Starting phenix.real_space_refine on Mon Aug 25 18:46:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vxf_32178/08_2025/7vxf_32178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vxf_32178/08_2025/7vxf_32178.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/7vxf_32178/08_2025/7vxf_32178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vxf_32178/08_2025/7vxf_32178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vxf_32178/08_2025/7vxf_32178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vxf_32178/08_2025/7vxf_32178.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= -0.003 sd= 0.164 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 19214 2.51 5 N 5012 2.21 5 O 5709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30079 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Chain: "C" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 8301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8301 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 51, 'TRANS': 1007} Chain breaks: 6 Chain: "D" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 5 Time building chain proxies: 6.59, per 1000 atoms: 0.22 Number of scatterers: 30079 At special positions: 0 Unit cell: (161.764, 150.834, 263.413, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 5709 8.00 N 5012 7.00 C 19214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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 B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 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: 2.38 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7156 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 46 sheets defined 31.3% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.584A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.941A 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 403 through 407 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.636A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.763A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.543A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.582A 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: 3.590A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.801A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.177A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.689A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.651A 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: 3.941A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.583A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.561A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1154 removed outlier: 4.116A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A1154 " --> pdb=" O GLU A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'C' and resid 20 through 53 removed outlier: 4.041A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.742A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.947A pdb=" N GLU C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.512A 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: 4.071A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.929A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 removed outlier: 3.849A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 removed outlier: 3.796A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.611A pdb=" N ARG C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 194 removed outlier: 3.674A pdb=" N MET C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.545A pdb=" N TYR C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.732A 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: 4.000A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.802A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.508A 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: 3.738A pdb=" N ASP C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 removed outlier: 4.072A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.610A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.671A pdb=" N PHE C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 370 " --> pdb=" O MET C 366 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) removed outlier: 4.309A 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: 3.568A pdb=" N VAL C 404 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.744A pdb=" N ILE C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.640A pdb=" N ASN C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 466 removed outlier: 3.999A 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: 3.881A pdb=" N GLU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 removed outlier: 4.127A pdb=" N SER C 502 " --> pdb=" O CYS C 498 " (cutoff:3.500A) removed outlier: 3.848A 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: 3.513A pdb=" N THR C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 3.540A 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: 3.656A pdb=" N GLN C 552 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 556 " --> pdb=" O GLN C 552 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 removed outlier: 3.519A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.588A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.693A pdb=" N TRP C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.590A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 removed outlier: 4.009A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.128A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.688A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.776A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 780 removed outlier: 3.553A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 Processing helix chain 'B' and resid 849 through 854 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.582A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.072A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.608A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.173A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.657A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.939A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.639A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.522A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1154 removed outlier: 4.050A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS B1154 " --> pdb=" O GLU B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1161 removed outlier: 3.588A pdb=" N HIS B1159 " --> pdb=" O TYR B1155 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B1160 " --> pdb=" O PHE B1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.526A pdb=" N THR D 299 " --> pdb=" O PRO D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.111A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 