Starting phenix.real_space_refine on Fri Mar 6 09:26:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w99_32362/03_2026/7w99_32362.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w99_32362/03_2026/7w99_32362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w99_32362/03_2026/7w99_32362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w99_32362/03_2026/7w99_32362.map" model { file = "/net/cci-nas-00/data/ceres_data/7w99_32362/03_2026/7w99_32362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w99_32362/03_2026/7w99_32362.cif" } resolution = 3.4 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= 0.007 sd= 0.108 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 143 5.16 5 C 18970 2.51 5 N 4982 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 204 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29737 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "A" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "B" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "D" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Time building chain proxies: 5.78, per 1000 atoms: 0.19 Number of scatterers: 29737 At special positions: 0 Unit cell: (159.578, 172.694, 240.46, 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 143 16.00 O 5642 8.00 N 4982 7.00 C 18970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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=2.03 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=2.05 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 B 133 " - pdb=" SG CYS B 141 " distance=2.04 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 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: 2.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7076 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 51 sheets defined 30.2% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.785A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.673A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.514A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.537A pdb=" N VAL C 772 " --> pdb=" O THR C 768 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.763A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.503A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.980A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.952A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.806A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.638A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1142 through 1147 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.071A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.697A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.672A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.541A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.669A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.567A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.696A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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: 3.822A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (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: 3.587A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.019A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.631A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 53 removed outlier: 3.825A pdb=" N ALA B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 removed outlier: 3.556A pdb=" N VAL B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.636A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.628A pdb=" N SER B 106 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.616A pdb=" N ILE B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 172 Processing helix chain 'B' and resid 172 through 194 Proline residue: B 178 - end of helix removed outlier: 3.606A pdb=" N GLU B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 220 through 252 removed outlier: 3.756A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.742A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.565A pdb=" N TYR B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 removed outlier: 3.621A pdb=" N VAL B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 318 removed outlier: 3.744A pdb=" N PHE B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.677A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.617A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 397 through 414 removed outlier: 3.855A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.632A pdb=" N LEU B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 446 removed outlier: 3.895A pdb=" N ASN B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 512 through 533 removed outlier: 4.057A pdb=" N TYR B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.808A pdb=" N GLY B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 removed outlier: 3.587A pdb=" N ALA B 569 " --> pdb=" O PRO B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.743A pdb=" N THR B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.096A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.815A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.518A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.734A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.577A pdb=" N ASN D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.513A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.931A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 758 through 780 removed outlier: 3.556A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN D 764 " --> pdb=" O CYS D 760 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 773 " --> pdb=" O GLY D 769 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.517A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.529A pdb=" N TYR D 873 " --> pdb=" O MET D 869 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR D 883 " --> pdb=" O ALA D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 891 removed outlier: 4.177A pdb=" N GLY D 891 " --> pdb=" O PHE D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.873A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 