Starting phenix.real_space_refine on Mon Aug 25 09:04:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8e_39043/08_2025/8y8e_39043.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8e_39043/08_2025/8y8e_39043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y8e_39043/08_2025/8y8e_39043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8e_39043/08_2025/8y8e_39043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y8e_39043/08_2025/8y8e_39043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8e_39043/08_2025/8y8e_39043.map" } resolution = 3.62 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= 0.002 sd= 0.029 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 159 5.16 5 C 16881 2.51 5 N 4381 2.21 5 O 5219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26640 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 8787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 8787 Classifications: {'peptide': 1183} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1126} Chain breaks: 4 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 637 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ASN:plan1': 10, 'PHE:plan': 16, 'ARG:plan': 4, 'TRP:plan': 4, 'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 301 Chain: "B" Number of atoms: 8858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 8858 Classifications: {'peptide': 1183} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1126} Chain breaks: 4 Unresolved non-hydrogen bonds: 406 Unresolved non-hydrogen angles: 519 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'TYR:plan': 7, 'ARG:plan': 11, 'ASN:plan1': 8, 'PHE:plan': 9, 'GLU:plan': 4, 'HIS:plan': 3, 'GLN:plan1': 8, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 257 Chain: "A" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 8771 Classifications: {'peptide': 1172} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1115} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 8, 'PHE:plan': 10, 'ARG:plan': 8, 'GLU:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 8, 'GLN:plan1': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 249 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.77, per 1000 atoms: 0.25 Number of scatterers: 26640 At special positions: 0 Unit cell: (139.4, 149.24, 214.84, 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 159 16.00 O 5219 8.00 N 4381 7.00 C 16881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=66, symmetry=0 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 188 " " NAG A1302 " - " ASN A 192 " " NAG A1303 " - " ASN A 725 " " NAG A1304 " - " ASN A 58 " " NAG B1301 " - " ASN B 725 " " NAG B1302 " - " ASN B 793 " " NAG B1303 " - " ASN B1211 " " NAG B1304 " - " ASN B 132 " " NAG B1305 " - " ASN B 188 " " NAG B1306 " - " ASN B 192 " " NAG B1307 " - " ASN B 664 " " NAG C1301 " - " ASN C 188 " " NAG C1302 " - " ASN C 664 " " NAG C1303 " - " ASN C 725 " " NAG C1304 " - " ASN C 58 " " NAG C1305 " - " ASN C 924 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6672 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 63 sheets defined 22.8% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.765A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.681A pdb=" N ASP C 400 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 401 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 397 through 402' Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 442 through 448 removed outlier: 4.209A pdb=" N ARG C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.521A pdb=" N VAL C 482 " --> pdb=" O ASP C 478 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 478 through 483' Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 605 through 610 removed outlier: 3.625A pdb=" N TYR C 609 " --> pdb=" O ASN C 605 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER C 610 " --> pdb=" O ASP C 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 605 through 610' Processing helix chain 'C' and resid 611 through 613 No H-bonds generated for 'chain 'C' and resid 611 through 613' Processing helix chain 'C' and resid 699 through 704 Processing helix chain 'C' and resid 814 through 819 Processing helix chain 'C' and resid 822 through 830 removed outlier: 4.151A pdb=" N HIS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP C 827 " --> pdb=" O ALA C 823 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 833 No H-bonds generated for 'chain 'C' and resid 831 through 833' Processing helix chain 'C' and resid 836 through 858 removed outlier: 3.662A pdb=" N ALA C 858 " --> pdb=" O GLN C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 882 Processing helix chain 'C' and resid 901 through 909 removed outlier: 3.544A pdb=" N ASN C 909 " --> pdb=" O ASP C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 924 removed outlier: 4.073A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 920 " --> pdb=" O VAL C 916 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 940 removed outlier: 3.527A pdb=" N VAL C 937 " --> pdb=" O ASP C 933 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 940 " --> pdb=" O CYS C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 968 removed outlier: 3.677A pdb=" N TYR C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 959 " --> pdb=" O ILE C 955 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C 960 " --> pdb=" O SER C 956 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA C 961 " --> pdb=" O GLY C 957 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C 966 " --> pdb=" O ALA C 962 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET C 967 " --> pdb=" O THR C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 987 removed outlier: 3.504A pdb=" N ASN C 982 " --> pdb=" O PRO C 978 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 983 " --> pdb=" O PHE C 979 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1000 Processing helix chain 'C' and resid 1002 through 1008 removed outlier: 4.064A pdb=" N ASN C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1018 removed outlier: 4.232A pdb=" N ILE C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLN C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1045 Processing helix chain 'C' and resid 1046 through 1049 Processing helix chain 'C' and resid 1057 through 1065 removed outlier: 3.755A pdb=" N SER C1063 " --> pdb=" O GLN C1059 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG C1064 " --> pdb=" O GLU C1060 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU C1065 " --> pdb=" O ILE C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1111 removed outlier: 3.766A pdb=" N ILE C1074 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN C1111 " --> pdb=" O ILE C1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 1179 through 1183 removed outlier: 3.601A pdb=" N ASP C1182 " --> pdb=" O LYS C1179 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.626A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.587A pdb=" N ILE B 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 375 through 379' Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.911A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.561A pdb=" N VAL B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 605 through 608 removed outlier: 3.656A pdb=" N LEU B 608 " --> pdb=" O ASN B 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 605 through 608' Processing helix chain 'B' and resid 696 through 700 Processing helix chain 'B' and resid 813 through 818 removed outlier: 4.027A pdb=" N VAL B 818 " --> pdb=" O CYS B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 830 removed outlier: 3.864A pdb=" N HIS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 828 " --> pdb=" O ALA B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 862 removed outlier: 3.722A pdb=" N LEU B 849 " --> pdb=" O GLU B 845 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 857 " --> pdb=" O THR B 853 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA B 858 " --> pdb=" O GLN B 854 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 860 " --> pdb=" O GLN B 856 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 882 removed outlier: 4.220A pdb=" N ILE B 882 " --> pdb=" O VAL B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 909 removed outlier: 4.387A pdb=" N LEU B 906 " --> pdb=" O PRO B 902 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 925 removed outlier: 3.554A pdb=" N ASN B 923 " --> pdb=" O VAL B 919 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 964 Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.544A pdb=" N PHE B 968 " --> pdb=" O ALA B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 978 through 987 removed outlier: 3.862A pdb=" N TYR B 985 " --> pdb=" O LEU B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 990 No H-bonds generated for 'chain 'B' and resid 988 through 990' Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.936A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1018 removed outlier: 4.553A pdb=" N ILE B1015 " --> pdb=" O ALA B1011 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN B1017 " --> pdb=" O LEU B1013 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY B1018 " --> pdb=" O SER B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1021 No H-bonds generated for 'chain 'B' and resid 1019 through 1021' Processing helix chain 'B' and resid 1023 through 1046 removed outlier: 4.070A pdb=" N LEU B1043 " --> pdb=" O ALA B1039 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B1044 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B1046 " --> pdb=" O SER B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1049 No H-bonds generated for 'chain 'B' and resid 1047 through 1049' Processing helix chain 'B' and resid 1057 through 1062 removed outlier: 3.588A pdb=" N LEU B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1113 removed outlier: 3.671A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B1101 " --> pdb=" O THR B1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.596A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.867A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.942A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.618A pdb=" N GLY A 449 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.500A pdb=" N VAL A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 removed outlier: 3.884A pdb=" N VAL A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 701 " --> pdb=" O CYS A 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 696 through 701' Processing helix chain 'A' and resid 813 through 818 Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.583A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 860 Processing helix chain 'A' and resid 878 through 882 removed outlier: 3.945A pdb=" N ASN A 881 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.856A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 940 removed outlier: 3.850A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 6.608A pdb=" N LEU A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU A1013 " --> pdb=" O ASN A1009 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1021 No H-bonds generated for 'chain 'A' and resid 1019 through 1021' Processing helix chain 'A' and resid 1023 through 1045 Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.533A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1057 through 1062 removed outlier: 3.534A pdb=" N ILE A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1113 removed outlier: 5.275A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1202 removed outlier: 3.618A pdb=" N ASN A1201 " --> pdb=" O SER A1198 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A1202 " --> pdb=" O ASP A1199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1198 through 1202' Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 removed outlier: 4.086A pdb=" N