737 through 743 removed outlier: 4.054A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS D 743 " --> pdb=" O THR D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 755 removed outlier: 3.721A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 780 removed outlier: 3.597A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 825 Processing helix chain 'D' and resid 849 through 854 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 891 removed outlier: 4.025A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 899 No H-bonds generated for 'chain 'D' and resid 897 through 899' Processing helix chain 'D' and resid 900 through 909 removed outlier: 4.043A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 3.899A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.678A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 removed outlier: 3.715A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.092A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1157 removed outlier: 4.269A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1158 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.770A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.776A 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: 4.475A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.778A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.555A 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: 3.516A 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: 3.771A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 4.024A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.747A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (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: 5.683A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 672 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 4.060A 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: 3.681A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.734A 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: 3.624A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.528A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.561A pdb=" N LEU C 142 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.093A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.595A pdb=" N THR C 347 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.748A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.369A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.578A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.694A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 318 removed outlier: 3.549A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 removed outlier: 4.036A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 566 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.792A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 653 through 655 removed outlier: 5.616A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.549A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.641A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.562A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 27 through 30 removed outlier: 3.816A pdb=" N ALA D 27 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE D 194 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.644A pdb=" N THR D 51 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 275 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.842A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 241 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS D 131 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL D 126 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AE1, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.836A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 324 through 327 removed outlier: 6.939A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 354 through 357 removed outlier: 4.368A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU D 513 " --> pdb=" O CYS D 432 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N CYS D 432 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 378 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA D 435 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR D 376 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.037A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.826A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.650A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.375A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1120 through 1122 removed outlier: 3.650A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1094 through 1097 1030 hydrogen bonds defined for protein. 2898 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: 6.45 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9715 1.35 - 1.46: 7584 1.46 - 1.58: 13310 1.58 - 1.70: 0 1.70 - 1.82: 195 Bond restraints: 30804 Sorted by residual: bond pdb=" C LEU D 229 " pdb=" N PRO D 230 " ideal model delta sigma weight residual 1.334 1.437 -0.103 2.34e-02 1.83e+03 1.92e+01 bond pdb=" C PRO D 25 " pdb=" N PRO D 26 " ideal model delta sigma weight residual 1.334 1.433 -0.100 2.34e-02 1.83e+03 1.81e+01 bond pdb=" C CYS D 336 " pdb=" N PRO D 337 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.44e+01 bond pdb=" C PRO B 25 " pdb=" N PRO B 26 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.71e+00 bond pdb=" C PRO A 25 " pdb=" N PRO A 26 " ideal model delta sigma weight residual 1.334 1.392 -0.059 2.34e-02 1.83e+03 6.25e+00 ... (remaining 30799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 41626 2.34 - 4.69: 231 4.69 - 7.03: 26 7.03 - 9.38: 3 9.38 - 11.72: 3 Bond angle restraints: 41889 Sorted by residual: angle pdb=" C LYS A 790 " pdb=" N THR A 791 " pdb=" CA THR A 791 " ideal model delta sigma weight residual 120.94 132.07 -11.13 1.90e+00 2.77e-01 3.43e+01 angle pdb=" N ALA A 292 " pdb=" CA ALA A 292 " pdb=" C ALA A 292 " ideal model delta sigma weight residual 110.80 99.08 11.72 2.13e+00 2.20e-01 3.03e+01 angle pdb=" N ALA B 292 " pdb=" CA ALA B 292 " pdb=" C ALA B 292 " ideal model delta sigma weight residual 110.80 100.34 10.46 2.13e+00 2.20e-01 2.41e+01 angle pdb=" N CYS A 291 " pdb=" CA CYS A 291 " pdb=" C CYS A 291 " ideal model delta sigma weight residual 108.73 116.16 -7.43 1.63e+00 3.76e-01 2.08e+01 angle pdb=" CA CYS D 361 " pdb=" C CYS D 361 " pdb=" N VAL D 362 " ideal model delta sigma weight residual 115.79 120.51 -4.72 1.34e+00 5.57e-01 1.24e+01 ... (remaining 41884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 17855 15.99 - 31.97: 307 31.97 - 47.96: 112 47.96 - 63.94: 28 63.94 - 79.93: 15 Dihedral angle restraints: 18317 sinusoidal: 7197 harmonic: 11120 Sorted by residual: dihedral pdb=" CA THR D 531 " pdb=" C THR D 