918 removed outlier: 3.742A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.593A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.781A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (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 977 through 982 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.681A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA D1016 " --> pdb=" O LEU D1012 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D1030 " --> pdb=" O ALA D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1147 Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.601A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.565A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.592A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.592A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.421A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 324 through 327 Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.554A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.642A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 565 through 566 removed outlier: 7.202A pdb=" N PHE C 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.179A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.574A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'C' and resid 788 through 789 removed outlier: 7.041A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.813A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.771A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.753A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 141 through 143 removed outlier: 6.342A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 259 " --> pdb=" O HIS A 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.510A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.694A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.261A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.261A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.103A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.840A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.947A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AD9, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.319A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 347 through 352 removed outlier: 5.884A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 28 through 31 removed outlier: 8.359A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 268 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG D 190 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.641A pdb=" N VAL D 47 " --> pdb=" O TYR D 279 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 83 through 85 removed outlier: 3.829A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 311 through 319 removed outlier: 6.994A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 324 through 327 removed outlier: 4.044A pdb=" N GLU D 324 " --> pdb=" O CYS D 538 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.874A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.126A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.806A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 718 through 722 Processing sheet with id=AF4, first strand: chain 'D' and resid 718 through 722 removed outlier: 7.062A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D1047 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'D' and resid 1121 through 1122 1129 hydrogen bonds defined for protein. 3141 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: 6.81 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9659 1.35 - 1.48: 7968 1.48 - 1.61: 12623 1.61 - 1.74: 0 1.74 - 1.87: 194 Bond restraints: 30444 Sorted by residual: bond pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.17e-02 7.31e+03 7.36e+00 bond pdb=" C VAL A 860 " pdb=" N LEU A 861 " ideal model delta sigma weight residual 1.331 1.303 0.028 1.48e-02 4.57e+03 3.57e+00 bond pdb=" CB CYS D 525 " pdb=" SG CYS D 525 " ideal model delta sigma weight residual 1.808 1.868 -0.060 3.30e-02 9.18e+02 3.33e+00 bond pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.16e-02 7.43e+03 2.97e+00 bond pdb=" N SER B 19 " pdb=" CA SER B 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 30439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 39987 1.33 - 2.67: 1151 2.67 - 4.00: 127 4.00 - 5.33: 121 5.33 - 6.66: 10 Bond angle restraints: 41396 Sorted by residual: angle pdb=" N SER A 151 " pdb=" CA SER A 151 " pdb=" CB SER A 151 " ideal model delta sigma weight residual 114.17 109.87 4.30 1.14e+00 7.69e-01 1.42e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 120.79 125.91 -5.12 1.39e+00 5.18e-01 1.36e+01 angle pdb=" C ARG A 214 " pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta sigma weight residual 121.19 126.98 -5.79 1.59e+00 3.96e-01 1.33e+01 angle pdb=" C LYS A 147 " pdb=" CA LYS A 147 " pdb=" CB LYS A 147 " ideal model delta sigma weight residual 110.96 115.65 -4.69 1.54e+00 4.22e-01 9.27e+00 angle pdb=" N LYS A 147 " pdb=" CA LYS A 147 " pdb=" C LYS A 147 " ideal model delta sigma weight residual 110.97 107.91 3.06 1.09e+00 8.42e-01 7.90e+00 ... (remaining 41391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16896 17.99 - 35.99: 1012 35.99 - 53.98: 151 53.98 - 71.97: 43 71.97 - 89.97: 34 Dihedral angle restraints: 18136 sinusoidal: 7139 harmonic: 10997 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 34.20 58.80 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CA ARG A 214 " pdb=" C ARG A 214 " pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta harmonic sigma weight residual -180.00 -147.96 -32.04 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual 93.00 44.66 48.34 1 1.00e+01 1.00e-02 3.22e+01 ... (remaining 18133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3039 0.033 - 0.066: 1099 0.066 - 0.099: 234 0.099 - 0.132: 226 0.132 - 0.165: 18 Chirality restraints: 4616 Sorted by residual: chirality pdb=" CA ILE A 896 " pdb=" N ILE A 896 " pdb=" C ILE A 896 " pdb=" CB ILE A 896 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA ILE A 714 " pdb=" N ILE A 714 " pdb=" C ILE A 714 " pdb=" CB ILE A 714 