ARG C 34 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 76 " --> pdb=" O ARG C 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.168A pdb=" N THR C 48 " --> pdb=" O THR C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.271A pdb=" N VAL C 55 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 104 removed outlier: 3.581A pdb=" N ILE C 102 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 202 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 111 through 112 Processing sheet with id=AA7, first strand: chain 'C' and resid 126 through 127 removed outlier: 3.808A pdb=" N CYS C 151 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 267 through 268 removed outlier: 4.447A pdb=" N LEU C 267 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL C 280 " --> pdb=" O LEU C 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 305 through 307 Processing sheet with id=AB1, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AB2, first strand: chain 'C' and resid 346 through 348 removed outlier: 3.505A pdb=" N ARG C 347 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 427 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 346 through 348 removed outlier: 3.505A pdb=" N ARG C 347 " --> pdb=" O VAL C 388 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 459 through 462 Processing sheet with id=AB5, first strand: chain 'C' and resid 467 through 468 removed outlier: 3.668A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 504 through 506 Processing sheet with id=AB7, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AB8, first strand: chain 'C' and resid 632 through 636 removed outlier: 4.146A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 691 through 692 removed outlier: 3.803A pdb=" N CYS C 719 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 742 through 746 Processing sheet with id=AC2, first strand: chain 'C' and resid 802 through 804 removed outlier: 3.533A pdb=" N LEU C1133 " --> pdb=" O ILE C1144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 809 through 811 removed outlier: 4.467A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1162 through 1163 removed outlier: 4.104A pdb=" N CYS C1163 " --> pdb=" O THR C1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 1177 through 1178 Processing sheet with id=AC6, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.640A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AC8, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.660A pdb=" N LYS B 105 " --> pdb=" O TRP B 257 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B 202 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 200 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 110 through 112 Processing sheet with id=AD1, first strand: chain 'B' and resid 188 through 189 removed outlier: 3.987A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS B 234 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 161 through 162 removed outlier: 5.997A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 302 through 303 removed outlier: 3.508A pdb=" N GLY B 302 " --> pdb=" O PHE B 681 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 681 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AD5, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.853A pdb=" N ARG B 347 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 388 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 365 through 371 removed outlier: 6.862A pdb=" N TYR B 426 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE B 368 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLN B 424 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N CYS B 370 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N SER B 422 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 427 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AD8, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.289A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 504 through 506 Processing sheet with id=AE1, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.630A pdb=" N GLY B 550 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 620 through 624 Processing sheet with id=AE3, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.539A pdb=" N PHE B 713 " --> pdb=" O VAL B 720 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 742 through 746 Processing sheet with id=AE5, first strand: chain 'B' and resid 790 through 791 Processing sheet with id=AE6, first strand: chain 'B' and resid 801 through 804 removed outlier: 3.579A pdb=" N GLY B1140 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B1142 " --> pdb=" O GLN B1135 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1163 through 1164 removed outlier: 3.608A pdb=" N MET B1205 " --> pdb=" O GLY B1169 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1176 through 1177 removed outlier: 3.615A pdb=" N THR B1187 " --> pdb=" O TYR B1176 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AF1, first strand: chain 'A' and resid 60 through 68 removed outlier: 3.645A pdb=" N LEU A 61 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 266 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 65 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 262 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 261 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE A 200 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 106 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 198 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 199 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE A 209 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER A 225 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.701A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 124 through 126 removed outlier: 3.993A pdb=" N ILE A 124 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 139 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 137 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 189 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 187 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 150 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.771A pdb=" N GLY A 302 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 681 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 304 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 309 through 310 removed outlier: 3.582A pdb=" N GLY A 675 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 316 through 317 removed outlier: 3.859A pdb=" N VAL A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 631 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 667 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AF8, first strand: chain 'A' and resid 346 through 349 removed outlier: 3.504A pdb=" N ASN A 591 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 382 through 383 removed outlier: 3.656A pdb=" N THR A 602 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 460 through 462 Processing sheet with id=AG2, first strand: chain 'A' and resid 466 through 467 removed outlier: 4.410A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 538 " --> pdb=" O CYS A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.810A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.765A pdb=" N ILE A 788 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A1156 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'A' and resid 797 through 804 removed outlier: 3.896A pdb=" N ALA A 797 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A1147 " --> pdb=" O ALA A 797 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 803 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A1141 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.229A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 1162 through 1163 Processing sheet with id=AG8, first strand: chain 'A' and resid 1170 through 1171 removed outlier: 3.823A pdb=" N ALA A1171 " --> pdb=" O VAL A1203 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A1203 " --> pdb=" O ALA A1171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'A' and resid 1175 through 1179 655 hydrogen bonds defined for protein. 1794 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: 6.13 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8619 1.34 - 1.46: 6578 1.46 - 1.58: 11871 1.58 - 1.70: 0 1.70 - 1.81: 179 Bond restraints: 27247 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 27242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 36393 1.27 - 2.54: 647 2.54 - 3.81: 155 3.81 - 5.08: 9 5.08 - 6.35: 5 Bond angle restraints: 37209 Sorted by residual: angle pdb=" C PRO A 394 " pdb=" N ASN A 395 " pdb=" CA ASN A 395 " ideal model delta sigma weight residual 120.38 123.61 -3.23 1.37e+00 5.33e-01 5.56e+00 angle pdb=" N ILE A1130 " pdb=" CA ILE A1130 " pdb=" C ILE A1130 " ideal model delta sigma weight residual 111.48 109.30 2.18 9.40e-01 1.13e+00 5.36e+00 angle pdb=" C GLY B 957 " pdb=" N TYR B 958 " pdb=" CA TYR B 958 " ideal model delta sigma weight residual 121.54 125.77 -4.23 1.91e+00 2.74e-01 4.89e+00 angle pdb=" N GLY A 16 " pdb=" CA GLY A 16 " pdb=" C GLY A 16 " ideal model delta sigma weight residual 113.18 118.35 -5.17 2.37e+00 1.78e-01 4.75e+00 angle pdb=" N PRO A1067 " pdb=" CA PRO A1067 " pdb=" C PRO A1067 " ideal model delta sigma weight residual 110.70 113.16 -2.46 1.22e+00 6.72e-01 4.08e+00 ... (remaining 37204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 15876 17.88 - 35.75: 492 35.75 - 53.63: 85 53.63 - 71.50: 14 71.50 - 89.38: 3 Dihedral angle restraints: 16470 sinusoidal: 6108 harmonic: 10362 Sorted by residual: dihedral pdb=" CA PHE A1008 " pdb=" C PHE A1008 " pdb=" N ASN A1009 " pdb=" CA ASN A1009 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ILE A 15 " pdb=" C ILE A 15 " pdb=" N GLY A 16 " pdb=" CA GLY A 16 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PRO B 325 " pdb=" C PRO B 325 " pdb=" N ASP B 326 " pdb=" CA ASP B 326 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 16467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2690 0.030 - 0.060: 1074 0.060 - 0.089: 266 0.089 - 0.119: 284 0.119 - 0.149: 8 Chirality restraints: 4322 Sorted by residual: chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 924 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE B 32 " pdb=" N ILE B 32 " pdb=" C ILE B 32 " pdb=" CB ILE B 32 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE C 627 " pdb=" N ILE C 627 " pdb=" C ILE C 627 " pdb=" CB ILE C 627 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 4319 not shown) Planarity restraints: 4837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 324 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO B 325 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 325 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 325 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1066 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C1067 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C1067 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C1067 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO B1067 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B1067 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B1067 " 0.017 5.00e-02 4.00e+02 ... (remaining 4834 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2496 2.75 - 3.29: 26583 3.29 - 3.82: 41938 3.82 - 4.36: 46772 4.36 - 4.90: 80911 Nonbonded interactions: 198700 Sorted by model distance: nonbonded pdb=" O VAL A 700 " pdb=" OG SER A 705 " model vdw 2.211 3.040 nonbonded pdb=" O VAL B 113 " pdb=" OG1 THR B 116 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR B 123 " pdb=" OE1 GLN B 140 " model vdw 2.230 3.040 nonbonded pdb=" O GLY C 976 " pdb=" OH TYR B1176 " model vdw 2.237 3.040 nonbonded pdb=" O VAL B 636 " pdb=" OG1 THR B 666 " model vdw 2.242 3.040 ... (remaining 