531 " pdb=" N ASN D 532 " pdb=" CA ASN D 532 " ideal model delta harmonic sigma weight residual -180.00 -153.12 -26.88 0 5.00e+00 4.00e-02 2.89e+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 56.40 36.60 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CA LEU A 241 " pdb=" C LEU A 241 " pdb=" N HIS A 242 " pdb=" CA HIS A 242 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 18314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3861 0.049 - 0.098: 571 0.098 - 0.147: 233 0.147 - 0.196: 3 0.196 - 0.245: 3 Chirality restraints: 4671 Sorted by residual: 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 2.27 0.24 2.00e-01 2.50e+01 1.49e+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 1.40e+00 chirality pdb=" CA ALA B 292 " pdb=" N ALA B 292 " pdb=" C ALA B 292 " pdb=" CB ALA B 292 " both_signs ideal model delta sigma weight residual False 2.48 2.72 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 4668 not shown) Planarity restraints: 5431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 290 " -0.014 2.00e-02 2.50e+03 2.86e-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=" C ASP B 294 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO B 295 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO A 295 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.031 5.00e-02 4.00e+02 ... (remaining 5428 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 85 2.40 - 3.03: 16361 3.03 - 3.65: 42558 3.65 - 4.28: 64323 4.28 - 4.90: 107518 Nonbonded interactions: 230845 Sorted by model distance: nonbonded pdb=" O GLY A 103 " pdb=" CE1 HIS A 242 " model vdw 1.780 3.260 nonbonded pdb=" OG1 THR D 108 " pdb=" O ASN D 234 " model vdw 2.197 3.040 nonbonded pdb=" OG SER D 746 " pdb=" OE1 GLU D 748 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR D 33 " pdb=" O GLY D 219 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR A 912 " pdb=" NE2 GLN A1106 " model vdw 2.262 3.120 ... (remaining 230840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 470 or resid 491 through 1161)) selection = chain 'B' selection = (chain 'D' and (resid 14 through 470 or resid 491 through 1161)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.450 Find NCS groups from input model: 0.420 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4765 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 30843 Z= 0.106 Angle : 0.480 11.725 41967 Z= 0.276 Chirality : 0.041 0.245 4671 Planarity : 0.003 0.055 5431 Dihedral : 8.026 79.929 11044 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.97 % Favored : 95.89 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.11), residues: 3774 helix: -3.28 (0.10), residues: 946 sheet: -0.51 (0.17), residues: 655 loop : -1.11 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 102 TYR 0.016 0.001 TYR A 495 PHE 0.017 0.001 PHE D 59 TRP 0.018 0.001 TRP A 436 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00195 (30804) covalent geometry : angle 0.47929 (41889) SS BOND : bond 0.00222 ( 39) SS BOND : angle 0.88866 ( 78) hydrogen bonds : bond 0.30799 ( 1030) hydrogen bonds : angle 9.84247 ( 2898) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 858 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.4327 (p0) cc_final: 0.4028 (p0) REVERT: A 574 ASP cc_start: 0.7620 (p0) cc_final: 0.7347 (p0) REVERT: A 584 ILE cc_start: 0.7384 (mt) cc_final: 0.7055 (mp) REVERT: A 693 ILE cc_start: 0.8623 (pt) cc_final: 0.8298 (pt) REVERT: A 714 ILE cc_start: 0.8527 (mp) cc_final: 0.8259 (mt) REVERT: B 305 SER cc_start: 0.8401 (t) cc_final: 0.8177 (t) REVERT: B 1033 VAL cc_start: 0.8081 (t) cc_final: 0.7687 (t) REVERT: D 159 VAL cc_start: 0.3726 (t) cc_final: 0.3468 (t) REVERT: D 710 ASN cc_start: 0.6325 (p0) cc_final: 0.6092 (p0) REVERT: D 1102 TRP cc_start: 0.6782 (m100) cc_final: 0.6484 (m100) outliers start: 1 outliers final: 0 residues processed: 859 average time/residue: 0.1930 time to fit residues: 261.9076 Evaluate side-chains 406 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.0670 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 overall best weight: 2.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 280 ASN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 690 GLN A 787 GLN A 955 ASN A1088 HIS C 24 GLN C 60 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS C 380 GLN C 401 HIS C 417 HIS C 505 HIS B 30 ASN B 211 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS D 30 ASN D 69 HIS D 121 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN D 655 HIS D 675 GLN D 762 GLN D 824 ASN D1005 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1088 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.168042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.132881 restraints weight = 95609.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.136111 restraints weight = 46107.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.136691 restraints weight = 26431.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.137251 restraints weight = 19191.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.137453 restraints weight = 16145.072| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 30843 Z= 0.188 Angle : 0.652 9.627 41967 Z= 0.345 Chirality : 0.046 0.199 4671 Planarity : 0.005 0.051 5431 Dihedral : 4.064 24.864 4087 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.75 % Favored : 98.22 % Rotamer: Outliers : 1.94 % Allowed : 8.88 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.12), residues: 3774 helix: -0.62 (0.14), residues: 970 sheet: -0.30 (0.17), residues: 703 loop : -0.88 (0.12), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 765 TYR 0.026 0.002 TYR D 741 PHE 0.038 0.002 PHE A 55 TRP 0.016 0.001 TRP A1102 HIS 0.016 0.002 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00393 (30804) covalent geometry : angle 0.64929 (41889) SS BOND : bond 0.00690 ( 39) SS BOND : angle 1.52664 ( 78) hydrogen bonds : bond 0.05433 ( 1030) hydrogen bonds : angle 6.05220 ( 2898) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 455 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.6490 (p0) cc_final: 0.6197 (p0) REVERT: A 206 LYS cc_start: 0.8171 (tptt) cc_final: 0.7939 (tptt) REVERT: A 305 SER cc_start: 0.7738 (t) cc_final: 0.7304 (p) REVERT: A 559 PHE cc_start: 0.6058 (m-10) cc_final: 0.4733 (m-10) REVERT: A 596 SER cc_start: 0.8722 (m) cc_final: 0.8064 (p) REVERT: A 902 MET cc_start: 0.8414 (mmm) cc_final: 0.8126 (mmm) REVERT: A 976 VAL cc_start: 0.8153 (t) cc_final: 0.7953 (t) REVERT: A 978 ASN cc_start: 0.8129 (m110) cc_final: 0.7402 (m-40) REVERT: A 992 GLN cc_start: 0.8757 (mm110) cc_final: 0.8474 (mm110) REVERT: C 38 ASP cc_start: 0.6267 (OUTLIER) cc_final: 0.6025 (t0) REVERT: C 39 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5443 (mp) REVERT: C 