D 1017 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7719 (tm-30) REVERT: D 1030 SER cc_start: 0.9265 (m) cc_final: 0.8913 (t) REVERT: D 1037 SER cc_start: 0.9238 (t) cc_final: 0.8974 (p) REVERT: D 1050 MET cc_start: 0.8429 (ptm) cc_final: 0.8186 (ptm) REVERT: D 1092 GLU cc_start: 0.8052 (tt0) cc_final: 0.7122 (pp20) REVERT: D 1139 ASP cc_start: 0.7598 (t0) cc_final: 0.7295 (t0) REVERT: B 118 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8256 (tp) REVERT: B 379 CYS cc_start: 0.2509 (OUTLIER) cc_final: 0.1521 (p) REVERT: B 918 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7744 (mp0) outliers start: 52 outliers final: 42 residues processed: 289 average time/residue: 0.1730 time to fit residues: 83.1407 Evaluate side-chains 293 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 1146 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 366 optimal weight: 0.7980 chunk 332 optimal weight: 1.9990 chunk 165 optimal weight: 20.0000 chunk 58 optimal weight: 0.0040 chunk 309 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 90 optimal weight: 0.0020 chunk 306 optimal weight: 0.0470 chunk 169 optimal weight: 4.9990 chunk 319 optimal weight: 6.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.149565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.113269 restraints weight = 94213.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.114557 restraints weight = 56779.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115637 restraints weight = 31008.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115683 restraints weight = 26644.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.115866 restraints weight = 24557.664| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.8194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30656 Z= 0.105 Angle : 0.551 14.966 41708 Z= 0.281 Chirality : 0.042 0.158 4648 Planarity : 0.004 0.043 5393 Dihedral : 4.202 35.376 4060 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.41 % Allowed : 16.67 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.05 (0.14), residues: 3747 helix: 1.26 (0.16), residues: 1051 sheet: -0.04 (0.19), residues: 699 loop : -0.71 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 393 TYR 0.022 0.001 TYR A 421 PHE 0.032 0.001 PHE D 186 TRP 0.046 0.002 TRP A 104 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00230 (30618) covalent geometry : angle 0.54841 (41632) SS BOND : bond 0.00287 ( 38) SS BOND : angle 1.42181 ( 76) hydrogen bonds : bond 0.03465 ( 1077) hydrogen bonds : angle 4.98927 ( 3066) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5619.26 seconds wall clock time: 97 minutes 24.81 seconds (5844.81 seconds total)