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 4613 not shown) Planarity restraints: 5375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 599 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO C 600 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 600 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 600 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 130 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C VAL C 130 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL C 130 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS C 131 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 283 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO B 284 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " 0.018 5.00e-02 4.00e+02 ... (remaining 5372 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 323 2.64 - 3.21: 26511 3.21 - 3.77: 43677 3.77 - 4.34: 62475 4.34 - 4.90: 103405 Nonbonded interactions: 236391 Sorted by model distance: nonbonded pdb=" O GLN C 755 " pdb=" OG SER A 968 " model vdw 2.076 3.040 nonbonded pdb=" O GLN A 755 " pdb=" OG SER D 968 " model vdw 2.079 3.040 nonbonded pdb=" OG SER D 708 " pdb=" OG SER D 711 " model vdw 2.140 3.040 nonbonded pdb=" OG1 THR A 883 " pdb=" OH TYR D 707 " model vdw 2.186 3.040 nonbonded pdb=" O VAL C1040 " pdb=" OG SER D1030 " model vdw 2.202 3.040 ... (remaining 236386 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' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.920 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 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 : 0.004 0.060 30486 Z= 0.172 Angle : 0.595 6.664 41480 Z= 0.335 Chirality : 0.042 0.165 4616 Planarity : 0.003 0.036 5375 Dihedral : 12.548 89.967 10934 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.12 % Allowed : 1.61 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.11), residues: 3733 helix: -2.51 (0.11), residues: 998 sheet: -2.18 (0.17), residues: 684 loop : -2.16 (0.12), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.012 0.001 TYR A 707 PHE 0.018 0.001 PHE A 906 TRP 0.005 0.001 TRP B 203 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00374 (30444) covalent geometry : angle 0.59355 (41396) SS BOND : bond 0.00444 ( 42) SS BOND : angle 1.05241 ( 84) hydrogen bonds : bond 0.26843 ( 1122) hydrogen bonds : angle 9.18060 ( 3141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 694 time to evaluate : 0.932 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: C 94 SER cc_start: 0.8302 (m) cc_final: 0.7983 (p) REVERT: C 133 PHE cc_start: 0.6678 (m-80) cc_final: 0.6476 (m-10) REVERT: C 140 PHE cc_start: 0.4865 (p90) cc_final: 0.3835 (p90) REVERT: C 141 LEU cc_start: 0.6148 (mt) cc_final: 0.5921 (mt) REVERT: C 166 CYS cc_start: 0.6476 (OUTLIER) cc_final: 0.6010 (t) REVERT: C 236 THR cc_start: 0.8867 (p) cc_final: 0.8566 (t) REVERT: C 258 TRP cc_start: 0.4894 (m-10) cc_final: 0.4228 (m-10) REVERT: C 357 ARG cc_start: 0.5471 (ttt180) cc_final: 0.5055 (mpt-90) REVERT: C 369 TYR cc_start: 0.6019 (t80) cc_final: 0.5606 (p90) REVERT: C 541 PHE cc_start: 0.5919 (m-80) cc_final: 0.5164 (m-80) REVERT: C 557 LYS cc_start: 0.7190 (mttt) cc_final: 0.6759 (mtpp) REVERT: C 585 LEU cc_start: 0.7657 (mt) cc_final: 0.7322 (mt) REVERT: C 673 SER cc_start: 0.8509 (p) cc_final: 0.8042 (m) REVERT: C 747 THR cc_start: 0.8908 (m) cc_final: 0.8681 (p) REVERT: C 748 GLU cc_start: 0.7534 (mp0) cc_final: 0.7208 (mp0) REVERT: C 941 THR cc_start: 0.7683 (m) cc_final: 0.7373 (p) REVERT: C 1047 TYR cc_start: 0.8595 (m-80) cc_final: 0.7937 (m-80) REVERT: A 118 LEU cc_start: 0.7872 (mt) cc_final: 0.7632 (mt) REVERT: A 129 LYS cc_start: 0.7067 (mttm) cc_final: 0.6841 (tptp) REVERT: A 170 TYR cc_start: 0.8254 (t80) cc_final: 0.7591 (t80) REVERT: A 287 ASP cc_start: 0.8335 (t0) cc_final: 0.8000 (m-30) REVERT: A 368 LEU cc_start: 0.6810 (tp) cc_final: 0.6385 (tp) REVERT: A 436 TRP cc_start: 0.5393 (t60) cc_final: 0.4937 (t60) REVERT: A 508 TYR cc_start: 0.6982 (m-80) cc_final: 0.6409 (m-80) REVERT: A 869 MET cc_start: 0.8614 (mtt) cc_final: 0.8405 (mtt) REVERT: A 896 ILE cc_start: 0.6835 (mt) cc_final: 0.6543 (mt) REVERT: A 941 THR cc_start: 0.6803 (m) cc_final: 0.6226 (p) REVERT: B 95 LEU cc_start: 0.6159 (mt) cc_final: 0.5764 (tt) REVERT: B 114 LYS cc_start: 0.6179 (mttt) cc_final: 0.5933 (tttt) REVERT: B 131 LYS cc_start: 0.3236 (pttt) cc_final: 0.3032 (pttm) REVERT: B 177 ARG cc_start: 0.3721 (ttp80) cc_final: 0.3124 (ttt90) REVERT: B 215 TYR cc_start: 0.2183 (m-80) cc_final: 0.1961 (m-80) REVERT: B 323 MET cc_start: 0.5935 (mmt) cc_final: 0.5609 (mmt) REVERT: B 462 MET cc_start: 0.4519 (mtp) cc_final: 0.4088 (ttm) REVERT: B 474 MET cc_start: 0.0337 (tpp) cc_final: -0.0197 (mmm) REVERT: B 555 PHE cc_start: 0.4120 (t80) cc_final: 0.3727 (t80) REVERT: D 48 LEU cc_start: 0.8239 (tp) cc_final: 0.8010 (mt) REVERT: D 170 TYR cc_start: 0.7122 (t80) cc_final: 0.6596 (t80) REVERT: D 216 LEU cc_start: 0.7607 (tp) cc_final: 0.7352 (tp) REVERT: D 274 THR cc_start: 0.8846 (m) cc_final: 0.8577 (m) REVERT: D 390 LEU cc_start: 0.6877 (mp) cc_final: 0.6294 (tp) REVERT: D 532 ASN cc_start: 0.8429 (p0) cc_final: 0.8088 (t0) REVERT: D 751 ASN cc_start: 0.8493 (m-40) cc_final: 0.8226 (m-40) outliers start: 4 outliers final: 1 residues processed: 697 average time/residue: 0.1997 time to fit residues: 218.2136 Evaluate side-chains 369 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain D residue 391 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 HIS C 519 HIS C 564 GLN C 655 HIS ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 183 GLN A 188 ASN A 394 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 655 HIS A 919 ASN A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 49 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 159 ASN B 241 HIS B 472 GLN ** B 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 HIS B 572 ASN D 137 ASN D 165 ASN D 334 ASN D 787 GLN D 895 GLN D 935 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.157369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.127900 restraints weight = 83370.854| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.03 