84 PRO cc_start: 0.6265 (Cg_exo) cc_final: 0.6007 (Cg_endo) REVERT: C 85 LEU cc_start: 0.2810 (mp) cc_final: 0.1580 (pp) REVERT: C 323 MET cc_start: -0.1168 (mmm) cc_final: -0.1635 (mtm) REVERT: C 408 MET cc_start: -0.0748 (mtt) cc_final: -0.1065 (mtp) REVERT: C 455 MET cc_start: -0.2374 (tmm) cc_final: -0.3014 (tmm) REVERT: B 46 SER cc_start: 0.8279 (m) cc_final: 0.7825 (t) REVERT: B 62 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7823 (p) REVERT: B 129 LYS cc_start: 0.7509 (mttt) cc_final: 0.7096 (mmmt) REVERT: B 170 TYR cc_start: 0.6676 (t80) cc_final: 0.6469 (t80) REVERT: B 365 TYR cc_start: 0.4374 (m-80) cc_final: 0.2043 (t80) REVERT: B 699 LEU cc_start: 0.7598 (mt) cc_final: 0.7296 (mt) REVERT: B 884 SER cc_start: 0.9216 (m) cc_final: 0.8942 (p) REVERT: B 1141 LEU cc_start: 0.7711 (tt) cc_final: 0.7487 (tp) REVERT: D 238 PHE cc_start: 0.6760 (p90) cc_final: 0.6374 (p90) REVERT: D 241 LEU cc_start: 0.6889 (tp) cc_final: 0.6475 (mp) REVERT: D 1031 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7185 (mt-10) outliers start: 65 outliers final: 38 residues processed: 506 average time/residue: 0.1984 time to fit residues: 163.0213 Evaluate side-chains 370 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 328 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 743 CYS Chi-restraints excluded: chain D residue 875 SER Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 305 optimal weight: 0.0170 chunk 178 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 297 optimal weight: 9.9990 chunk 294 optimal weight: 9.9990 chunk 225 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 314 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 overall best weight: 2.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 49 HIS ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A1088 HIS A1106 GLN A1159 HIS C 61 ASN C 524 GLN B 30 ASN B 66 HIS B 207 HIS B 498 GLN B 563 GLN B 655 HIS B 913 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN B1088 HIS B1106 GLN D 148 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 HIS D 321 GLN D 703 ASN D 779 GLN D 856 ASN D 914 ASN D 955 ASN D1002 GLN D1054 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.163538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.126868 restraints weight = 97391.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.130014 restraints weight = 50953.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.130642 restraints weight = 26065.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.131135 restraints weight = 21589.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.131205 restraints weight = 19344.002| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 30843 Z= 0.181 Angle : 0.644 12.289 41967 Z= 0.334 Chirality : 0.046 0.191 4671 Planarity : 0.005 0.048 5431 Dihedral : 4.259 28.477 4087 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.81 % Favored : 97.16 % Rotamer: Outliers : 2.42 % Allowed : 9.69 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.13), residues: 3774 helix: 0.38 (0.16), residues: 982 sheet: -0.19 (0.17), residues: 692 loop : -0.86 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 237 TYR 0.027 0.002 TYR C 252 PHE 0.034 0.002 PHE A 55 TRP 0.032 0.002 TRP A 104 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00409 (30804) covalent geometry : angle 0.64053 (41889) SS BOND : bond 0.00518 ( 39) SS BOND : angle 1.74083 ( 78) hydrogen bonds : bond 0.04758 ( 1030) hydrogen bonds : angle 5.40435 ( 2898) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 377 time to evaluate : 1.233 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 34 ARG cc_start: 0.6749 (mtt90) cc_final: 0.6046 (mpt180) REVERT: A 88 ASP cc_start: 0.6488 (p0) cc_final: 0.6246 (p0) REVERT: A 305 SER cc_start: 0.8324 (t) cc_final: 0.7965 (p) REVERT: A 596 SER cc_start: 0.8951 (m) cc_final: 0.8311 (p) REVERT: A 697 MET cc_start: 0.7346 (tpt) cc_final: 0.6579 (ttt) REVERT: A 699 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8306 (mm) REVERT: A 780 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7611 (tt0) REVERT: A 791 THR cc_start: 0.7477 (m) cc_final: 0.7156 (t) REVERT: A 978 ASN cc_start: 0.8407 (m110) cc_final: 0.7919 (m-40) REVERT: A 992 GLN cc_start: 0.8756 (mm110) cc_final: 0.8545 (mp10) REVERT: A 1130 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8591 (tp) REVERT: C 85 LEU cc_start: 0.3059 (mp) cc_final: 0.1903 (pp) REVERT: C 323 MET cc_start: -0.0890 (mmm) cc_final: -0.1338 (mtm) REVERT: C 383 MET cc_start: 0.3631 (tmm) cc_final: 0.3345 (tmm) REVERT: C 536 GLU cc_start: 0.4993 (OUTLIER) cc_final: 0.4588 (pt0) REVERT: B 119 ILE cc_start: 0.8660 (mp) cc_final: 0.8341 (pt) REVERT: B 129 LYS cc_start: 0.7827 (mttt) cc_final: 0.7615 (mmtt) REVERT: B 227 VAL cc_start: 0.8732 (t) cc_final: 0.8531 (m) REVERT: B 266 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6696 (m-80) REVERT: B 365 TYR cc_start: 0.4404 (m-80) cc_final: 0.1991 (t80) REVERT: B 699 LEU cc_start: 0.8130 (mt) cc_final: 0.7729 (mt) REVERT: B 856 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7945 (t0) REVERT: B 884 SER cc_start: 0.9433 (m) cc_final: 0.9125 (p) REVERT: B 904 TYR cc_start: 0.7671 (t80) cc_final: 0.7021 (t80) REVERT: B 957 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: B 992 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8341 (mt0) REVERT: D 729 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8696 (m) REVERT: D 954 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8099 (tm-30) outliers start: 81 outliers final: 44 residues processed: 437 average time/residue: 0.1877 time to fit residues: 137.2429 Evaluate side-chains 356 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 305 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 328 TRP Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 743 CYS Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 967 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 371 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 319 optimal weight: 9.9990 chunk 334 optimal weight: 0.5980 chunk 128 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 487 ASN A 498 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS C 24 GLN C 221 GLN C 330 ASN C 505 HIS B 14 GLN B 30 ASN B 394 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN D 498 GLN D 914 ASN D1125 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.155992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.118518 restraints weight = 98052.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.120862 restraints weight = 46666.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.122393 restraints weight = 28065.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.123379 restraints weight = 19919.