198695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 36 or (resid 39 through 40 and (na \ me N or name CA or name C or name O or name CB )) or resid 41 or (resid 42 and ( \ name N or name CA or name C or name O or name CB )) or resid 43 through 48 or (r \ esid 49 through 52 and (name N or name CA or name C or name O or name CB )) or r \ esid 53 or (resid 54 through 55 and (name N or name CA or name C or name O or na \ me CB )) or resid 56 or (resid 57 through 58 and (name N or name CA or name C or \ name O or name CB )) or resid 59 through 61 or (resid 62 and (name N or name CA \ or name C or name O or name CB )) or resid 63 through 68 or (resid 69 and (name \ N or name CA or name C or name O or name CB )) or resid 70 through 72 or (resid \ 73 through 75 and (name N or name CA or name C or name O or name CB )) or resid \ 76 through 88 or (resid 89 and (name N or name CA or name C or name O or name C \ B )) or resid 90 through 93 or (resid 94 through 95 and (name N or name CA or na \ me C or name O or name CB )) or resid 96 through 97 or (resid 98 and (name N or \ name CA or name C or name O or name CB )) or resid 99 through 101 or (resid 102 \ and (name N or name CA or name C or name O or name CB )) or resid 103 through 10 \ 4 or (resid 105 and (name N or name CA or name C or name O or name CB )) or resi \ d 106 through 120 or (resid 121 and (name N or name CA or name C or name O or na \ me CB )) or resid 122 through 123 or (resid 124 and (name N or name CA or name C \ or name O or name CB )) or resid 125 through 128 or (resid 129 through 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 through 138 or \ (resid 139 through 140 and (name N or name CA or name C or name O or name CB )) \ or resid 141 or (resid 142 through 143 and (name N or name CA or name C or name \ O or name CB )) or resid 144 or (resid 145 through 148 and (name N or name CA o \ r name C or name O or name CB )) or resid 149 through 154 or (resid 155 and (nam \ e N or name CA or name C or name O or name CB )) or resid 156 through 157 or (re \ sid 158 and (name N or name CA or name C or name O or name CB )) or resid 159 th \ rough 163 or (resid 164 and (name N or name CA or name C or name O or name CB )) \ or resid 165 through 168 or (resid 169 through 170 and (name N or name CA or na \ me C or name O or name CB )) or resid 171 or (resid 172 and (name N or name CA o \ r name C or name O or name CB )) or resid 173 through 181 or (resid 182 and (nam \ e N or name CA or name C or name O or name CB )) or resid 183 through 184 or (re \ sid 185 through 186 and (name N or name CA or name C or name O or name CB )) or \ resid 187 through 195 or (resid 196 and (name N or name CA or name C or name O o \ r name CB )) or resid 197 through 199 or (resid 200 and (name N or name CA or na \ me C or name O or name CB )) or resid 201 through 211 or (resid 212 through 214 \ and (name N or name CA or name C or name O or name CB )) or resid 215 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 221 or (resid 222 through 224 and (name N or name CA or name C or name O or na \ me CB )) or resid 225 or (resid 226 and (name N or name CA or name C or name O o \ r name CB )) or resid 227 through 233 or (resid 234 through 235 and (name N or n \ ame CA or name C or name O or name CB )) or resid 237 through 239 or (resid 240 \ and (name N or name CA or name C or name O or name CB )) or resid 241 through 24 \ 4 or resid 254 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB )) or resid 258 through 260 or (resid 261 and (name N or name CA \ or name C or name O or name CB )) or resid 262 or (resid 263 and (name N or name \ CA or name C or name O or name CB )) or resid 264 or (resid 265 and (name N or \ name CA or name C or name O or name CB )) or resid 266 through 279 or (resid 280 \ and (name N or name CA or name C or name O or name CB )) or resid 281 through 2 \ 84 or (resid 285 and (name N or name CA or name C or name O or name CB )) or res \ id 286 through 292 or (resid 293 and (name N or name CA or name C or name O or n \ ame CB )) or resid 294 through 316 or (resid 317 through 320 and (name N or name \ CA or name C or name O or name CB )) or resid 321 through 347 or (resid 348 and \ (name N or name CA or name C or name O or name CB )) or resid 349 through 352 o \ r (resid 353 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 54 through 383 or (resid 384 and (name N or name CA or name C or name O or name \ CB )) or resid 385 through 399 or (resid 400 through 401 and (name N or name CA \ or name C or name O or name CB )) or resid 402 through 407 or (resid 408 through \ 410 and (name N or name CA or name C or name O or name CB )) or resid 411 throu \ gh 424 or (resid 425 and (name N or name CA or name C or name O or name CB )) or \ resid 426 through 436 or (resid 437 and (name N or name CA or name C or name O \ or name CB )) or resid 438 or (resid 439 and (name N or name CA or name C or nam \ e O or name CB )) or resid 440 through 460 or (resid 461 through 462 and (name N \ or name CA or name C or name O or name CB )) or resid 463 through 491 or (resid \ 492 through 493 and (name N or name CA or name C or name O or name CB )) or res \ id 494 through 553 or (resid 554 and (name N or name CA or name C or name O or n \ ame CB )) or resid 555 through 557 or resid 563 through 589 or (resid 590 and (n \ ame N or name CA or name C or name O or name CB )) or resid 591 or (resid 592 an \ d (name N or name CA or name C or name O or name CB )) or resid 593 through 608 \ or (resid 609 and (name N or name CA or name C or name O or name CB )) or resid \ 610 or (resid 611 through 612 and (name N or name CA or name C or name O or name \ CB )) or resid 613 through 626 or (resid 627 and (name N or name CA or name C o \ r name O or name CB )) or resid 628 through 641 or (resid 642 through 646 and (n \ ame N or name CA or name C or name O or name CB )) or resid 647 through 649 or ( \ resid 650 and (name N or name CA or name C or name O or name CB )) or resid 651 \ through 657 or (resid 658 through 661 and (name N or name CA or name C or name O \ or name CB )) or resid 662 through 672 or (resid 673 and (name N or name CA or \ name C or name O or name CB )) or resid 674 through 682 or (resid 683 through 68 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 685 through \ 697 or (resid 698 and (name N or name CA or name C or name O or name CB )) or re \ sid 699 or (resid 700 and (name N or name CA or name C or name O or name CB )) o \ r resid 701 through 703 or (resid 704 and (name N or name CA or name C or name O \ or name CB )) or resid 705 through 762 or (resid 763 through 765 and (name N or \ name CA or name C or name O or name CB )) or resid 766 through 771 or (resid 77 \ 2 through 773 and (name N or name CA or name C or name O or name CB )) or resid \ 774 through 777 or (resid 778 and (name N or name CA or name C or name O or name \ CB )) or resid 779 or (resid 780 and (name N or name CA or name C or name O or \ name CB )) or resid 781 or (resid 786 and (name N or name CA or name C or name O \ or name CB )) or resid 787 through 793 or (resid 794 and (name N or name CA or \ name C or name O or name CB )) or resid 795 through 799 or (resid 800 and (name \ N or name CA or name C or name O or name CB )) or resid 801 through 808 or (resi \ d 809 through 810 and (name N or name CA or name C or name O or name CB )) or re \ sid 811 through 819 or (resid 820 and (name N or name CA or name C or name O or \ name CB )) or resid 821 through 834 or (resid 835 and (name N or name CA or name \ C or name O or name CB )) or resid 836 through 853 or (resid 854 and (name N or \ name CA or name C or name O or name CB )) or resid 855 or (resid 856 and (name \ N or name CA or name C or name O or name CB )) or resid 857 through 860 or (resi \ d 861 through 863 and (name N or name CA or name C or name O or name CB )) or re \ sid 864 through 870 or (resid 871 through 872 and (name N or name CA or name C o \ r name O or name CB )) or resid 873 through 883 or (resid 884 and (name N or nam \ e CA or name C or name O or name CB )) or resid 885 through 890 or (resid 891 an \ d (name N or name CA or name C or name O or name CB )) or resid 892 through 902 \ or (resid 903 through 904 and (name N or name CA or name C or name O or name CB \ )) or resid 905 through 911 or (resid 912 and (name N or name CA or name C or na \ me O or name CB )) or resid 913 through 924 or (resid 925 through 926 and (name \ N or name CA or name C or name O or name CB )) or resid 927 through 929 or (resi \ d 930 through 935 and (name N or name CA or name C or name O or name CB )) or re \ sid 936 through 953 or (resid 954 and (name N or name CA or name C or name O or \ name CB )) or resid 955 through 957 or (resid 958 through 963 and (name N or nam \ e CA or name C or name O or name CB )) or resid 964 through 967 or (resid 968 an \ d (name N or name CA or name C or name O or name CB )) or resid 969 through 983 \ or (resid 984 through 986 and (name N or name CA or name C or name O or name CB \ )) or resid 987 through 992 or (resid 993 through 994 and (name N or name CA or \ name C or name O or name CB )) or resid 995 through 999 or (resid 1000 through 1 \ 008 and (name N or name CA or name C or name O or name CB )) or resid 1009 or (r \ esid 1010 through 1013 and (name N or name CA or name C or name O or name CB )) \ or resid 1014 through 1019 or (resid 1020 through 1021 and (name N or name CA or \ name C or name O or name CB )) or resid 1022 through 1037 or (resid 1038 throug \ h 1039 and (name N or name CA or name C or name O or name CB )) or resid 1040 th \ rough 1058 or (resid 1059 and (name N or name CA or name C or name O or name CB \ )) or resid 1060 through 1061 or (resid 1062 and (name N or name CA or name C or \ name O or name CB )) or resid 1063 or (resid 1064 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1065 or (resid 1066 and (name N or name CA \ or name C or name O or name CB )) or resid 1067 through 1068 or (resid 1069 thro \ ugh 1073 and (name N or name CA or name C or name O or name CB )) or resid 1074 \ through 1075 or (resid 1076 and (name N or name CA or name C or name O or name C \ B )) or resid 1077 through 1111 or (resid 1112 and (name N or name CA or name C \ or name O or name CB )) or resid 1113 through 1128 or (resid 1129 through 1130 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1131 through 11 \ 44 or (resid 1145 and (name N or name CA or name C or name O or name CB )) or re \ sid 1146 through 1150 or (resid 1151 through 1155 and (name N or name CA or name \ C or name O or name CB )) or resid 1156 through 1178 or (resid 1179 through 118 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 1182 through \ 1183 or (resid 1184 through 1187 and (name N or name CA or name C or name O or \ name CB )) or resid 1188 through 1304)) selection = (chain 'B' and ((resid 14 and (name N or name CA or name C or name O or name CB \ )) or resid 15 through 36 or (resid 39 through 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 49 or (resid 50 through 52 and (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 66 or (re \ sid 67 and (name N or name CA or name C or name O or name CB )) or resid 68 or ( \ resid 69 and (name N or name CA or name C or name O or name CB )) or resid 70 th \ rough 72 or (resid 73 through 75 and (name N or name CA or name C or name O or n \ ame CB )) or resid 76 through 79 or (resid 80 and (name N or name CA or name C o \ r name O or name CB )) or resid 81 through 88 or (resid 89 and (name N or name C \ A or name C or name O or name CB )) or resid 90 or (resid 91 and (name N or name \ CA or name C or name O or name CB )) or resid 92 through 93 or (resid 94 throug \ h 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 104 or (resid 105 and (name N or name CA or name C or name O o \ r name CB )) or resid 106 through 