r_work: 0.3797 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 30486 Z= 0.235 Angle : 0.681 8.874 41480 Z= 0.356 Chirality : 0.048 0.226 4616 Planarity : 0.005 0.052 5375 Dihedral : 4.571 47.035 4052 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.82 % Allowed : 9.24 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.12), residues: 3733 helix: -0.38 (0.15), residues: 1009 sheet: -1.21 (0.18), residues: 700 loop : -1.61 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 44 TYR 0.022 0.002 TYR D 495 PHE 0.033 0.002 PHE D 497 TRP 0.014 0.002 TRP C1102 HIS 0.008 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00541 (30444) covalent geometry : angle 0.67629 (41396) SS BOND : bond 0.00732 ( 42) SS BOND : angle 1.85246 ( 84) hydrogen bonds : bond 0.05036 ( 1122) hydrogen bonds : angle 5.80102 ( 3141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 440 time to evaluate : 0.958 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: C 166 CYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5616 (p) REVERT: C 236 THR cc_start: 0.8558 (p) cc_final: 0.8294 (t) REVERT: C 357 ARG cc_start: 0.5868 (ttt180) cc_final: 0.5436 (mpt-90) REVERT: C 1111 GLU cc_start: 0.7334 (pt0) cc_final: 0.7014 (pt0) REVERT: A 173 GLN cc_start: 0.6008 (OUTLIER) cc_final: 0.5381 (pp30) REVERT: A 508 TYR cc_start: 0.7292 (m-80) cc_final: 0.6990 (m-80) REVERT: A 750 SER cc_start: 0.8624 (m) cc_final: 0.8258 (t) REVERT: A 1040 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 1045 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8450 (mmtm) REVERT: A 1091 ARG cc_start: 0.8800 (ptp-110) cc_final: 0.8456 (ttm-80) REVERT: B 114 LYS cc_start: 0.6361 (mttt) cc_final: 0.6104 (tttt) REVERT: B 152 MET cc_start: -0.2585 (mmm) cc_final: -0.2805 (mmm) REVERT: B 323 MET cc_start: 0.5488 (mmt) cc_final: 0.4857 (mmm) REVERT: B 383 MET cc_start: 0.5111 (mtt) cc_final: 0.4595 (mmm) REVERT: B 462 MET cc_start: 0.4642 (mtp) cc_final: 0.4254 (ttm) REVERT: B 474 MET cc_start: 0.0284 (tpp) cc_final: -0.0074 (mmm) REVERT: B 555 PHE cc_start: 0.3624 (t80) cc_final: 0.3421 (t80) REVERT: D 128 ILE cc_start: 0.8683 (mp) cc_final: 0.8295 (pt) REVERT: D 365 TYR cc_start: 0.7886 (m-80) cc_final: 0.7665 (m-80) REVERT: D 387 LEU cc_start: 0.7981 (tp) cc_final: 0.7701 (tp) REVERT: D 532 ASN cc_start: 0.8655 (p0) cc_final: 0.8315 (t0) REVERT: D 658 ASN cc_start: 0.7840 (m-40) cc_final: 0.7625 (m-40) REVERT: D 1041 ASP cc_start: 0.8013 (t0) cc_final: 0.7730 (t0) outliers start: 60 outliers final: 36 residues processed: 483 average time/residue: 0.1908 time to fit residues: 147.1274 Evaluate side-chains 349 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 310 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 203 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 186 optimal weight: 0.0070 chunk 159 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 253 optimal weight: 0.8980 chunk 288 optimal weight: 0.0270 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 895 GLN C1054 GLN C1119 ASN A 173 GLN A 394 ASN A 919 ASN A 965 GLN A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN D 334 ASN D 655 HIS D1010 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.159429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.129454 restraints weight = 82590.948| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.99 r_work: 0.3828 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30486 Z= 0.110 Angle : 0.533 7.938 41480 Z= 0.275 Chirality : 0.044 0.199 4616 Planarity : 0.004 0.045 5375 Dihedral : 4.035 32.842 4052 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.67 % Allowed : 11.63 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 3733 helix: 0.58 (0.16), residues: 1009 sheet: -0.67 (0.18), residues: 720 loop : -1.26 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 44 TYR 0.030 0.001 TYR D 495 PHE 0.022 0.001 PHE A 565 TRP 0.017 0.001 TRP C 436 HIS 0.022 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00242 (30444) covalent geometry : angle 0.52969 (41396) SS BOND : bond 0.00369 ( 42) SS BOND : angle 1.34271 ( 84) hydrogen bonds : bond 0.03965 ( 1122) hydrogen bonds : angle 5.18446 ( 3141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 391 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 THR cc_start: 0.8554 (p) cc_final: 0.8294 (t) REVERT: C 273 ARG cc_start: 0.8260 (mmp80) cc_final: 0.8058 (mmp80) REVERT: C 357 ARG cc_start: 0.5816 (ttt180) cc_final: 0.5414 (mpt-90) REVERT: C 439 ASN cc_start: 0.5583 (p0) cc_final: 0.4685 (t0) REVERT: C 776 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8632 (ttpp) REVERT: C 1047 TYR cc_start: 0.8813 (m-80) cc_final: 0.8049 (m-80) REVERT: A 287 ASP cc_start: 0.8396 (t0) cc_final: 0.8143 (m-30) REVERT: A 516 GLU cc_start: 0.4546 (OUTLIER) cc_final: 0.4270 (pm20) REVERT: A 750 SER cc_start: 0.8562 (m) cc_final: 0.8269 (t) REVERT: A 1040 VAL cc_start: 0.9084 (m) cc_final: 0.8735 (p) REVERT: A 1091 ARG cc_start: 0.8712 (ptp-110) cc_final: 0.8444 (ttm-80) REVERT: B 35 GLU cc_start: 0.6318 (mt-10) cc_final: 0.5786 (tp30) REVERT: B 41 TYR cc_start: 0.6078 (m-10) cc_final: 0.5642 (m-10) REVERT: B 50 TYR cc_start: 0.7801 (t80) cc_final: 0.7557 (t80) REVERT: B 177 ARG cc_start: 0.3369 (ttp80) cc_final: 0.2834 (ttt-90) REVERT: B 323 MET cc_start: 0.5754 (mmt) cc_final: 0.5095 (mmm) REVERT: B 474 MET cc_start: 0.0154 (tpp) cc_final: -0.0207 (tpp) REVERT: B 475 LYS cc_start: 0.7653 (mttm) cc_final: 0.7245 (mttm) REVERT: D 317 ASN cc_start: 0.8608 (m-40) cc_final: 0.8406 (t0) REVERT: D 532 ASN cc_start: 0.8658 (p0) cc_final: 0.8371 (t0) REVERT: D 546 LEU cc_start: 0.7261 (tp) cc_final: 0.6991 (mp) REVERT: D 568 ASP cc_start: 0.7980 (t0) cc_final: 0.7732 (t70) REVERT: D 750 SER cc_start: 0.9321 (t) cc_final: 0.9025 (p) REVERT: D 1041 ASP cc_start: 0.7815 (t0) cc_final: 0.7551 (t0) outliers start: 55 outliers final: 30 residues processed: 429 average time/residue: 0.1909 time to fit residues: 132.3953 Evaluate side-chains 356 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 325 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 130 optimal weight: 5.9990 chunk 303 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 296 optimal weight: 0.0870 chunk 372 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 198 optimal weight: 0.5980 chunk 243 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 362 optimal weight: 3.