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.123945 restraints weight = 16027.102| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 30843 Z= 0.209 Angle : 0.662 12.811 41967 Z= 0.340 Chirality : 0.047 0.178 4671 Planarity : 0.005 0.093 5431 Dihedral : 4.542 21.313 4087 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 2.48 % Allowed : 11.58 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.13), residues: 3774 helix: 0.52 (0.16), residues: 1014 sheet: -0.19 (0.18), residues: 695 loop : -0.95 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 765 TYR 0.022 0.002 TYR A 160 PHE 0.027 0.002 PHE D 970 TRP 0.018 0.002 TRP D 104 HIS 0.008 0.002 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00478 (30804) covalent geometry : angle 0.65857 (41889) SS BOND : bond 0.00478 ( 39) SS BOND : angle 1.70644 ( 78) hydrogen bonds : bond 0.04315 ( 1030) hydrogen bonds : angle 5.32716 ( 2898) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 345 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6707 (mtt90) cc_final: 0.6365 (mmm160) REVERT: A 86 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: A 88 ASP cc_start: 0.5926 (p0) cc_final: 0.5587 (p0) REVERT: A 200 TYR cc_start: 0.6642 (t80) cc_final: 0.6424 (t80) REVERT: A 205 SER cc_start: 0.8269 (t) cc_final: 0.7899 (p) REVERT: A 275 PHE cc_start: 0.8431 (m-10) cc_final: 0.8211 (m-80) REVERT: A 571 ASP cc_start: 0.7518 (t70) cc_final: 0.7211 (t70) REVERT: A 596 SER cc_start: 0.9142 (m) cc_final: 0.8440 (p) REVERT: A 699 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8500 (mm) REVERT: A 803 SER cc_start: 0.8881 (m) cc_final: 0.8580 (p) REVERT: A 900 MET cc_start: 0.8715 (mmm) cc_final: 0.8172 (mtp) REVERT: A 978 ASN cc_start: 0.8400 (m110) cc_final: 0.8072 (m-40) REVERT: C 323 MET cc_start: -0.0510 (mmm) cc_final: -0.1057 (mtm) REVERT: C 536 GLU cc_start: 0.4113 (OUTLIER) cc_final: 0.3854 (pt0) REVERT: C 606 TRP cc_start: 0.2274 (p90) cc_final: 0.0949 (p90) REVERT: B 759 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7602 (t80) REVERT: B 764 ASN cc_start: 0.8578 (t0) cc_final: 0.8197 (m-40) REVERT: B 787 GLN cc_start: 0.7792 (mp10) cc_final: 0.7575 (mt0) REVERT: B 904 TYR cc_start: 0.7860 (t80) cc_final: 0.7363 (t80) REVERT: B 1019 ARG cc_start: 0.7708 (tpt90) cc_final: 0.7451 (tpt170) REVERT: D 177 MET cc_start: 0.0841 (mtp) cc_final: 0.0591 (mtp) REVERT: D 238 PHE cc_start: 0.7213 (p90) cc_final: 0.6553 (p90) REVERT: D 243 ILE cc_start: 0.4777 (mt) cc_final: 0.3587 (mt) REVERT: D 278 LYS cc_start: 0.8062 (tttt) cc_final: 0.7770 (mttm) REVERT: D 604 THR cc_start: 0.8199 (p) cc_final: 0.7975 (t) REVERT: D 808 ASP cc_start: 0.6813 (t0) cc_final: 0.6164 (m-30) REVERT: D 859 THR cc_start: 0.8733 (m) cc_final: 0.8497 (p) REVERT: D 954 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7903 (mt0) outliers start: 83 outliers final: 45 residues processed: 409 average time/residue: 0.1889 time to fit residues: 129.0032 Evaluate side-chains 321 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 743 CYS Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 1030 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 141 optimal weight: 7.9990 chunk 355 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 312 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.154543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.119372 restraints weight = 99192.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.121627 restraints weight = 48544.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.122771 restraints weight = 29636.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.123901 restraints weight = 22606.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.124468 restraints weight = 18200.404| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.7144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 30843 Z= 0.177 Angle : 0.606 11.465 41967 Z= 0.312 Chirality : 0.045 0.154 4671 Planarity : 0.004 0.050 5431 Dihedral : 4.424 23.294 4087 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 2.39 % Allowed : 13.01 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.13), residues: 3774 helix: 0.64 (0.16), residues: 1015 sheet: -0.08 (0.18), residues: 679 loop : -1.04 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 319 TYR 0.024 0.002 TYR D 160 PHE 0.043 0.002 PHE B 275 TRP 0.026 0.002 TRP D 104 HIS 0.007 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00405 (30804) covalent geometry : angle 0.60237 (41889) SS BOND : bond 0.00698 ( 39) SS BOND : angle 1.73492 ( 78) hydrogen bonds : bond 0.04049 ( 1030) hydrogen bonds : angle 5.16867 ( 2898) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 296 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8053 (tpt90) cc_final: 0.7403 (mmt90) REVERT: A 86 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: A 200 TYR cc_start: 0.6568 (t80) cc_final: 0.6311 (t80) REVERT: A 241 LEU cc_start: 0.7869 (pp) cc_final: 0.7638 (tp) REVERT: A 265 TYR cc_start: 0.5198 (p90) cc_final: 0.4814 (p90) REVERT: A 452 LEU cc_start: 0.7594 (mp) cc_final: 0.7384 (mp) REVERT: A 571 ASP cc_start: 0.7610 (t70) cc_final: 0.7244 (t70) REVERT: A 803 SER cc_start: 0.8823 (m) cc_final: 0.8537 (p) REVERT: A 900 MET cc_start: 0.8645 (mmm) cc_final: 0.8054 (mtt) REVERT: A 918 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: A 992 GLN cc_start: 0.8655 (mp10) cc_final: 0.8352 (mp10) REVERT: C 323 MET cc_start: -0.0954 (mmm) cc_final: -0.1177 (mtm) REVERT: C 536 GLU cc_start: 0.4486 (OUTLIER) cc_final: 0.4042 (pt0) REVERT: C 606 TRP cc_start: 0.2170 (p90) cc_final: 0.0814 (p90) REVERT: B 904 TYR cc_start: 0.7847 (t80) cc_final: 0.7186 (t80) REVERT: B 1019 ARG cc_start: 0.7750 (tpt90) cc_final: 0.7538 (tpt170) REVERT: D 238 PHE cc_start: 0.7464 (p90) cc_final: 0.6931 (p90) REVERT: D 278 LYS cc_start: 0.8206 (tttt) cc_final: 0.7983 (mttm) REVERT: D 740 MET cc_start: 0.8618 (tpp) cc_final: 0.8353 (tpp) REVERT: D 808 ASP cc_start: 0.6753 (t0) cc_final: 0.6219 (m-30) REVERT: D 859 THR cc_start: 0.8765 (m) cc_final: 0.8435 (p) REVERT: D 954 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7976 (mt0) REVERT: D 1031 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7113 (mp0) outliers start: 80 outliers final: 56 residues processed: 355 average time/residue: 0.1938 time to fit residues: 114.3341 Evaluate side-chains 325 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 265 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 743 CYS Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1040 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 94 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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** B 762 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.154943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.120224 restraints weight = 96973.