118 or (resid 119 and (name N or name CA or na \ me C or name O or name CB )) or resid 120 or (resid 121 and (name N or name CA o \ r name C or name O or name CB )) or resid 122 through 123 or (resid 124 and (nam \ e N or name CA or name C or name O or name CB )) or resid 125 through 128 or (re \ sid 129 through 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 through 138 or (resid 139 through 140 and (name N or name CA or name C \ or name O or name CB )) or resid 141 or (resid 142 through 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 or (resid 145 through 148 \ and (name N or name CA or name C or name O or name CB )) or resid 149 through 15 \ 4 or (resid 155 and (name N or name CA or name C or name O or name CB )) or resi \ d 156 or (resid 157 through 158 and (name N or name CA or name C or name O or na \ me CB )) or resid 159 or (resid 160 and (name N or name CA or name C or name O o \ r name CB )) or resid 161 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 181 or (resid 182 and (name N \ or name CA or name C or name O or name CB )) or resid 183 through 192 or (resid \ 193 and (name N or name CA or name C or name O or name CB )) or resid 194 throug \ h 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 197 through 199 or (resid 200 and (name N or name CA or name C or name O o \ r name CB )) or resid 201 through 211 or (resid 212 through 214 and (name N or n \ ame CA or name C or name O or name CB )) or resid 215 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 or (resid \ 220 and (name N or name CA or name C or name O or name CB )) or resid 221 or (re \ sid 222 through 224 and (name N or name CA or name C or name O or name CB )) or \ resid 225 through 235 or resid 237 through 239 or (resid 240 and (name N or name \ CA or name C or name O or name CB )) or resid 241 through 256 or (resid 257 and \ (name N or name CA or name C or name O or name CB )) or resid 258 through 260 o \ r (resid 261 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 62 or (resid 263 and (name N or name CA or name C or name O or name CB )) or res \ id 264 through 284 or (resid 285 and (name N or name CA or name C or name O or n \ ame CB )) or resid 286 through 289 or (resid 290 and (name N or name CA or name \ C or name O or name CB )) or resid 291 through 292 or (resid 293 and (name N or \ name CA or name C or name O or name CB )) or resid 294 through 316 or (resid 317 \ through 320 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 21 through 341 or (resid 342 and (name N or name CA or name C or name O or name \ CB )) or resid 343 through 358 or (resid 359 and (name N or name CA or name C or \ name O or name CB )) or resid 360 through 367 or (resid 368 and (name N or name \ CA or name C or name O or name CB )) or resid 369 through 374 or (resid 375 and \ (name N or name CA or name C or name O or name CB )) or resid 376 through 390 o \ r (resid 391 through 392 and (name N or name CA or name C or name O or name CB ) \ ) or resid 393 through 394 or (resid 395 and (name N or name CA or name C or nam \ e O or name CB )) or resid 396 through 397 or (resid 398 and (name N or name CA \ or name C or name O or name CB )) or resid 399 through 400 or (resid 401 and (na \ me N or name CA or name C or name O or name CB )) or resid 402 through 408 or (r \ esid 409 through 410 and (name N or name CA or name C or name O or name CB )) or \ resid 411 through 412 or (resid 413 through 414 and (name N or name CA or name \ C or name O or name CB )) or resid 415 through 424 or (resid 425 and (name N or \ name CA or name C or name O or name CB )) or resid 426 through 438 or (resid 439 \ and (name N or name CA or name C or name O or name CB )) or resid 440 through 4 \ 43 or (resid 444 and (name N or name CA or name C or name O or name CB )) or res \ id 445 through 446 or (resid 447 through 448 and (name N or name CA or name C or \ name O or name CB )) or resid 449 through 466 or (resid 467 and (name N or name \ CA or name C or name O or name CB )) or resid 468 through 483 or resid 490 thro \ ugh 501 or (resid 502 and (name N or name CA or name C or name O or name CB )) o \ r resid 519 through 520 or (resid 521 and (name N or name CA or name C or name O \ or name CB )) or resid 522 through 589 or (resid 590 and (name N or name CA or \ name C or name O or name CB )) or resid 591 through 626 or (resid 627 and (name \ N or name CA or name C or name O or name CB )) or resid 628 through 633 or (resi \ d 634 and (name N or name CA or name C or name O or name CB )) or resid 635 thro \ ugh 643 or (resid 644 through 646 and (name N or name CA or name C or name O or \ name CB )) or resid 647 through 649 or (resid 650 and (name N or name CA or name \ C or name O or name CB )) or resid 651 through 658 or (resid 659 through 661 an \ d (name N or name CA or name C or name O or name CB )) or resid 662 through 665 \ or (resid 666 and (name N or name CA or name C or name O or name CB )) or resid \ 667 through 677 or (resid 678 through 680 and (name N or name CA or name C or na \ me O or name CB )) or resid 681 through 682 or (resid 683 through 684 and (name \ N or name CA or name C or name O or name CB )) or resid 685 through 690 or (resi \ d 691 and (name N or name CA or name C or name O or name CB )) or resid 692 thro \ ugh 703 or (resid 704 and (name N or name CA or name C or name O or name CB )) o \ r resid 705 through 710 or (resid 711 and (name N or name CA or name C or name O \ or name CB )) or resid 712 or (resid 713 and (name N or name CA or name C or na \ me O or name CB )) or resid 714 through 728 or (resid 729 and (name N or name CA \ or name C or name O or name CB )) or resid 730 through 734 or (resid 735 and (n \ ame N or name CA or name C or name O or name CB )) or resid 736 through 743 or ( \ resid 744 through 745 and (name N or name CA or name C or name O or name CB )) o \ r resid 746 through 763 or (resid 764 through 765 and (name N or name CA or name \ C or name O or name CB )) or resid 766 through 769 or (resid 770 and (name N or \ name CA or name C or name O or name CB )) or resid 771 or (resid 772 through 77 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 774 through \ 775 or (resid 776 through 778 and (name N or name CA or name C or name O or name \ CB )) or resid 779 through 781 or (resid 786 and (name N or name CA or name C o \ r name O or name CB )) or resid 787 through 790 or (resid 791 and (name N or nam \ e CA or name C or name O or name CB )) or resid 792 through 793 or (resid 794 an \ d (name N or name CA or name C or name O or name CB )) or resid 795 through 799 \ or (resid 800 and (name N or name CA or name C or name O or name CB )) or resid \ 801 through 819 or (resid 820 and (name N or name CA or name C or name O or name \ CB )) or resid 821 through 834 or (resid 835 and (name N or name CA or name C o \ r name O or name CB )) or resid 836 or (resid 837 and (name N or name CA or name \ C or name O or name CB )) or resid 838 through 871 or (resid 872 and (name N or \ name CA or name C or name O or name CB )) or resid 873 through 874 or (resid 87 \ 5 through 876 and (name N or name CA or name C or name O or name CB )) or resid \ 877 through 890 or (resid 891 and (name N or name CA or name C or name O or name \ CB )) or resid 892 through 893 or (resid 894 and (name N or name CA or name C o \ r name O or name CB )) or resid 895 through 903 or (resid 904 and (name N or nam \ e CA or name C or name O or name CB )) or resid 905 through 924 or (resid 925 th \ rough 926 and (name N or name CA or name C or name O or name CB )) or resid 927 \ through 936 or (resid 937 and (name N or name CA or name C or name O or name CB \ )) or resid 938 through 957 or (resid 958 through 963 and (name N or name CA or \ name C or name O or name CB )) or resid 964 through 967 or (resid 968 and (name \ N or name CA or name C or name O or name CB )) or resid 969 through 980 or (resi \ d 981 and (name N or name CA or name C or name O or name CB )) or resid 982 thro \ ugh 983 or (resid 984 through 986 and (name N or name CA or name C or name O or \ name CB )) or resid 987 or (resid 988 and (name N or name CA or name C or name O \ or name CB )) or resid 989 through 991 or (resid 992 through 994 and (name N or \ name CA or name C or name O or name CB )) or resid 995 through 997 or (resid 99 \ 8 through 1008 and (name N or name CA or name C or name O or name CB )) or resid \ 1009 or (resid 1010 through 1013 and (name N or name CA or name C or name O or \ name CB )) or resid 1014 through 1019 or (resid 1020 through 1021 and (name N or \ name CA or name C or name O or name CB )) or resid 1022 through 1049 or (resid \ 1050 and (name N or name CA or name C or name O or name CB )) or resid 1051 thro \ ugh 1055 or (resid 1056 and (name N or name CA or name C or name O or name CB )) \ or resid 1057 through 1065 or (resid 1066 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1067 through 1068 or (resid 1069 through 1073 and ( \ name N or name CA or name C or name O or name CB )) or resid 1074 through 1111 o \ r (resid 1112 and (name N or name CA or name C or name O or name CB )) or resid \ 1113 through 1116 or (resid 1117 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1118 through 1125 or (resid 1126 and (name N or name CA or na \ me C or name O or name CB )) or resid 1127 through 1153 or (resid 1154 through 1 \ 155 and (name N or name CA or name C or name O or name CB )) or resid 1156 throu \ gh 1167 or (resid 1168 and (name N or name CA or name C or name O or name CB )) \ or resid 1169 through 1178 or (resid 1179 through 1181 and (name N or name CA or \ name C or name O or name CB )) or resid 1182 through 1183 or (resid 1184 throug \ h 1187 and (name N or name CA or name C or name O or name CB )) or resid 1188 th \ rough 1191 or (resid 1192 and (name N or name CA or name C or name O or name CB \ )) or resid 1193 through 1196 or (resid 1197 and (name N or name CA or name C or \ name O or name CB )) or resid 1198 through 1204 or (resid 1205 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1206 through 1217 or (resid 12 \ 18 and (name N or name CA or name C or name O or name CB )) or resid 1219 throug \ h 1304)) selection = (chain 'C' and (resid 14 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 36 or resid 39 through 41 or (resi \ d 42 and (name N or name CA or name C or name O or name CB )) or resid 43 throug \ h 48 or (resid 49 through 52 and (name N or name CA or name C or name O or name \ CB )) or resid 53 or (resid 54 through 55 and (name N or name CA or name C or na \ me O or name CB )) or resid 56 or (resid 57 through 58 and (name N or name CA or \ name C or name O or name CB )) or resid 59 through 66 or (resid 67 and (name N \ or name CA or name C or name O or name CB )) or resid 68 through 78 or (resid 79 \ through 80 and (name N or name CA or name C or name O or name CB )) or resid 81 \ through 97 or (resid 98 and (name N or name CA or name C or name O or name CB ) \ ) or resid 99 through 118 or (resid 119 and (name N or name CA or name C or name \ O or name CB )) or resid 120 through 125 or (resid 126 and (name N or name CA o \ r name C or name O or name CB )) or resid 127 through 146 or (resid 147 through \ 148 and (name N or name CA or name C or name O or name CB )) or resid 149 throug \ h 159 or (resid 160 and (name N or name CA or name C or name O or name CB )) or \ resid 161 through 168 or (resid 169 through 170 and (name N or name CA or name C \ or name O or name CB )) or resid 171 through 184 or (resid 185 through 186 and \ (name N or name CA or name C or name O or name CB )) or resid 187 through 192 or \ (resid 193 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 4 through 212 or (resid 213 through 214 and (name N or name CA or name C or name \ O or name CB )) or resid 215 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 