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 487 ASN A 919 ASN A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 895 GLN D 901 GLN D 914 ASN D1010 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.159167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.129380 restraints weight = 81985.729| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.97 r_work: 0.3831 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 30486 Z= 0.109 Angle : 0.514 8.538 41480 Z= 0.266 Chirality : 0.043 0.199 4616 Planarity : 0.003 0.045 5375 Dihedral : 3.864 24.905 4051 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.94 % Allowed : 12.42 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 3733 helix: 0.92 (0.16), residues: 1024 sheet: -0.33 (0.18), residues: 716 loop : -1.10 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 44 TYR 0.036 0.001 TYR D 495 PHE 0.029 0.001 PHE D 497 TRP 0.023 0.001 TRP C 436 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00240 (30444) covalent geometry : angle 0.50957 (41396) SS BOND : bond 0.00438 ( 42) SS BOND : angle 1.55357 ( 84) hydrogen bonds : bond 0.03569 ( 1122) hydrogen bonds : angle 4.89658 ( 3141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 374 time to evaluate : 1.075 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: C 236 THR cc_start: 0.8463 (p) cc_final: 0.8235 (t) REVERT: C 357 ARG cc_start: 0.5890 (ttt180) cc_final: 0.5456 (mpt-90) REVERT: C 439 ASN cc_start: 0.5607 (p0) cc_final: 0.4768 (t0) REVERT: C 574 ASP cc_start: 0.8428 (p0) cc_final: 0.8169 (p0) REVERT: C 646 ARG cc_start: 0.6047 (tpm170) cc_final: 0.5013 (mmt180) REVERT: C 776 LYS cc_start: 0.8850 (ttpp) cc_final: 0.8611 (ttpp) REVERT: C 1047 TYR cc_start: 0.8825 (m-80) cc_final: 0.8058 (m-80) REVERT: C 1111 GLU cc_start: 0.7127 (pt0) cc_final: 0.6817 (pt0) REVERT: A 170 TYR cc_start: 0.7796 (t80) cc_final: 0.7425 (t80) REVERT: A 287 ASP cc_start: 0.8412 (t0) cc_final: 0.8148 (m-30) REVERT: A 516 GLU cc_start: 0.4331 (OUTLIER) cc_final: 0.4086 (pm20) REVERT: A 750 SER cc_start: 0.8573 (m) cc_final: 0.8342 (t) REVERT: A 979 ASP cc_start: 0.8077 (t0) cc_final: 0.7863 (t0) REVERT: A 1040 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8785 (p) REVERT: B 35 GLU cc_start: 0.6321 (mt-10) cc_final: 0.5775 (tp30) REVERT: B 323 MET cc_start: 0.5846 (mmt) cc_final: 0.5132 (mmm) REVERT: B 462 MET cc_start: 0.5589 (ttm) cc_final: 0.4829 (mmm) REVERT: B 474 MET cc_start: 0.0109 (tpp) cc_final: -0.0182 (tpp) REVERT: B 475 LYS cc_start: 0.7562 (mttm) cc_final: 0.7210 (mttm) REVERT: D 170 TYR cc_start: 0.6884 (t80) cc_final: 0.6636 (t80) REVERT: D 424 LYS cc_start: 0.6543 (tptt) cc_final: 0.6072 (ttmt) REVERT: D 453 TYR cc_start: 0.4584 (p90) cc_final: 0.4208 (p90) REVERT: D 532 ASN cc_start: 0.8660 (p0) cc_final: 0.8379 (t0) REVERT: D 546 LEU cc_start: 0.7397 (tp) cc_final: 0.7132 (mp) REVERT: D 750 SER cc_start: 0.9346 (t) cc_final: 0.9115 (p) REVERT: D 780 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: D 1041 ASP cc_start: 0.7801 (t0) cc_final: 0.7540 (t0) outliers start: 64 outliers final: 39 residues processed: 413 average time/residue: 0.1837 time to fit residues: 122.9336 Evaluate side-chains 362 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 320 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 118 optimal weight: 9.9990 chunk 347 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 73 optimal weight: 0.1980 chunk 230 optimal weight: 20.0000 chunk 376 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS A 239 GLN A 437 ASN A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN D 14 GLN D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.153151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.123176 restraints weight = 83159.553| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.80 r_work: 0.3748 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 30486 Z= 0.207 Angle : 0.628 9.278 41480 Z= 0.328 Chirality : 0.046 0.260 4616 Planarity : 0.004 0.047 5375 Dihedral : 4.505 23.840 4050 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.54 % Allowed : 13.93 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 3733 helix: 0.85 (0.17), residues: 980 sheet: -0.33 (0.19), residues: 701 loop : -1.16 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 44 TYR 0.048 0.002 TYR B 41 PHE 0.025 0.002 PHE A 43 TRP 0.020 0.002 TRP A 258 HIS 0.005 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00483 (30444) covalent geometry : angle 0.62399 (41396) SS BOND : bond 0.00493 ( 42) SS BOND : angle 1.74330 ( 84) hydrogen bonds : bond 0.04485 ( 1122) hydrogen bonds : angle 5.13644 ( 3141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 350 time to evaluate : 1.134 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: C 357 ARG cc_start: 0.5969 (ttt180) cc_final: 0.5486 (mpt-90) REVERT: C 776 LYS cc_start: 0.8899 (ttpp) cc_final: 0.8641 (ttpp) REVERT: C 900 MET cc_start: 0.8908 (mtp) cc_final: 0.8667 (mtp) REVERT: C 1111 GLU cc_start: 0.7379 (pt0) cc_final: 0.7111 (pt0) REVERT: A 170 TYR cc_start: 0.8036 (t80) cc_final: 0.7720 (t80) REVERT: A 386 LYS cc_start: 0.6349 (mmpt) cc_final: 0.6060 (mmpt) REVERT: A 750 SER cc_start: 0.8679 (m) cc_final: 0.8387 (t) REVERT: A 855 PHE cc_start: 0.5962 (m-80) cc_final: 0.5725 (m-80) REVERT: A 858 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9001 (mt) REVERT: A 1040 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8771 (p) REVERT: B 35 GLU cc_start: 0.6496 (mt-10) cc_final: 0.5974 (tp30) REVERT: B 41 TYR cc_start: 0.5936 (m-10) cc_final: 0.5455 (m-10) REVERT: B 42 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: B 253 PRO cc_start: 0.1980 (Cg_exo) cc_final: 0.1778 (Cg_endo) REVERT: B 474 MET cc_start: 0.0126 (tpp) cc_final: -0.0090 (tpp) REVERT: B 475 LYS cc_start: 0.7577 (mttm) cc_final: 0.7133 (mttm) REVERT: D 317 ASN cc_start: 0.8340 (t0) cc_final: 0.7816 (t0) REVERT: D 532 ASN cc_start: 0.8799 (p0) cc_final: 0.8592 (t0) outliers start: 84 outliers final: 56 residues processed: 406 average time/residue: 0.1864 time to fit residues: 123.9659 Evaluate side-chains 359 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 300 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 175 optimal weight: 2.9990 chunk 233 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 163 optimal weight: 0.0040 chunk 31 optimal weight: 9.9990 chunk 272 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 345 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN D 245 HIS D 334 ASN D 460 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 895 GLN D1010 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 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 = 0.4332 r_free = 0.4332 target = 0.154376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.124394 restraints weight = 82282.882| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.93 r_work: 0.3758 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30486 Z= 0.144 Angle : 0.561 11.763 41480 Z= 0.290 Chirality : 0.044 0.204 4616 Planarity : 0.004 0.057 5375 Dihedral : 4.226 25.330 4050 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.12 % Allowed : 15.20 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 3733 helix: 1.04 (0.17), residues: 998 sheet: -0.28 (0.19), residues: 720 loop : -1.12 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 44 TYR 0.024 0.001 TYR B 41 PHE 0.018 0.001 PHE A 43 TRP 0.013 0.001 TRP C 436 HIS 0.003 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00336 (30444) covalent geometry : angle 0.55437 (41396) SS BOND : bond 0.00414 ( 42) SS BOND : angle 1.92068 ( 84) hydrogen bonds : bond 0.03860 ( 1122) hydrogen bonds : angle 4.92913 ( 3141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 328 time to evaluate : 1.054 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: C 552 LEU cc_start: 0.8428 (mt) cc_final: 0.8075 (mp) REVERT: C 572 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.7947 (p) REVERT: C 776 LYS cc_start: 0.8912 (ttpp) cc_final: 0.8641 (ttpp) REVERT: C 900 MET cc_start: 0.8747 (mtp) cc_final: 0.8529 (mtp) REVERT: C 1047 TYR cc_start: 0.8808 (m-80) cc_final: 0.7992 (m-80) REVERT: C 1111 GLU cc_start: 0.7441 (pt0) cc_final: 0.7118 (pt0) REVERT: A 170 TYR cc_start: 0.7999 (t80) cc_final: 0.7706 (t80) REVERT: A 392 PHE cc_start: 0.5469 (OUTLIER) cc_final: 0.3619 (m-80) REVERT: A 750 SER cc_start: 0.8593 (m) cc_final: 0.8361 (t) REVERT: A 858 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8948 (mt) REVERT: A 1040 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8860 (p) REVERT: B 35 GLU cc_start: 0.6468 (mt-10) cc_final: 0.6002 (tp30) REVERT: B 41 TYR cc_start: 0.6062 (m-10) cc_final: 0.5602 (m-10) REVERT: B 462 MET cc_start: 0.5250 (ttm) cc_final: 0.4822 (mmm) REVERT: B 475 LYS cc_start: 0.7631 (mttm) cc_final: 0.7240 (mttm) REVERT: D 317 ASN cc_start: 0.8429 (t0) cc_final: 0.7931 (t0) REVERT: D 532 ASN cc_start: 0.8754 (p0) cc_final: 0.8543 (t0) REVERT: D 546 LEU cc_start: 0.7394 (tp) cc_final: 0.7064 (mp) REVERT: D 1041 ASP cc_start: 0.7828 (t0) cc_final: 0.7622 (t0) REVERT: D 1072 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8146 (mt-10) outliers start: 70 outliers final: 54 residues processed: 373 average time/residue: 0.1839 time to fit residues: 112.9668 Evaluate side-chains 343 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 284 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 135 optimal weight: 2.9990 chunk 346 optimal weight: 0.2980 chunk 214 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 301 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 414 GLN A 487 ASN A 564 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A1010 GLN A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.154415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.124572 restraints weight = 82534.492| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.91 r_work: 0.3754 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30486 Z= 0.135 Angle : 0.564 16.047 41480 Z= 0.290 Chirality : 0.044 0.223 4616 Planarity : 0.004 0.051 5375 Dihedral : 4.207 35.253 4050 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.21 % Allowed : 16.05 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3733 helix: 1.15 (0.17), residues: 998 sheet: -0.25 (0.19), residues: 727 loop : -1.10 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 44 TYR 0.020 0.001 TYR B 41 PHE 0.027 0.001 PHE D 429 TRP 0.015 0.001 TRP C 436 HIS 0.003 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00311 (30444) covalent geometry : angle 0.55410 (41396) SS BOND : bond 0.00497 ( 42) SS BOND : angle 2.34902 ( 84) hydrogen bonds : bond 0.03787 ( 1122) hydrogen bonds : angle 4.85606 ( 3141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 316 time to evaluate : 1.095 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: C 153 MET cc_start: 0.0724 (tpt) cc_final: 0.0375 (tpt) REVERT: C 357 ARG cc_start: 0.6552 (ttt-90) cc_final: 0.5123 (mpt-90) REVERT: C 776 LYS cc_start: 0.8902 (ttpp) cc_final: 0.8633 (ttpp) REVERT: C 900 MET cc_start: 0.8768 (mtp) cc_final: 0.8550 (mtp) REVERT: C 1047 TYR cc_start: 0.8796 (m-80) cc_final: 0.7981 (m-80) REVERT: C 1111 GLU cc_start: 0.7468 (pt0) cc_final: 0.7205 (pt0) REVERT: A 170 TYR cc_start: 0.8028 (t80) cc_final: 0.7751 (t80) REVERT: A 392 PHE cc_start: 0.5479 (OUTLIER) cc_final: 0.3588 (m-80) REVERT: A 571 ASP cc_start: 0.6680 (m-30) cc_final: 0.6453 (t0) REVERT: A 750 SER cc_start: 0.8321 (m) cc_final: 0.8111 (t) REVERT: A 858 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8906 (mt) REVERT: A 1040 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8815 (p) REVERT: B 35 GLU cc_start: 0.6338 (mt-10) cc_final: 0.5964 (tp30) REVERT: B 323 MET cc_start: 0.5668 (mmt) cc_final: 0.5464 (mtm) REVERT: B 462 MET cc_start: 0.5493 (ttm) cc_final: 0.4992 (mmm) REVERT: B 475 LYS cc_start: 0.7444 (mttm) cc_final: 0.7232 (mmtm) REVERT: D 164 ASN cc_start: 0.5628 (p0) cc_final: 0.5191 (p0) REVERT: D 532 ASN cc_start: 0.8733 (p0) cc_final: 0.8511 (t0) REVERT: D 546 LEU