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.122505 restraints weight = 46882.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.123709 restraints weight = 28362.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 74)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.124729 restraints weight = 21428.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.125270 restraints weight = 17159.553| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.7384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30843 Z= 0.125 Angle : 0.562 10.372 41967 Z= 0.283 Chirality : 0.043 0.158 4671 Planarity : 0.004 0.048 5431 Dihedral : 4.153 21.467 4087 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.81 % Favored : 97.16 % Rotamer: Outliers : 2.21 % Allowed : 13.67 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.13), residues: 3774 helix: 0.90 (0.16), residues: 1028 sheet: -0.08 (0.18), residues: 659 loop : -0.93 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.028 0.001 TYR D 495 PHE 0.029 0.001 PHE B 275 TRP 0.021 0.001 TRP B 104 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00288 (30804) covalent geometry : angle 0.55843 (41889) SS BOND : bond 0.00312 ( 39) SS BOND : angle 1.56899 ( 78) hydrogen bonds : bond 0.03686 ( 1030) hydrogen bonds : angle 4.95671 ( 2898) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 291 time to evaluate : 1.227 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 241 LEU cc_start: 0.7852 (pp) cc_final: 0.7565 (tp) REVERT: A 452 LEU cc_start: 0.7635 (mp) cc_final: 0.7425 (mp) REVERT: A 571 ASP cc_start: 0.7588 (t70) cc_final: 0.7178 (t70) REVERT: A 803 SER cc_start: 0.8786 (m) cc_final: 0.8508 (p) REVERT: A 900 MET cc_start: 0.8542 (mmm) cc_final: 0.8166 (mtp) REVERT: A 918 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: A 979 ASP cc_start: 0.8319 (m-30) cc_final: 0.8099 (m-30) REVERT: A 992 GLN cc_start: 0.8517 (mp10) cc_final: 0.8176 (mp10) REVERT: C 323 MET cc_start: -0.0904 (mmm) cc_final: -0.1392 (ptp) REVERT: C 455 MET cc_start: -0.2289 (tmm) cc_final: -0.2551 (tmm) REVERT: C 536 GLU cc_start: 0.4545 (OUTLIER) cc_final: 0.3678 (pm20) REVERT: C 606 TRP cc_start: 0.2154 (p90) cc_final: 0.0738 (p90) REVERT: B 365 TYR cc_start: 0.4166 (m-80) cc_final: 0.2044 (t80) REVERT: B 856 ASN cc_start: 0.8507 (t0) cc_final: 0.8142 (t0) REVERT: B 900 MET cc_start: 0.8408 (mpp) cc_final: 0.8168 (mtm) REVERT: B 904 TYR cc_start: 0.7861 (t80) cc_final: 0.7153 (t80) REVERT: D 202 LYS cc_start: 0.6655 (mmtm) cc_final: 0.6324 (mmtm) REVERT: D 238 PHE cc_start: 0.7344 (p90) cc_final: 0.6774 (p90) REVERT: D 278 LYS cc_start: 0.8470 (tttt) cc_final: 0.8171 (tttp) REVERT: D 563 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6466 (mm-40) REVERT: D 808 ASP cc_start: 0.6787 (t0) cc_final: 0.6240 (m-30) REVERT: D 859 THR cc_start: 0.8755 (m) cc_final: 0.8387 (p) REVERT: D 1031 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6842 (mp0) outliers start: 74 outliers final: 50 residues processed: 345 average time/residue: 0.1913 time to fit residues: 109.9105 Evaluate side-chains 318 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 264 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 563 GLN Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 743 CYS Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1031 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 255 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 343 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 320 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 250 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 367 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN B 762 GLN B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.153742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.118755 restraints weight = 98938.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.121031 restraints weight = 48440.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.122513 restraints weight = 29017.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.123363 restraints weight = 21374.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.123821 restraints weight = 17319.026| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.7708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 30843 Z= 0.140 Angle : 0.573 11.493 41967 Z= 0.289 Chirality : 0.044 0.154 4671 Planarity : 0.004 0.048 5431 Dihedral : 4.167 28.559 4087 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 2.39 % Allowed : 13.58 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.13), residues: 3774 helix: 0.95 (0.16), residues: 1026 sheet: -0.14 (0.18), residues: 664 loop : -0.90 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.022 0.001 TYR D 741 PHE 0.027 0.002 PHE B 275 TRP 0.019 0.001 TRP B 104 HIS 0.015 0.001 HIS D 242 Details of bonding type rmsd covalent geometry : bond 0.00323 (30804) covalent geometry : angle 0.56952 (41889) SS BOND : bond 0.00287 ( 39) SS BOND : angle 1.47875 ( 78) hydrogen bonds : bond 0.03633 ( 1030) hydrogen bonds : angle 4.90825 ( 2898) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 280 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1263 (mmm) cc_final: 0.0888 (mmm) REVERT: A 205 SER cc_start: 0.8080 (t) cc_final: 0.7635 (p) REVERT: A 452 LEU cc_start: 0.7555 (mp) cc_final: 0.7333 (mp) REVERT: A 571 ASP cc_start: 0.7718 (t70) cc_final: 0.7314 (t70) REVERT: A 803 SER cc_start: 0.8758 (m) cc_final: 0.8479 (p) REVERT: A 900 MET cc_start: 0.8645 (mmm) cc_final: 0.8258 (mtp) REVERT: A 918 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: A 979 ASP cc_start: 0.8368 (m-30) cc_final: 0.8117 (m-30) REVERT: A 992 GLN cc_start: 0.8555 (mp10) cc_final: 0.8236 (mp10) REVERT: C 67 ASP cc_start: 0.5388 (OUTLIER) cc_final: 0.5110 (p0) REVERT: C 323 MET cc_start: -0.0644 (mmm) cc_final: -0.1154 (ptp) REVERT: C 536 GLU cc_start: 0.4586 (OUTLIER) cc_final: 0.3637 (pm20) REVERT: C 606 TRP cc_start: 0.2326 (p90) cc_final: 0.1765 (p90) REVERT: B 54 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8331 (mm) REVERT: B 796 ASP cc_start: 0.7202 (p0) cc_final: 0.6866 (p0) REVERT: B 856 ASN cc_start: 0.8562 (t0) cc_final: 0.8295 (t0) REVERT: B 904 TYR cc_start: 0.7790 (t80) cc_final: 0.7067 (t80) REVERT: B 992 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8337 (mt0) REVERT: D 229 LEU cc_start: 0.7685 (tp) cc_final: 0.7462 (tp) REVERT: D 238 PHE cc_start: 0.7516 (p90) cc_final: 0.6907 (p90) REVERT: D 278 LYS cc_start: 0.8547 (tttt) cc_final: 0.8213 (tttp) REVERT: D 563 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6349 (mt0) REVERT: D 808 ASP cc_start: 0.6748 (t0) cc_final: 0.6214 (m-30) REVERT: D 859 THR cc_start: 0.8776 (m) cc_final: 0.8376 (p) REVERT: D 1031 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6838 (mp0) outliers start: 80 outliers final: 58 residues processed: 337 average time/residue: 0.1867 time to fit residues: 105.6822 Evaluate side-chains 325 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 563 GLN Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1040 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 128 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 291 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 319 optimal weight: 8.9990 chunk 237 optimal weight: 0.6980 chunk 364 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 260 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 264 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** C 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.154206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.119373 restraints weight = 99144.