222 or (resid 223 through \ 224 and (name N or name CA or name C or name O or name CB )) or resid 225 throug \ h 233 or (resid 234 through 235 and (name N or name CA or name C or name O or na \ me CB )) or resid 237 through 244 or resid 254 through 264 or (resid 265 and (na \ me N or name CA or name C or name O or name CB )) or resid 266 through 279 or (r \ esid 280 and (name N or name CA or name C or name O or name CB )) or resid 281 t \ hrough 289 or (resid 290 and (name N or name CA or name C or name O or name CB ) \ ) or resid 291 through 311 or (resid 312 and (name N or name CA or name C or nam \ e O or name CB )) or resid 313 through 317 or (resid 318 through 320 and (name N \ or name CA or name C or name O or name CB )) or resid 321 through 341 or (resid \ 342 and (name N or name CA or name C or name O or name CB )) or resid 343 throu \ gh 352 or (resid 353 and (name N or name CA or name C or name O or name CB )) or \ resid 354 through 358 or (resid 359 and (name N or name CA or name C or name O \ or name CB )) or resid 360 through 367 or (resid 368 and (name N or name CA or n \ ame C or name O or name CB )) or resid 369 through 374 or (resid 375 and (name N \ or name CA or name C or name O or name CB )) or resid 376 through 383 or (resid \ 384 and (name N or name CA or name C or name O or name CB )) or resid 385 throu \ gh 390 or (resid 391 through 392 and (name N or name CA or name C or name O or n \ ame CB )) or resid 393 through 394 or (resid 395 and (name N or name CA or name \ C or name O or name CB )) or resid 396 or (resid 397 through 398 and (name N or \ name CA or name C or name O or name CB )) or resid 399 or (resid 400 through 401 \ and (name N or name CA or name C or name O or name CB )) or resid 402 through 4 \ 07 or (resid 408 through 410 and (name N or name CA or name C or name O or name \ CB )) or resid 411 through 413 or (resid 414 and (name N or name CA or name C or \ name O or name CB )) or resid 415 through 436 or (resid 437 and (name N or name \ CA or name C or name O or name CB )) or resid 438 through 443 or (resid 444 and \ (name N or name CA or name C or name O or name CB )) or resid 445 or (resid 446 \ through 448 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 49 through 460 or (resid 461 through 462 and (name N or name CA or name C or nam \ e O or name CB )) or resid 463 through 466 or (resid 467 and (name N or name CA \ or name C or name O or name CB )) or resid 468 through 483 or resid 490 through \ 501 or (resid 502 and (name N or name CA or name C or name O or name CB )) or re \ sid 519 through 520 or (resid 521 and (name N or name CA or name C or name O or \ name CB )) or resid 522 through 591 or (resid 592 and (name N or name CA or name \ C or name O or name CB )) or resid 593 through 608 or (resid 609 and (name N or \ name CA or name C or name O or name CB )) or resid 610 or (resid 611 through 61 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 613 through \ 633 or (resid 634 and (name N or name CA or name C or name O or name CB )) or re \ sid 635 through 641 or (resid 642 through 646 and (name N or name CA or name C o \ r name O or name CB )) or resid 647 or (resid 648 and (name N or name CA or name \ C or name O or name CB )) or resid 649 through 657 or (resid 658 through 661 an \ d (name N or name CA or name C or name O or name CB )) or resid 662 through 665 \ or (resid 666 and (name N or name CA or name C or name O or name CB )) or resid \ 667 through 672 or (resid 673 and (name N or name CA or name C or name O or name \ CB )) or resid 674 through 677 or (resid 678 through 680 and (name N or name CA \ or name C or name O or name CB )) or resid 681 through 690 or (resid 691 and (n \ ame N or name CA or name C or name O or name CB )) or resid 692 through 699 or ( \ resid 700 and (name N or name CA or name C or name O or name CB )) or resid 701 \ through 712 or (resid 713 and (name N or name CA or name C or name O or name CB \ )) or resid 714 through 728 or (resid 729 and (name N or name CA or name C or na \ me O or name CB )) or resid 730 through 734 or (resid 735 and (name N or name CA \ or name C or name O or name CB )) or resid 736 through 743 or (resid 744 throug \ h 745 and (name N or name CA or name C or name O or name CB )) or resid 746 thro \ ugh 762 or (resid 763 through 765 and (name N or name CA or name C or name O or \ name CB )) or resid 766 through 769 or (resid 770 and (name N or name CA or name \ C or name O or name CB )) or resid 771 through 775 or (resid 776 through 778 an \ d (name N or name CA or name C or name O or name CB )) or resid 779 through 790 \ or (resid 791 and (name N or name CA or name C or name O or name CB )) or resid \ 792 through 808 or (resid 809 through 810 and (name N or name CA or name C or na \ me O or name CB )) or resid 811 through 836 or (resid 837 and (name N or name CA \ or name C or name O or name CB )) or resid 838 through 853 or (resid 854 and (n \ ame N or name CA or name C or name O or name CB )) or resid 855 or (resid 856 an \ d (name N or name CA or name C or name O or name CB )) or resid 857 through 858 \ or (resid 859 through 863 and (name N or name CA or name C or name O or name CB \ )) or resid 864 through 874 or (resid 875 through 876 and (name N or name CA or \ name C or name O or name CB )) or resid 877 through 883 or (resid 884 and (name \ N or name CA or name C or name O or name CB )) or resid 885 through 893 or (resi \ d 894 and (name N or name CA or name C or name O or name CB )) or resid 895 thro \ ugh 902 or (resid 903 through 904 and (name N or name CA or name C or name O or \ name CB )) or resid 905 through 929 or (resid 930 through 935 and (name N or nam \ e CA or name C or name O or name CB )) or resid 936 or (resid 937 and (name N or \ name CA or name C or name O or name CB )) or resid 938 through 958 or (resid 95 \ 9 through 963 and (name N or name CA or name C or name O or name CB )) or resid \ 964 through 985 or (resid 986 and (name N or name CA or name C or name O or name \ CB )) or resid 987 or (resid 988 and (name N or name CA or name C or name O or \ name CB )) or resid 989 through 991 or (resid 992 through 994 and (name N or nam \ e CA or name C or name O or name CB )) or resid 995 through 997 or (resid 998 th \ rough 1008 and (name N or name CA or name C or name O or name CB )) or resid 100 \ 9 through 1012 or (resid 1013 and (name N or name CA or name C or name O or name \ CB )) or resid 1014 through 1037 or (resid 1038 through 1039 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1040 through 1049 or (resid 1050 \ and (name N or name CA or name C or name O or name CB )) or resid 1051 through \ 1055 or (resid 1056 and (name N or name CA or name C or name O or name CB )) or \ resid 1057 through 1061 or (resid 1062 and (name N or name CA or name C or name \ O or name CB )) or resid 1063 or (resid 1064 and (name N or name CA or name C or \ name O or name CB )) or resid 1065 through 1072 or (resid 1073 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1074 through 1075 or (resid 10 \ 76 and (name N or name CA or name C or name O or name CB )) or resid 1077 throug \ h 1116 or (resid 1117 and (name N or name CA or name C or name O or name CB )) o \ r resid 1118 through 1125 or (resid 1126 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1127 through 1128 or (resid 1129 through 1130 and (na \ me N or name CA or name C or name O or name CB )) or resid 1131 through 1144 or \ (resid 1145 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 46 through 1150 or (resid 1151 through 1155 and (name N or name CA or name C or \ name O or name CB )) or resid 1156 through 1161 or (resid 1162 and (name N or na \ me CA or name C or name O or name CB )) or resid 1163 through 1167 or (resid 116 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 1169 through \ 1191 or (resid 1192 and (name N or name CA or name C or name O or name CB )) or \ resid 1193 through 1196 or (resid 1197 and (name N or name CA or name C or name \ O or name CB )) or resid 1198 through 1204 or (resid 1205 and (name N or name C \ A or name C or name O or name CB )) or resid 1206 through 1217 or (resid 1218 an \ d (name N or name CA or name C or name O or name CB )) or resid 1219 through 130 \ 4)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.580 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27329 Z= 0.097 Angle : 0.434 6.351 37389 Z= 0.230 Chirality : 0.041 0.149 4322 Planarity : 0.003 0.036 4821 Dihedral : 8.473 89.377 9600 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.45 % Allowed : 6.48 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % 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 aren not related in a simple way. whole: -3.40 (0.12), residues: 3506 helix: -1.12 (0.19), residues: 632 sheet: -1.99 (0.22), residues: 519 loop : -2.84 (0.11), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.009 0.001 TYR A1148 PHE 0.006 0.001 PHE A 681 TRP 0.012 0.001 TRP C 344 HIS 0.001 0.000 HIS C 799 Details of bonding type rmsd covalent geometry : bond 0.00190 (27247) covalent geometry : angle 0.43307 (37209) SS BOND : bond 0.00093 ( 66) SS BOND : angle 0.47318 ( 132) hydrogen bonds : bond 0.23133 ( 646) hydrogen bonds : angle 8.14034 ( 1794) link_NAG-ASN : bond 0.00229 ( 16) link_NAG-ASN : angle 0.92915 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 539 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 291 GLN cc_start: 0.7353 (mt0) cc_final: 0.7122 (mt0) REVERT: C 323 ASN cc_start: 0.8181 (p0) cc_final: 0.7751 (p0) REVERT: C 641 TYR cc_start: 0.7227 (m-80) cc_final: 0.6935 (m-10) REVERT: C 658 PHE cc_start: 0.6755 (p90) cc_final: 0.6373 (p90) REVERT: C 676 ARG cc_start: 0.6436 (mmm-85) cc_final: 0.5952 (mmt90) REVERT: C 716 TYR cc_start: 0.7887 (t80) cc_final: 0.6273 (t80) REVERT: C 845 GLU cc_start: 0.6606 (tm-30) cc_final: 0.6289 (tm-30) REVERT: C 870 ASN cc_start: 0.6715 (m-40) cc_final: 0.6483 (m110) REVERT: C 906 LEU cc_start: 0.7877 (tp) cc_final: 0.7660 (tt) REVERT: C 936 CYS cc_start: 0.7466 (t) cc_final: 0.6981 (t) REVERT: C 952 GLU cc_start: 0.6853 (tp30) cc_final: 0.6554 (tp30) REVERT: C 979 PHE cc_start: 0.5001 (OUTLIER) cc_final: 0.2025 (t80) REVERT: C 1026 LEU cc_start: 0.6547 (tp) cc_final: 0.6294 (mp) REVERT: B 187 LYS cc_start: 0.6053 (ptpp) cc_final: 0.5166 (ptpp) REVERT: B 691 LEU cc_start: 0.7324 (tp) cc_final: 0.6952 (pp) REVERT: B 740 SER cc_start: 0.8084 (t) cc_final: 0.7882 (t) REVERT: B 813 ASP cc_start: 0.6082 (t0) cc_final: 0.5841 (t0) REVERT: B 850 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7453 (mt) REVERT: B 949 ILE cc_start: 0.7982 (pt) cc_final: 0.7563 (mm) REVERT: B 1028 LYS cc_start: 0.7406 (ttmt) cc_final: 0.7183 (ttmt) REVERT: B 1091 GLN cc_start: 0.6930 (mm-40) cc_final: 0.6628 (mm-40) REVERT: B 1093 LEU cc_start: 0.8199 (mt) cc_final: 0.7736 (mp) REVERT: A 427 TYR cc_start: 0.5997 (p90) cc_final: 0.5792 (p90) REVERT: A 553 GLU cc_start: 0.4485 (OUTLIER) cc_final: 0.4044 (pp20) REVERT: A 582 SER cc_start: 0.7940 (m) cc_final: 0.7587 (p) REVERT: A 700 VAL cc_start: 0.8138 (m) cc_final: 0.7756 (p) REVERT: A 845 GLU cc_start: 0.7052 (tt0) cc_final: 0.6818 (tt0) REVERT: A 856 GLN cc_start: 0.7357 (tt0) cc_final: 0.7077 (tt0) REVERT: A 871 LEU cc_start: 0.7765 (tp) cc_final: 0.7560 (tp) REVERT: A 884 PHE cc_start: 0.5745 (OUTLIER) cc_final: 0.5397 (t80) REVERT: A 906 LEU cc_start: 0.8571 (mp) cc_final: 0.7889 (tt) REVERT: A 920 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6913 (mm-30) REVERT: A 952 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6477 (mp0) REVERT: A 1008 PHE cc_start: 0.6775 (m-80) cc_final: 0.6279 (m-80) REVERT: A 1012 LEU cc_start: 0.8051 (pt) cc_final: 0.7723 (pp) REVERT: A 1030 GLN cc_start: 0.7405 (mm-40) cc_final: 0.7020 (mm-40) REVERT: A 1038 GLN cc_start: 0.7350 (pp30) cc_final: 0.7106 (pp30) REVERT: A 1060 GLU cc_start: 0.7140 (tt0) cc_final: 0.5650 (tt0) REVERT: A 1061 ILE cc_start: 0.7987 (pt) cc_final: 0.7773 (pt) REVERT: A 1085 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8309 (tp) REVERT: A 1100 LYS cc_start: 0.7764 (mmmt) cc_final: 0.7544 (tppt) REVERT: A 1144 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7661 (pt) outliers start: 70 outliers final: 29 residues processed: 594 average time/residue: 0.1706 time to fit residues: 163.2046 Evaluate side-chains 472 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 436 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 814 CYS Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 979 PHE Chi-restraints excluded: chain C residue 1191 TYR Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1144 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0070 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN C 371 ASN C 605 ASN C 709 GLN ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN C1001 GLN C1174 GLN C1211 ASN B 26 ASN B 152 GLN B 291 GLN B 355 ASN B 413 ASN B 709 GLN B 847 ASN B 870 ASN B 874 ASN B1009 ASN B1030 GLN B1117 GLN B1126 ASN B1181 ASN B1201 ASN A 201 HIS A 204 GLN A 343 ASN A 694 ASN A 826 HIS A 847 ASN A 854 GLN A 923 ASN A 954 GLN A1046 GLN A1079 ASN A1180 GLN A1211 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.210874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.173146 restraints weight = 58921.