cc_start: 0.7464 (tp) cc_final: 0.7078 (mp) REVERT: D 1041 ASP cc_start: 0.7842 (t0) cc_final: 0.7629 (t0) REVERT: D 1072 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8106 (mt-10) outliers start: 73 outliers final: 57 residues processed: 364 average time/residue: 0.1784 time to fit residues: 107.5934 Evaluate side-chains 356 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 295 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 379 CYS Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 66 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 374 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 774 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.153322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.123646 restraints weight = 82466.823| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.80 r_work: 0.3752 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30486 Z= 0.150 Angle : 0.584 16.231 41480 Z= 0.301 Chirality : 0.044 0.238 4616 Planarity : 0.004 0.050 5375 Dihedral : 4.286 35.269 4050 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.57 % Allowed : 16.02 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3733 helix: 1.11 (0.17), residues: 1002 sheet: -0.16 (0.19), residues: 701 loop : -1.13 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 44 TYR 0.021 0.001 TYR D 170 PHE 0.017 0.001 PHE A 32 TRP 0.015 0.001 TRP A 258 HIS 0.003 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00348 (30444) covalent geometry : angle 0.57546 (41396) SS BOND : bond 0.00332 ( 42) SS BOND : angle 2.29458 ( 84) hydrogen bonds : bond 0.03900 ( 1122) hydrogen bonds : angle 4.93176 ( 3141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 321 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.0747 (tpt) cc_final: 0.0368 (tpt) REVERT: C 357 ARG cc_start: 0.6650 (ttt-90) cc_final: 0.5328 (mpt-90) REVERT: C 436 TRP cc_start: 0.0124 (m100) cc_final: -0.0292 (m100) REVERT: C 572 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.7986 (p) REVERT: C 776 LYS cc_start: 0.8896 (ttpp) cc_final: 0.8613 (ttpp) REVERT: C 787 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: C 900 MET cc_start: 0.8829 (mtp) cc_final: 0.8604 (mtp) REVERT: C 1047 TYR cc_start: 0.8830 (m-80) cc_final: 0.8017 (m-80) REVERT: C 1111 GLU cc_start: 0.7517 (pt0) cc_final: 0.7262 (pt0) REVERT: A 386 LYS cc_start: 0.6681 (mmpt) cc_final: 0.6212 (mmpt) REVERT: A 392 PHE cc_start: 0.5673 (OUTLIER) cc_final: 0.3816 (m-80) REVERT: A 464 PHE cc_start: 0.7248 (t80) cc_final: 0.7043 (t80) REVERT: A 571 ASP cc_start: 0.6840 (m-30) cc_final: 0.6570 (t0) REVERT: A 858 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8914 (mt) REVERT: A 900 MET cc_start: 0.8831 (mtm) cc_final: 0.8297 (mtp) REVERT: A 979 ASP cc_start: 0.8104 (t0) cc_final: 0.7712 (t0) REVERT: A 983 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6812 (mtp180) REVERT: B 35 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5856 (tp30) REVERT: B 41 TYR cc_start: 0.6132 (m-10) cc_final: 0.5721 (m-10) REVERT: B 82 MET cc_start: 0.8047 (mmm) cc_final: 0.5793 (ptt) REVERT: B 253 PRO cc_start: 0.2307 (Cg_exo) cc_final: 0.2083 (Cg_endo) REVERT: B 462 MET cc_start: 0.5503 (ttm) cc_final: 0.4976 (mmm) REVERT: B 482 ARG cc_start: 0.5239 (mtm180) cc_final: 0.4840 (mtm110) REVERT: D 22 THR cc_start: 0.5958 (OUTLIER) cc_final: 0.5500 (p) REVERT: D 164 ASN cc_start: 0.5588 (p0) cc_final: 0.5079 (p0) REVERT: D 532 ASN cc_start: 0.8717 (p0) cc_final: 0.8475 (t0) REVERT: D 546 LEU cc_start: 0.7670 (tp) cc_final: 0.7332 (mp) REVERT: D 1041 ASP cc_start: 0.7857 (t0) cc_final: 0.7638 (t0) REVERT: D 1072 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8156 (mt-10) outliers start: 85 outliers final: 60 residues processed: 375 average time/residue: 0.1797 time to fit residues: 110.3869 Evaluate side-chains 364 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 298 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 200 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 363 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 233 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 564 GLN A 913 GLN A1113 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.153944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.124184 restraints weight = 81972.830| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.89 r_work: 0.3751 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30486 Z= 0.115 Angle : 0.536 10.953 41480 Z= 0.276 Chirality : 0.043 0.251 4616 Planarity : 0.004 0.057 5375 Dihedral : 4.077 20.993 4050 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.06 % Allowed : 16.96 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3733 helix: 1.18 (0.17), residues: 1005 sheet: -0.18 (0.19), residues: 726 loop : -1.11 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 44 TYR 0.022 0.001 TYR B 516 PHE 0.020 0.001 PHE A 32 TRP 0.014 0.001 TRP C 258 HIS 0.003 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00265 (30444) covalent geometry : angle 0.53257 (41396) SS BOND : bond 0.00373 ( 42) SS BOND : angle 1.43232 ( 84) hydrogen bonds : bond 0.03562 ( 1122) hydrogen bonds : angle 4.77490 ( 3141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 314 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 PHE cc_start: 0.7549 (m-80) cc_final: 0.7320 (m-80) REVERT: C 153 MET cc_start: 0.0756 (tpt) cc_final: 0.0447 (tpt) REVERT: C 357 ARG cc_start: 0.6701 (ttt-90) cc_final: 0.5322 (mpt-90) REVERT: C 436 TRP cc_start: 0.0182 (m100) cc_final: -0.0227 (m100) REVERT: C 547 THR cc_start: 0.8023 (p) cc_final: 0.7814 (t) REVERT: C 572 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.7946 (p) REVERT: C 646 ARG cc_start: 0.5403 (tpm170) cc_final: 0.5076 (tpm170) REVERT: C 776 LYS cc_start: 0.8895 (ttpp) cc_final: 0.8613 (ttpp) REVERT: C 787 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: C 900 MET cc_start: 0.8780 (mtp) cc_final: 0.8561 (mtp) REVERT: C 1047 TYR cc_start: 0.8791 (m-80) cc_final: 0.7963 (m-80) REVERT: C 1111 GLU cc_start: 0.7475 (pt0) cc_final: 0.7261 (pt0) REVERT: A 386 LYS cc_start: 0.6613 (mmpt) cc_final: 0.6213 (mmpt) REVERT: A 392 PHE cc_start: 