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.121789 restraints weight = 48183.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.123206 restraints weight = 28638.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.124155 restraints weight = 20944.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.124554 restraints weight = 17195.902| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.7849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30843 Z= 0.116 Angle : 0.551 11.935 41967 Z= 0.276 Chirality : 0.043 0.346 4671 Planarity : 0.004 0.051 5431 Dihedral : 4.089 26.168 4087 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 2.33 % Allowed : 13.85 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.13), residues: 3774 helix: 1.04 (0.16), residues: 1035 sheet: -0.18 (0.18), residues: 673 loop : -0.85 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.015 0.001 TYR D 170 PHE 0.024 0.001 PHE B 275 TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00264 (30804) covalent geometry : angle 0.54900 (41889) SS BOND : bond 0.00309 ( 39) SS BOND : angle 1.27794 ( 78) hydrogen bonds : bond 0.03490 ( 1030) hydrogen bonds : angle 4.81794 ( 2898) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 288 time to evaluate : 1.222 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 205 SER cc_start: 0.7944 (t) cc_final: 0.7495 (p) REVERT: A 571 ASP cc_start: 0.7720 (t70) cc_final: 0.7262 (t70) REVERT: A 803 SER cc_start: 0.8743 (m) cc_final: 0.8471 (p) REVERT: A 900 MET cc_start: 0.8629 (mmm) cc_final: 0.8202 (mtp) REVERT: A 918 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: A 979 ASP cc_start: 0.8287 (m-30) cc_final: 0.8049 (m-30) REVERT: A 992 GLN cc_start: 0.8504 (mp10) cc_final: 0.8228 (mp10) REVERT: C 323 MET cc_start: -0.0553 (mmm) cc_final: -0.0969 (ptp) REVERT: C 455 MET cc_start: -0.2409 (tmm) cc_final: -0.3483 (tmm) REVERT: C 536 GLU cc_start: 0.4439 (OUTLIER) cc_final: 0.3535 (pm20) REVERT: C 606 TRP cc_start: 0.2422 (p90) cc_final: 0.1859 (p90) REVERT: B 54 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8397 (mm) REVERT: B 365 TYR cc_start: 0.4141 (m-80) cc_final: 0.2066 (t80) REVERT: B 759 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7589 (t80) REVERT: B 796 ASP cc_start: 0.7171 (p0) cc_final: 0.6794 (p0) REVERT: B 856 ASN cc_start: 0.8572 (t0) cc_final: 0.8323 (t0) REVERT: B 900 MET cc_start: 0.8467 (mpp) cc_final: 0.8158 (mtm) REVERT: B 904 TYR cc_start: 0.7794 (t80) cc_final: 0.7028 (t80) REVERT: D 229 LEU cc_start: 0.7588 (tp) cc_final: 0.7358 (tp) REVERT: D 238 PHE cc_start: 0.7487 (p90) cc_final: 0.6861 (p90) REVERT: D 278 LYS cc_start: 0.8646 (tttt) cc_final: 0.8203 (tttp) REVERT: D 495 TYR cc_start: 0.2809 (m-80) cc_final: 0.2487 (m-80) REVERT: D 563 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6233 (mt0) REVERT: D 808 ASP cc_start: 0.6747 (t0) cc_final: 0.6251 (m-30) REVERT: D 859 THR cc_start: 0.8767 (m) cc_final: 0.8357 (p) REVERT: D 1031 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6836 (mp0) outliers start: 78 outliers final: 57 residues processed: 347 average time/residue: 0.1865 time to fit residues: 108.8564 Evaluate side-chains 324 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 563 GLN Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1086 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 342 optimal weight: 0.9990 chunk 235 optimal weight: 7.9990 chunk 374 optimal weight: 8.9990 chunk 325 optimal weight: 20.0000 chunk 266 optimal weight: 1.9990 chunk 259 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 487 ASN C 24 GLN C 330 ASN ** C 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.151273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.116635 restraints weight = 96866.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.118911 restraints weight = 46392.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.120175 restraints weight = 27457.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.121177 restraints weight = 20376.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.121708 restraints weight = 16501.907| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.8353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30843 Z= 0.164 Angle : 0.599 11.618 41967 Z= 0.304 Chirality : 0.045 0.311 4671 Planarity : 0.004 0.051 5431 Dihedral : 4.322 26.220 4087 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 2.24 % Allowed : 14.18 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.13), residues: 3774 helix: 0.98 (0.16), residues: 1025 sheet: -0.30 (0.18), residues: 687 loop : -0.92 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.015 0.002 TYR D 170 PHE 0.029 0.002 PHE B 275 TRP 0.016 0.001 TRP C 328 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00378 (30804) covalent geometry : angle 0.59533 (41889) SS BOND : bond 0.00419 ( 39) SS BOND : angle 1.55769 ( 78) hydrogen bonds : bond 0.03763 ( 1030) hydrogen bonds : angle 4.95065 ( 2898) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 292 time to evaluate : 1.195 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 86 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: A 177 MET cc_start: 0.1367 (mmm) cc_final: 0.0979 (mmm) REVERT: A 205 SER cc_start: 0.8039 (t) cc_final: 0.7649 (p) REVERT: A 571 ASP cc_start: 0.7736 (t70) cc_final: 0.7264 (t70) REVERT: A 803 SER cc_start: 0.8735 (m) cc_final: 0.8485 (p) REVERT: A 918 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: A 979 ASP cc_start: 0.8528 (m-30) cc_final: 0.8244 (m-30) REVERT: A 992 GLN cc_start: 0.8520 (mp10) cc_final: 0.8224 (mp10) REVERT: C 323 MET cc_start: -0.0618 (mmm) cc_final: -0.0931 (ptp) REVERT: C 536 GLU cc_start: 0.4886 (OUTLIER) cc_final: 0.4396 (pt0) REVERT: B 365 TYR cc_start: 0.4259 (m-80) cc_final: 0.1820 (t80) REVERT: B 759 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7763 (t80) REVERT: B 796 ASP cc_start: 