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.178587 restraints weight = 34455.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.180390 restraints weight = 20124.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.181877 restraints weight = 15971.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.181825 restraints weight = 15021.426| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27329 Z= 0.135 Angle : 0.552 10.968 37389 Z= 0.289 Chirality : 0.044 0.215 4322 Planarity : 0.004 0.057 4821 Dihedral : 5.768 58.203 4160 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.29 % Allowed : 11.31 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % 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 aren not related in a simple way. whole: -2.78 (0.13), residues: 3506 helix: -0.34 (0.20), residues: 662 sheet: -1.53 (0.22), residues: 556 loop : -2.55 (0.12), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 676 TYR 0.029 0.001 TYR C1148 PHE 0.032 0.001 PHE A 379 TRP 0.026 0.001 TRP A 971 HIS 0.010 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00284 (27247) covalent geometry : angle 0.54730 (37209) SS BOND : bond 0.00462 ( 66) SS BOND : angle 1.14767 ( 132) hydrogen bonds : bond 0.03932 ( 646) hydrogen bonds : angle 5.99506 ( 1794) link_NAG-ASN : bond 0.00294 ( 16) link_NAG-ASN : angle 1.31797 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 462 time to evaluate : 0.782 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 323 ASN cc_start: 0.8356 (p0) cc_final: 0.7970 (p0) REVERT: C 635 GLU cc_start: 0.7218 (tp30) cc_final: 0.6804 (tm-30) REVERT: C 641 TYR cc_start: 0.7309 (m-80) cc_final: 0.6536 (m-80) REVERT: C 674 SER cc_start: 0.8190 (m) cc_final: 0.7709 (p) REVERT: C 845 GLU cc_start: 0.6700 (tm-30) cc_final: 0.6399 (tm-30) REVERT: C 870 ASN cc_start: 0.6943 (m-40) cc_final: 0.6734 (m110) REVERT: C 879 VAL cc_start: 0.5896 (OUTLIER) cc_final: 0.5630 (t) REVERT: C 906 LEU cc_start: 0.7948 (tp) cc_final: 0.7720 (tt) REVERT: C 936 CYS cc_start: 0.7628 (t) cc_final: 0.7286 (t) REVERT: C 952 GLU cc_start: 0.7164 (tp30) cc_final: 0.6752 (tp30) REVERT: C 979 PHE cc_start: 0.4967 (OUTLIER) cc_final: 0.1762 (t80) REVERT: C 1135 GLN cc_start: 0.7394 (tp40) cc_final: 0.6730 (mm-40) REVERT: B 155 MET cc_start: 0.6130 (mmm) cc_final: 0.5904 (mmm) REVERT: B 187 LYS cc_start: 0.6354 (ptpp) cc_final: 0.5624 (mttt) REVERT: B 206 ARG cc_start: 0.7682 (ttm-80) cc_final: 0.7195 (mtt90) REVERT: B 289 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6752 (mm-30) REVERT: B 676 ARG cc_start: 0.7014 (ttm170) cc_final: 0.6186 (ttm170) REVERT: B 691 LEU cc_start: 0.7519 (tp) cc_final: 0.7188 (pp) REVERT: B 740 SER cc_start: 0.8319 (t) cc_final: 0.8044 (t) REVERT: B 838 ASN cc_start: 0.7576 (t0) cc_final: 0.7280 (m-40) REVERT: B 850 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7370 (mt) REVERT: B 949 ILE cc_start: 0.8087 (pt) cc_final: 0.7642 (mm) REVERT: B 1091 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6751 (mm-40) REVERT: B 1096 ILE cc_start: 0.8175 (tp) cc_final: 0.7962 (mm) REVERT: A 28 TYR cc_start: 0.7504 (t80) cc_final: 0.7135 (t80) REVERT: A 289 GLU cc_start: 0.5948 (pp20) cc_final: 0.5717 (pp20) REVERT: A 332 TRP cc_start: 0.6964 (t-100) cc_final: 0.6713 (t-100) REVERT: A 582 SER cc_start: 0.8117 (m) cc_final: 0.7742 (p) REVERT: A 700 VAL cc_start: 0.8440 (m) cc_final: 0.8062 (p) REVERT: A 856 GLN cc_start: 0.7439 (tt0) cc_final: 0.7198 (tt0) REVERT: A 884 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.5557 (t80) REVERT: A 906 LEU cc_start: 0.8542 (mp) cc_final: 0.7667 (tt) REVERT: A 920 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7112 (mm-30) REVERT: A 952 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: A 1008 PHE cc_start: 0.6893 (m-80) cc_final: 0.6387 (m-80) REVERT: A 1012 LEU cc_start: 0.8117 (pt) cc_final: 0.7638 (pp) REVERT: A 1060 GLU cc_start: 0.7092 (tt0) cc_final: 0.6761 (tt0) REVERT: A 1076 ARG cc_start: 0.6816 (tpp80) cc_final: 0.6581 (tpp80) REVERT: A 1085 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8300 (tp) outliers start: 94 outliers final: 60 residues processed: 530 average time/residue: 0.1563 time to fit residues: 133.1477 Evaluate side-chains 494 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 428 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 814 CYS Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 979 PHE Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1191 TYR Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1128 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 83 optimal weight: 10.0000 chunk 230 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 254 optimal weight: 9.9990 chunk 222 optimal weight: 1.9990 chunk 280 optimal weight: 0.1980 chunk 50 optimal weight: 40.0000 chunk 225 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 HIS B1201 ASN A 201 HIS A 483 ASN A 923 ASN A1079 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.210123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.172582 restraints weight = 58163.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.177662 restraints weight = 33700.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.180323 restraints weight = 19469.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.181013 restraints weight = 14778.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.181139 restraints weight = 14133.962| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27329 Z= 0.138 Angle : 0.544 9.363 37389 Z= 0.284 Chirality : 0.043 0.209 4322 Planarity : 0.004 0.052 4821 Dihedral : 5.605 58.294 4146 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.61 % Allowed : 12.64 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % 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 aren not related in a simple way. whole: -2.62 (0.14), residues: 3506 helix: -0.12 (0.21), residues: 663 sheet: -1.52 (0.21), residues: 589 loop : -2.45 (0.12), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 763 TYR 0.032 0.001 TYR C1148 PHE 0.025 0.001 PHE A 224 TRP 0.022 0.001 TRP B 332 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00294 (27247) covalent geometry : angle 0.53971 (37209) SS BOND : bond 0.00535 ( 66) SS BOND : angle 1.06272 ( 132) hydrogen bonds : bond 0.03776 ( 646) hydrogen bonds : angle 5.62130 ( 1794) link_NAG-ASN : bond 0.00314 ( 16) link_NAG-ASN : angle 1.40325 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 444 time to evaluate : 0.659 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 323 ASN cc_start: 0.8335 (p0) cc_final: 0.7967 (p0) REVERT: C 622 TYR cc_start: 0.7212 (p90) cc_final: 0.6913 (p90) REVERT: C 674 SER cc_start: 0.8221 (m) cc_final: 0.7792 (p) REVERT: C 813 ASP cc_start: 0.6747 (m-30) cc_final: 0.6546 (t70) REVERT: C 845 GLU cc_start: 0.6734 (tm-30) cc_final: 0.6452 (tm-30) REVERT: C 870 ASN cc_start: 0.7011 (m-40) cc_final: 0.6806 (m110) REVERT: C 936 CYS cc_start: 0.7641 (t) cc_final: 0.7336 (t) REVERT: C 952 GLU cc_start: 0.7169 (tp30) cc_final: 0.6804 (tp30) REVERT: C 979 PHE cc_start: 0.4987 (OUTLIER) cc_final: 0.1731 (t80) REVERT: C 1131 LEU cc_start: 0.7280 (pt) cc_final: 0.6932 (pt) REVERT: C 1135 GLN cc_start: 0.7570 (tp40) cc_final: 0.6993 (mm-40) REVERT: B 155 MET cc_start: 0.6242 (mmm) cc_final: 0.5968 (mmm) REVERT: B 187 LYS cc_start: 0.6483 (ptpp) cc_final: 0.5564 (mtmt) REVERT: B 206 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7230 (mtt-85) REVERT: B 289 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6786 (mm-30) REVERT: B 691 LEU cc_start: 0.7518 (tp) cc_final: 0.7124 (pp) REVERT: B 694 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8322 (p0) REVERT: B 740 SER cc_start: 0.8350 (t) cc_final: 0.8102 (t) REVERT: B 813 ASP cc_start: 0.6005 (t0) cc_final: 0.5764 (m-30) REVERT: B 838 ASN cc_start: 0.7659 (t0) cc_final: 0.7308 (m-40) REVERT: B 850 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7382 (mt) REVERT: B 949 ILE cc_start: 0.8117 (pt) cc_final: 0.7689 (mm) REVERT: B 1091 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6836 (mm-40) REVERT: B 1096 ILE cc_start: 0.8185 (tp) cc_final: 0.7967 (mm) REVERT: A 28 TYR cc_start: 0.7502 (t80) cc_final: 0.7176 (t80) REVERT: A 201 HIS cc_start: 0.5757 (m-70) cc_final: 0.5389 (m-70) REVERT: A 289 GLU cc_start: 0.6073 (pp20) cc_final: 0.5852 (pp20) REVERT: A 332 TRP cc_start: 0.7009 (t-100) cc_final: 0.6722 (t-100) REVERT: A 358 THR cc_start: 0.8405 (m) cc_final: 0.8092 (t) REVERT: A 582 SER cc_start: 0.8173 (m) cc_final: 0.7775 (p) REVERT: A 590 SER cc_start: 0.7871 (t) cc_final: 0.7553 (p) REVERT: A 681 PHE cc_start: 0.6443 (t80) cc_final: 0.6163 (t80) REVERT: A 700 VAL cc_start: 0.8451 (m) cc_final: 0.8062 (p) REVERT: A 763 ARG cc_start: 0.6875 (mtm-85) cc_final: 0.6490 (mtt90) REVERT: A 794 PHE cc_start: 0.5169 (p90) cc_final: 0.4806 (p90) REVERT: A 820 SER cc_start: 0.6957 (t) cc_final: 0.6394 (p) REVERT: A 884 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.5616 (t80) REVERT: A 904 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6806 (mt-10) REVERT: A 906 LEU cc_start: 0.8440 (mp) cc_final: 0.8020 (tt) REVERT: A 920 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7144 (mm-30) REVERT: A 952 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6580 (mp0) REVERT: A 958 TYR cc_start: 0.8099 (m-10) cc_final: 0.7897 (m-10) REVERT: A 1012 LEU cc_start: 0.8122 (pt) cc_final: 0.7870 (pp) REVERT: A 1085 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8368 (tp) outliers start: 103 outliers final: 66 residues processed: 516 average time/residue: 0.1482 time to fit residues: 123.0767 Evaluate side-chains 498 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 426 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 814 CYS Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 979 PHE Chi-restraints excluded: chain C residue 1057 SER Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain C residue 1191 TYR Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 694 ASN Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1132 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 103 optimal weight: 0.4980 chunk 67 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 304 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 274 optimal weight: 3.9990 chunk 221 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 51 optimal weight: 40.