0.5573 (OUTLIER) cc_final: 0.3670 (m-80) REVERT: A 452 ARG cc_start: 0.6652 (mmm-85) cc_final: 0.6300 (mtp85) REVERT: A 571 ASP cc_start: 0.6945 (m-30) cc_final: 0.6663 (t0) REVERT: A 858 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8942 (mt) REVERT: A 900 MET cc_start: 0.8844 (mtm) cc_final: 0.8290 (mtp) REVERT: B 35 GLU cc_start: 0.6150 (mt-10) cc_final: 0.5867 (tp30) REVERT: B 41 TYR cc_start: 0.5861 (m-10) cc_final: 0.5451 (m-10) REVERT: B 82 MET cc_start: 0.8086 (mmm) cc_final: 0.5920 (ptt) REVERT: B 329 GLU cc_start: 0.5485 (OUTLIER) cc_final: 0.5157 (tp30) REVERT: B 462 MET cc_start: 0.5484 (ttm) cc_final: 0.4955 (mmm) REVERT: B 482 ARG cc_start: 0.5207 (mtm180) cc_final: 0.4927 (mtm180) REVERT: D 164 ASN cc_start: 0.5546 (p0) cc_final: 0.5027 (p0) REVERT: D 532 ASN cc_start: 0.8762 (p0) cc_final: 0.8515 (t0) REVERT: D 776 LYS cc_start: 0.8383 (tttp) cc_final: 0.8152 (tttp) REVERT: D 1041 ASP cc_start: 0.7955 (t0) cc_final: 0.7719 (t0) REVERT: D 1072 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: D 1119 ASN cc_start: 0.8238 (m110) cc_final: 0.7959 (p0) outliers start: 68 outliers final: 51 residues processed: 355 average time/residue: 0.1672 time to fit residues: 99.3212 Evaluate side-chains 355 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 298 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 194 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 310 optimal weight: 9.9990 chunk 44 optimal weight: 0.0570 chunk 22 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 279 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN A 564 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.152317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.122535 restraints weight = 82113.324| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.84 r_work: 0.3726 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30486 Z= 0.160 Angle : 0.594 17.494 41480 Z= 0.305 Chirality : 0.045 0.269 4616 Planarity : 0.004 0.124 5375 Dihedral : 4.306 32.312 4050 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.06 % Allowed : 16.96 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3733 helix: 1.12 (0.17), residues: 997 sheet: -0.12 (0.19), residues: 709 loop : -1.14 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 319 TYR 0.021 0.001 TYR A1138 PHE 0.019 0.002 PHE A 32 TRP 0.030 0.002 TRP A 353 HIS 0.004 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00375 (30444) covalent geometry : angle 0.58553 (41396) SS BOND : bond 0.00344 ( 42) SS BOND : angle 2.29292 ( 84) hydrogen bonds : bond 0.03896 ( 1122) hydrogen bonds : angle 4.91076 ( 3141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 306 time to evaluate : 0.942 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: C 357 ARG cc_start: 0.6605 (ttt-90) cc_final: 0.5292 (mpt-90) REVERT: C 436 TRP cc_start: -0.0078 (m100) cc_final: -0.0471 (m100) REVERT: C 572 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.7938 (p) REVERT: C 776 LYS cc_start: 0.8898 (ttpp) cc_final: 0.8606 (ttpp) REVERT: C 787 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7976 (mt0) REVERT: C 900 MET cc_start: 0.8870 (mtp) cc_final: 0.8642 (mtp) REVERT: C 1047 TYR cc_start: 0.8811 (m-80) cc_final: 0.7965 (m-80) REVERT: C 1111 GLU cc_start: 0.7603 (pt0) cc_final: 0.7346 (pt0) REVERT: A 319 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.7672 (tpp-160) REVERT: A 392 PHE cc_start: 0.5724 (OUTLIER) cc_final: 0.3858 (m-80) REVERT: A 571 ASP cc_start: 0.7084 (m-30) cc_final: 0.6763 (t0) REVERT: A 858 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8944 (mt) REVERT: A 900 MET cc_start: 0.8895 (mtm) cc_final: 0.8353 (mtp) REVERT: B 35 GLU cc_start: 0.6183 (mt-10) cc_final: 0.5906 (tp30) REVERT: B 41 TYR cc_start: 0.5925 (m-10) cc_final: 0.5440 (m-10) REVERT: B 82 MET cc_start: 0.8023 (mmm) cc_final: 0.5916 (ptt) REVERT: B 329 GLU cc_start: 0.5378 (OUTLIER) cc_final: 0.5040 (tt0) REVERT: B 462 MET cc_start: 0.5412 (ttm) cc_final: 0.4878 (mmm) REVERT: B 482 ARG cc_start: 0.5325 (mtm180) cc_final: 0.4984 (mtm110) REVERT: D 164 ASN cc_start: 0.5496 (p0) cc_final: 0.4856 (p0) REVERT: D 532 ASN cc_start: 0.8732 (p0) cc_final: 0.8491 (t0) REVERT: D 776 LYS cc_start: 0.8420 (tttp) cc_final: 0.8218 (tttp) REVERT: D 1041 ASP cc_start: 0.7989 (t0) cc_final: 0.7751 (t0) REVERT: D 1119 ASN cc_start: 0.8212 (m110) cc_final: 0.7980 (p0) outliers start: 68 outliers final: 56 residues processed: 351 average time/residue: 0.1700 time to fit residues: 99.2873 Evaluate side-chains 357 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 296 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 379 CYS Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 312 optimal weight: 9.9990 chunk 141 optimal weight: 0.3980 chunk 171 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 232 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 362 optimal weight: 1.9990 chunk 259 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 895 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.152752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.123210 restraints weight = 82406.727| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.84 r_work: 0.3733 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30486 Z= 0.139 Angle : 0.572 16.246 41480 Z= 0.294 Chirality : 0.044 0.272 4616 Planarity : 0.004 0.096 5375 Dihedral : 4.248 34.423 4050 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.09 % Allowed : 17.17 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3733 helix: 1.23 (0.17), residues: 992 sheet: -0.09 (0.19), residues: 709 loop : -1.16 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 319 TYR 0.020 0.001 TYR A1138 PHE 0.018 0.001 PHE A 32 TRP 0.026 0.001 TRP A 353 HIS 0.003 0.001 HIS D1048 Details of bonding type rmsd covalent geometry : bond 0.00324 (30444) covalent geometry : angle 0.56418 (41396) SS BOND : bond 0.00305 ( 42) SS BOND : angle 2.22855 ( 84) hydrogen bonds : bond 0.03726 ( 1122) hydrogen bonds : angle 4.86358 ( 3141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7470.35 seconds wall clock time: 128 minutes 43.59 seconds (7723.59 seconds total)