0.7333 (p0) cc_final: 0.6904 (p0) REVERT: B 856 ASN cc_start: 0.8551 (t0) cc_final: 0.8210 (t0) REVERT: B 900 MET cc_start: 0.8566 (mpp) cc_final: 0.8329 (mtm) REVERT: B 904 TYR cc_start: 0.7898 (t80) cc_final: 0.7113 (t80) REVERT: B 992 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8359 (mt0) REVERT: D 229 LEU cc_start: 0.7744 (tp) cc_final: 0.7504 (tp) REVERT: D 238 PHE cc_start: 0.7610 (p90) cc_final: 0.6965 (p90) REVERT: D 278 LYS cc_start: 0.8917 (tttt) cc_final: 0.8647 (tttm) REVERT: D 563 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6530 (mm-40) REVERT: D 596 SER cc_start: 0.8721 (m) cc_final: 0.8171 (p) REVERT: D 808 ASP cc_start: 0.6881 (t0) cc_final: 0.6472 (m-30) REVERT: D 859 THR cc_start: 0.8791 (m) cc_final: 0.8374 (p) REVERT: D 1031 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6964 (mp0) outliers start: 75 outliers final: 59 residues processed: 348 average time/residue: 0.1899 time to fit residues: 110.5129 Evaluate side-chains 330 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 265 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 563 GLN Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1156 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 5.9990 chunk 251 optimal weight: 7.9990 chunk 327 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 330 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 200 optimal weight: 0.5980 chunk 337 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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** C 60 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.151384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.117451 restraints weight = 97779.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.119455 restraints weight = 50513.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.120520 restraints weight = 29564.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.121138 restraints weight = 20998.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.121223 restraints weight = 18901.500| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.8611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30843 Z= 0.147 Angle : 0.575 12.648 41967 Z= 0.291 Chirality : 0.044 0.163 4671 Planarity : 0.004 0.057 5431 Dihedral : 4.258 25.573 4087 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 2.06 % Allowed : 14.75 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.13), residues: 3774 helix: 0.97 (0.16), residues: 1028 sheet: -0.28 (0.18), residues: 674 loop : -0.92 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 765 TYR 0.016 0.001 TYR D1138 PHE 0.026 0.001 PHE B 275 TRP 0.028 0.001 TRP B 104 HIS 0.005 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00339 (30804) covalent geometry : angle 0.57200 (41889) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.44328 ( 78) hydrogen bonds : bond 0.03615 ( 1030) hydrogen bonds : angle 4.94665 ( 2898) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 279 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8143 (t) cc_final: 0.7843 (p) REVERT: A 571 ASP cc_start: 0.7924 (t70) cc_final: 0.7437 (t70) REVERT: A 803 SER cc_start: 0.8714 (m) cc_final: 0.8471 (p) REVERT: A 855 PHE cc_start: 0.7506 (m-80) cc_final: 0.7295 (m-80) REVERT: A 918 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: A 992 GLN cc_start: 0.8536 (mp10) cc_final: 0.8242 (mp10) REVERT: C 228 HIS cc_start: 0.5171 (OUTLIER) cc_final: 0.4871 (m-70) REVERT: C 323 MET cc_start: -0.0272 (mmm) cc_final: -0.0808 (ptp) REVERT: C 455 MET cc_start: -0.2275 (tmm) cc_final: -0.3178 (tmm) REVERT: C 536 GLU cc_start: 0.4887 (OUTLIER) cc_final: 0.3987 (pm20) REVERT: B 365 TYR cc_start: 0.4150 (m-80) cc_final: 0.1717 (t80) REVERT: B 759 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7675 (t80) REVERT: B 900 MET cc_start: 0.8547 (mpp) cc_final: 0.8312 (mtm) REVERT: B 904 TYR cc_start: 0.7845 (t80) cc_final: 0.7066 (t80) REVERT: B 992 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8412 (mt0) REVERT: D 229 LEU cc_start: 0.7732 (tp) cc_final: 0.7443 (tp) REVERT: D 238 PHE cc_start: 0.7751 (p90) cc_final: 0.7151 (p90) REVERT: D 241 LEU cc_start: 0.7278 (tp) cc_final: 0.6123 (mt) REVERT: D 278 LYS cc_start: 0.8771 (tttt) cc_final: 0.8499 (tttm) REVERT: D 563 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6664 (mt0) REVERT: D 592 PHE cc_start: 0.7341 (p90) cc_final: 0.6695 (p90) REVERT: D 596 SER cc_start: 0.8734 (m) cc_final: 0.8219 (p) REVERT: D 808 ASP cc_start: 0.6917 (t0) cc_final: 0.6575 (m-30) REVERT: D 859 THR cc_start: 0.8778 (m) cc_final: 0.8362 (p) REVERT: D 1031 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6913 (mp0) outliers start: 69 outliers final: 56 residues processed: 332 average time/residue: 0.1861 time to fit residues: 104.1366 Evaluate side-chains 323 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 261 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 563 GLN Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1156 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 311 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 359 optimal weight: 3.9990 chunk 76 optimal weight: 0.0970 chunk 55 optimal weight: 6.9990 chunk 219 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 331 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.150420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.116511 restraints weight = 98889.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.118423 restraints weight = 51787.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.119437 restraints weight = 30034.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.120382 restraints weight = 21415.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.120195 restraints weight = 19555.204| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.8816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 30843 Z= 0.158 Angle : 0.599 11.820 41967 Z= 0.304 Chirality : 0.044 0.231 4671 Planarity : 0.004 0.051 5431 Dihedral : 4.347 30.485 4087 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.76 % Rotamer: Outliers : 2.12 % Allowed : 15.26 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -0.49 (0.13), residues: 3774 helix: 0.97 (0.16), residues: 1018 sheet: -0.32 (0.18), residues: 688 loop : -0.98 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.021 0.002 TYR D 741 PHE 0.025 0.002 PHE B 275 TRP 0.047 0.002 TRP C 473 HIS 0.004 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00367 (30804) covalent geometry : angle 0.59413 (41889) SS BOND : bond 0.00345 ( 39) SS BOND : angle 1.81636 ( 78) hydrogen bonds : bond 0.03682 ( 1030) hydrogen bonds : angle 4.97473 ( 2898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7133.54 seconds wall clock time: 123 minutes 44.66 seconds (7424.66 seconds total)