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN B1201 ASN A 642 ASN A 923 ASN A1079 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.210420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.172970 restraints weight = 58367.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.177533 restraints weight = 33436.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.180892 restraints weight = 20716.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.180618 restraints weight = 16597.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.180628 restraints weight = 16938.029| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27329 Z= 0.117 Angle : 0.536 11.117 37389 Z= 0.276 Chirality : 0.043 0.206 4322 Planarity : 0.004 0.050 4821 Dihedral : 5.483 57.909 4142 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.71 % Allowed : 13.52 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % 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 aren not related in a simple way. whole: -2.44 (0.14), residues: 3506 helix: 0.05 (0.21), residues: 663 sheet: -1.54 (0.21), residues: 598 loop : -2.29 (0.13), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1076 TYR 0.030 0.001 TYR C1148 PHE 0.031 0.001 PHE A 224 TRP 0.026 0.001 TRP A 971 HIS 0.005 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00248 (27247) covalent geometry : angle 0.53155 (37209) SS BOND : bond 0.00455 ( 66) SS BOND : angle 0.98794 ( 132) hydrogen bonds : bond 0.03388 ( 646) hydrogen bonds : angle 5.39241 ( 1794) link_NAG-ASN : bond 0.00257 ( 16) link_NAG-ASN : angle 1.37921 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 434 time to evaluate : 0.983 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 202 PHE cc_start: 0.6415 (p90) cc_final: 0.6108 (p90) REVERT: C 323 ASN cc_start: 0.8318 (p0) cc_final: 0.7937 (p0) REVERT: C 622 TYR cc_start: 0.7282 (p90) cc_final: 0.6904 (p90) REVERT: C 674 SER cc_start: 0.8155 (m) cc_final: 0.7774 (p) REVERT: C 813 ASP cc_start: 0.6781 (m-30) cc_final: 0.6504 (m-30) REVERT: C 845 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6352 (tm-30) REVERT: C 870 ASN cc_start: 0.6952 (m-40) cc_final: 0.6695 (m110) REVERT: C 882 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.7017 (mp) REVERT: C 936 CYS cc_start: 0.7703 (t) cc_final: 0.7418 (t) REVERT: C 952 GLU cc_start: 0.7169 (tp30) cc_final: 0.6747 (tp30) REVERT: C 979 PHE cc_start: 0.5027 (OUTLIER) cc_final: 0.1741 (t80) REVERT: C 1028 LYS cc_start: 0.7684 (mtmt) cc_final: 0.7477 (mtmt) REVERT: C 1131 LEU cc_start: 0.7289 (pt) cc_final: 0.6918 (pt) REVERT: C 1135 GLN cc_start: 0.7600 (tp40) cc_final: 0.7117 (mm-40) REVERT: B 151 CYS cc_start: 0.5251 (m) cc_final: 0.4926 (m) REVERT: B 187 LYS cc_start: 0.6490 (ptpp) cc_final: 0.5150 (ptpp) REVERT: B 206 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7323 (mtt-85) REVERT: B 289 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6844 (mm-30) REVERT: B 691 LEU cc_start: 0.7498 (tp) cc_final: 0.7134 (pp) REVERT: B 740 SER cc_start: 0.8408 (t) cc_final: 0.8183 (t) REVERT: B 813 ASP cc_start: 0.6047 (t0) cc_final: 0.5783 (m-30) REVERT: B 850 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7421 (mt) REVERT: B 1009 ASN cc_start: 0.7239 (m-40) cc_final: 0.7016 (m-40) REVERT: B 1091 GLN cc_start: 0.7105 (mm-40) cc_final: 0.6834 (mm-40) REVERT: B 1093 LEU cc_start: 0.8347 (mt) cc_final: 0.7944 (mp) REVERT: B 1185 MET cc_start: 0.2789 (OUTLIER) cc_final: 0.2548 (tmm) REVERT: A 28 TYR cc_start: 0.7552 (t80) cc_final: 0.7213 (t80) REVERT: A 201 HIS cc_start: 0.5778 (m-70) cc_final: 0.5454 (m-70) REVERT: A 289 GLU cc_start: 0.6241 (pp20) cc_final: 0.6009 (pp20) REVERT: A 358 THR cc_start: 0.8408 (m) cc_final: 0.8108 (t) REVERT: A 582 SER cc_start: 0.8200 (m) cc_final: 0.7797 (p) REVERT: A 681 PHE cc_start: 0.6505 (t80) cc_final: 0.6256 (t80) REVERT: A 700 VAL cc_start: 0.8454 (m) cc_final: 0.8047 (p) REVERT: A 820 SER cc_start: 0.7080 (t) cc_final: 0.6847 (t) REVERT: A 884 PHE cc_start: 0.6024 (OUTLIER) cc_final: 0.5702 (t80) REVERT: A 906 LEU cc_start: 0.8506 (mp) cc_final: 0.7822 (tt) REVERT: A 920 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7190 (mm-30) REVERT: A 952 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: A 1012 LEU cc_start: 0.8111 (pt) cc_final: 0.7826 (pp) REVERT: A 1030 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7299 (mm-40) REVERT: A 1085 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8395 (tp) outliers start: 106 outliers final: 79 residues processed: 510 average time/residue: 0.1684 time to fit residues: 138.0838 Evaluate side-chains 513 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 427 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 746 TYR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 814 CYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 979 PHE Chi-restraints excluded: chain C residue 994 MET Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain C residue 1191 TYR Chi-restraints excluded: chain C residue 1197 ILE Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 940 PHE Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1176 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 225 optimal weight: 0.0770 chunk 156 optimal weight: 0.9990 chunk 325 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 94 optimal weight: 0.0470 chunk 15 optimal weight: 30.0000 chunk 200 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS A 923 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.209586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.172114 restraints weight = 58235.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.176904 restraints weight = 33540.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.180365 restraints weight = 19698.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.179873 restraints weight = 16346.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.180474 restraints weight = 15600.207| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27329 Z= 0.103 Angle : 0.531 10.886 37389 Z= 0.271 Chirality : 0.043 0.254 4322 Planarity : 0.004 0.052 4821 Dihedral : 5.360 57.327 4142 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.64 % Allowed : 14.19 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % 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 aren not related in a simple way. whole: -2.29 (0.14), residues: 3506 helix: 0.22 (0.21), residues: 657 sheet: -1.41 (0.21), residues: 602 loop : -2.22 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 54 TYR 0.028 0.001 TYR C1148 PHE 0.032 0.001 PHE A 224 TRP 0.031 0.001 TRP B 332 HIS 0.005 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00226 (27247) covalent geometry : angle 0.52752 (37209) SS BOND : bond 0.00313 ( 66) SS BOND : angle 0.89869 ( 132) hydrogen bonds : bond 0.03210 ( 646) hydrogen bonds : angle 5.23474 ( 1794) link_NAG-ASN : bond 0.00285 ( 16) link_NAG-ASN : angle 1.31244 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 433 time to evaluate : 0.919 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 319 ARG cc_start: 0.7462 (mmt-90) cc_final: 0.7137 (mmt180) REVERT: C 323 ASN cc_start: 0.8279 (p0) cc_final: 0.7914 (p0) REVERT: C 674 SER cc_start: 0.8132 (m) cc_final: 0.7743 (p) REVERT: C 813 ASP cc_start: 0.6727 (m-30) cc_final: 0.6433 (m-30) REVERT: C 845 GLU cc_start: 0.6649 (tm-30) cc_final: 0.6358 (tm-30) REVERT: C 870 ASN cc_start: 0.6982 (m-40) cc_final: 0.6741 (m110) REVERT: C 882 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.7001 (mp) REVERT: C 952 GLU cc_start: 0.7175 (tp30) cc_final: 0.6757 (tp30) REVERT: C 979 PHE cc_start: 0.4928 (OUTLIER) cc_final: 0.1771 (t80) REVERT: C 1028 LYS cc_start: 0.7707 (mtmt) cc_final: 0.7466 (mtmm) REVERT: C 1076 ARG cc_start: 0.7770 (mtm110) cc_final: 0.7559 (mtp-110) REVERT: C 1130 ILE cc_start: 0.6926 (mp) cc_final: 0.6580 (mm) REVERT: C 1131 LEU cc_start: 0.7289 (pt) cc_final: 0.6912 (pt) REVERT: C 1135 GLN cc_start: 0.7607 (tp40) cc_final: 0.6951 (mm-40) REVERT: B 187 LYS cc_start: 0.6475 (ptpp) cc_final: 0.5105 (ptpp) REVERT: B 206 ARG cc_start: 0.7596 (ttm-80) cc_final: 0.7223 (mtt90) REVERT: B 289 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6846 (mm-30) REVERT: B 656 ILE cc_start: 0.5670 (mm) cc_final: 0.5409 (mm) REVERT: B 691 LEU cc_start: 0.7479 (tp) cc_final: 0.7112 (pp) REVERT: B 740 SER cc_start: 0.8379 (t) cc_final: 0.8143 (t) REVERT: B 813 ASP cc_start: 0.6075 (t0) cc_final: 0.5826 (m-30) REVERT: B 850 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7463 (mt) REVERT: B 949 ILE cc_start: 0.8132 (pt) cc_final: 0.7753 (mm) REVERT: B 1009 ASN cc_start: 0.7268 (m-40) cc_final: 0.7061 (m-40) REVERT: B 1091 GLN cc_start: 0.7149 (mm-40) cc_final: 0.6905 (mm-40) REVERT: B 1093 LEU cc_start: 0.8339 (mt) cc_final: 0.7919 (mp) REVERT: B 1185 MET cc_start: 0.2505 (OUTLIER) cc_final: 0.2037 (tmm) REVERT: A 28 TYR cc_start: 0.7487 (t80) cc_final: 0.7164 (t80) REVERT: A 201 HIS cc_start: 0.5751 (m-70) cc_final: 0.5450 (m-70) REVERT: A 289 GLU cc_start: 0.6349 (pp20) cc_final: 0.6106 (pp20) REVERT: A 358 THR cc_start: 0.8409 (m) cc_final: 0.8119 (t) REVERT: A 582 SER cc_start: 0.8183 (m) cc_final: 0.7788 (p) REVERT: A 681 PHE cc_start: 0.6508 (t80) cc_final: 0.6293 (t80) REVERT: A 700 VAL cc_start: 0.8458 (m) cc_final: 0.8056 (p) REVERT: A 794 PHE cc_start: 0.5098 (p90) cc_final: 0.4211 (p90) REVERT: A 822 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.6049 (m-80) REVERT: A 884 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.5716 (t80) REVERT: A 906 LEU cc_start: 0.8393 (mp) cc_final: 0.7729 (tt) REVERT: A 920 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7189 (mm-30) REVERT: A 952 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: A 1012 LEU cc_start: 0.8144 (pt) cc_final: 0.7872 (pp) REVERT: A 1030 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7447 (mm-40) REVERT: A 1059 GLN cc_start: 0.8059 (mm110) cc_final: 0.7622 (mm110) REVERT: A 1060 GLU cc_start: 0.7342 (tt0) cc_final: 0.6949 (tt0) REVERT: A 1085 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8412 (tp) outliers start: 104 outliers final: 81 residues processed: 504 average time/residue: 0.1614 time to fit residues: 131.8650 Evaluate side-chains 508 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 419 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 814 CYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 979 PHE Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain C residue 1191 TYR Chi-restraints excluded: chain C residue 1197 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 940 PHE Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 979 PHE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1045 GLN Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1176 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 156 optimal weight: 0.0670 chunk 22 optimal weight: 6.9990 chunk 111 optimal weight: 0.1980 chunk 254 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 324 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 overall best weight: 1.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 ASN C 694 ASN ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 ASN B1201 ASN A 595 ASN ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 ASN ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 ASN A1136 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.204969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.166770 restraints weight = 57612.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.172838 restraints weight = 33945.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.174177 restraints weight = 19127.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.175275 restraints weight = 15318.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.175501 restraints weight = 14522.184| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27329 Z= 0.231 Angle : 0.666 11.672 37389 Z= 0.350 Chirality : 0.047 0.266 4322 Planarity : 0.005 0.058 4821 Dihedral : 6.060 58.078 4142 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 4.45 % Allowed : 13.98 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % 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 aren not related in a simple way. whole: -2.61 (0.14), residues: 3506 helix: -0.30 (0.20), residues: 647 sheet: -1.64 (0.22), residues: 567 loop : -2.32 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 693 TYR 0.027 0.002 TYR B 958 PHE 0.037 0.002 PHE B 764 TRP 0.037 0.002 TRP A 344 HIS 0.009 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00484 (27247) covalent geometry : angle 0.65975 (37209) SS BOND : bond 0.00527 ( 66) SS BOND : angle 1.13152 ( 132) hydrogen bonds : bond 0.04517 ( 646) hydrogen bonds : angle 5.67246 ( 1794) link_NAG-ASN : bond 0.00463 ( 16) link_NAG-ASN : angle 2.11605 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 445 time to evaluate : 0.977 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 215 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6556 (p0) REVERT: C 323 ASN cc_start: 0.8380 (p0) cc_final: 0.8061 (p0) REVERT: C 674 SER cc_start: 0.8203 (m) cc_final: 0.7884 (p) REVERT: C 855 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6481 (mt) REVERT: C 882 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.7047 (mp) REVERT: C 952 GLU cc_start: 0.7221 (tp30) cc_final: 0.6801 (tp30) REVERT: C 979 PHE cc_start: 0.5048 (OUTLIER) cc_final: 0.2184 (t80) REVERT: C 1028 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7758 (mtmm) REVERT: C 1076 ARG cc_start: 0.7868 (mtm110) cc_final: 0.7458 (mtm110) REVERT: C 1096 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8119 (mm) REVERT: C 1135 GLN cc_start: 0.7626 (tp40) cc_final: 0.7002 (mm-40) REVERT: B 187 LYS cc_start: 0.6785 (ptpp) cc_final: 0.5663 (ptpp) REVERT: B 289 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6880 (mm-30) REVERT: B 768 GLU cc_start: 0.5972 (tm-30) cc_final: 0.5714 (tm-30) REVERT: B 813 ASP cc_start: 0.6170 (t0) cc_final: 0.5922 (m-30) REVERT: B 827 ASP cc_start: 0.7109 (m-30) cc_final: 0.6797 (m-30) REVERT: B 850 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7397 (mt) REVERT: B 1093 LEU cc_start: 0.8414 (mt) cc_final: 0.8051 (mp) REVERT: B 1096 ILE cc_start: 0.8281 (tp) cc_final: 0.8073 (mm) REVERT: A 28 TYR cc_start: 0.7692 (t80) cc_final: 0.7367 (t80) REVERT: A 201 HIS cc_start: 0.5695 (m-70) cc_final: 0.5461 (m-70) REVERT: A 289 GLU cc_start: 0.6579 (pp20) cc_final: 0.6348 (pp20) REVERT: A 427 TYR cc_start: 0.6288 (p90) cc_final: 0.5973 (p90) REVERT: A 582 SER cc_start: 0.8324 (m) cc_final: 0.7911 (p) REVERT: A 625 TYR cc_start: 0.6460 (m-80) cc_final: 0.5782 (m-80) REVERT: A 662 LEU cc_start: 0.8224 (mt) cc_final: 0.7850 (pt) REVERT: A 794 PHE cc_start: 0.5113 (p90) cc_final: 0.4022 (p90) REVERT: A 822 TYR cc_start: 0.6342 (m-80) cc_final: 0.6023 (m-80) REVERT: A 832 TYR cc_start: 0.7045 (m-80) cc_final: 0.6821 (m-80) REVERT: A 879 VAL cc_start: 0.7900 (m) cc_final: 0.7659 (t) REVERT: A 884 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.5755 (t80) REVERT: A 904 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6263 (mt-10) REVERT: A 906 LEU cc_start: 0.8419 (mp) cc_final: 0.7778 (tt) REVERT: A 920 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7245 (mm-30) REVERT: A 933 ASP cc_start: 0.7196 (t0) cc_final: 0.6982 (t0) REVERT: A 952 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: A 1012 LEU cc_start: 0.8161 (pt) cc_final: 0.7903 (pp) REVERT: A 1017 ASN cc_start: 0.7530 (m-40) cc_final: 0.7269 (m-40) REVERT: A 1030 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7488 (mm-40) REVERT: A 1059 GLN cc_start: 0.8207 (mm110) cc_final: 0.7918 (mm110) REVERT: A 1060 GLU cc_start: 0.7543 (tt0) cc_final: 0.7169 (tt0) REVERT: A 1135 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7063 (tm-30) outliers start: 127 outliers final: 90 residues processed: 529 average time/residue: 0.1569 time to fit residues: 134.5156 Evaluate side-chains 526 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 427 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 827 ASP Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 910 LYS Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 979 PHE Chi-restraints excluded: chain C residue 1057 SER Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1191 TYR Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain C residue 1197 ILE Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 694 ASN Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 876 HIS Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 940 PHE Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1036 ASN Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1135 GLN Chi-restraints excluded: chain A residue 1176 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 173 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 213 optimal weight: 0.5980 chunk 307 optimal weight: 0.0270 chunk 329 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 303 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 ASN B 26 ASN B 938 GLN A 642 ASN A 923 ASN A 954 GLN ** A1036 ASN ** 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 = 0.4620 r_free = 0.4620 target = 0.207507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.169610 restraints weight = 57673.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.174635 restraints weight = 32111.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.177981 restraints weight = 20816.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.178953 restraints weight = 14518.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.180266 restraints weight = 12887.347| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27329 Z= 0.112 Angle : 0.588 13.493 37389 Z= 0.297 Chirality : 0.044 0.354 4322 Planarity : 0.004 0.056 4821 Dihedral : 5.552 57.682 4135 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.50 % Allowed : 15.83 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % 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 aren not related in a simple way. whole: -2.37 (0.14), residues: 3506 helix: 0.05 (0.21), residues: 657 sheet: -1.57 (0.22), residues: 572 loop : -2.20 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 54 TYR 0.025 0.001 TYR C1148 PHE 0.035 0.001 PHE A 224 TRP 0.032 0.002 TRP A 344 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00245 (27247) covalent geometry : angle 0.58240 (37209) SS BOND : bond 0.00293 ( 66) SS BOND : angle 0.94428 ( 132) hydrogen bonds : bond 0.03450 ( 646) hydrogen bonds : angle 5.26963 ( 1794) link_NAG-ASN : bond 0.00328 ( 16) link_NAG-ASN : angle 2.01610 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 435 time to evaluate : 0.959 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 323 ASN cc_start: 0.8264 (p0) cc_final: 0.7910 (p0) REVERT: C 476 CYS cc_start: 0.3845 (OUTLIER) cc_final: 0.2013 (m) REVERT: C 674 SER cc_start: 0.8000 (m) cc_final: 0.7650 (p) REVERT: C 855 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6667 (mt) REVERT: C 862 MET cc_start: 0.6828 (mmm) cc_final: 0.6527 (mmm) REVERT: C 882 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7058 (mp) REVERT: C 952 GLU cc_start: 0.7203 (tp30) cc_final: 0.6795 (tp30) REVERT: C 979 PHE cc_start: 0.4867 (OUTLIER) cc_final: 0.2109 (t80) REVERT: C 1028 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7606 (mtmm) REVERT: C 1054 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7192 (mm) REVERT: C 1075 ASP cc_start: 0.7201 (t0) cc_final: 0.6995 (t0) REVERT: C 1096 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7944 (mm) REVERT: C 1131 LEU cc_start: 0.7316 (pt) cc_final: 0.7039 (pt) REVERT: C 1135 GLN cc_start: 0.7582 (tp40) cc_final: 0.6955 (mm-40) REVERT: B 90 TYR cc_start: 0.7222 (m-80) cc_final: 0.7004 (m-10) REVERT: B 187 LYS cc_start: 0.6592 (ptpp) cc_final: 0.5446 (ptpp) REVERT: B 289 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6836 (mm-30) REVERT: B 691 LEU cc_start: 0.7617 (tp) cc_final: 0.7100 (pp) REVERT: B 827 ASP cc_start: 0.7015 (m-30) cc_final: 0.6699 (m-30) REVERT: B 840 ASN cc_start: 0.8001 (m-40) cc_final: 0.7785 (m-40) REVERT: B 850 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7426 (mt) REVERT: B 1093 LEU cc_start: 0.8334 (mt) cc_final: 0.7935 (mp) REVERT: A 28 TYR cc_start: 0.7465 (t80) cc_final: 0.7179 (t80) REVERT: A 140 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6692 (tp-100) REVERT: A 201 HIS cc_start: 0.5699 (m-70) cc_final: 0.5456 (m-70) REVERT: A 289 GLU cc_start: 0.6465 (pp20) cc_final: 0.6242 (pp20) REVERT: A 427 TYR cc_start: 0.6089 (p90) cc_final: 0.5821 (p90) REVERT: A 582 SER cc_start: 0.8152 (m) cc_final: 0.7757 (p) REVERT: A 662 LEU cc_start: 0.8149 (mt) cc_final: 0.7822 (pt) REVERT: A 794 PHE cc_start: 0.5028 (p90) cc_final: 0.3927 (p90) REVERT: A 822 TYR cc_start: 0.6235 (m-80) cc_final: 0.5850 (m-80) REVERT: A 879 VAL cc_start: 0.7800 (m) cc_final: 0.7306 (t) REVERT: A 884 PHE cc_start: 0.6023 (OUTLIER) cc_final: 0.5800 (t80) REVERT: A 885 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7558 (mmmt) REVERT: A 906 LEU cc_start: 0.8397 (mp) cc_final: 0.7705 (tt) REVERT: A 920 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7194 (mm-30) REVERT: A 933 ASP cc_start: 0.7077 (t0) cc_final: 0.6825 (t0) REVERT: A 952 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: A 958 TYR cc_start: 0.8134 (m-10) cc_final: 0.7819 (m-10) REVERT: A 967 MET cc_start: 0.5742 (mtm) cc_final: 0.5462 (mtm) REVERT: A 1012 LEU cc_start: 0.8043 (pt) cc_final: 0.7699 (pp) REVERT: A 1017 ASN cc_start: 0.7288 (m-40) cc_final: 0.6999 (m-40) REVERT: A 1059 GLN cc_start: 0.8026 (mm110) cc_final: 0.7737 (mm110) REVERT: A 1060 GLU cc_start: 0.7398 (tt0) cc_final: 0.6816 (tt0) REVERT: A 1105 ARG cc_start: 0.6964 (tpm-80) cc_final: 0.6617 (tpm-80) outliers start: 100 outliers final: 65 residues processed: 504 average time/residue: 0.1602 time to fit residues: 130.1737 Evaluate side-chains 499 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 425 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 476 CYS Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 979 PHE Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1197 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 876 HIS Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 940 PHE Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1176 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 272 optimal weight: 2.9990 chunk 326 optimal weight: 1.9990 chunk 243 optimal weight: 0.0870 chunk 346 optimal weight: 6.9990 chunk 25 optimal weight: 0.0670 chunk 334 optimal weight: 3.9990 chunk 8 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 ASN ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 ASN C1122 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN A 923 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.208626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.170718 restraints weight = 58315.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.175983 restraints weight = 32517.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.178572 restraints weight = 21727.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.180358 restraints weight = 14839.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.181735 restraints weight = 12500.285| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27329 Z= 0.102 Angle : 0.578 12.881 37389 Z= 0.292 Chirality : 0.044 0.302 4322 Planarity : 0.004 0.059 4821 Dihedral : 5.338 56.904 4133 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 3.29 % Allowed : 15.90 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % 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 aren not related in a simple way. whole: -2.21 (0.14), residues: 3506 helix: 0.25 (0.21), residues: 661 sheet: -1.44 (0.22), residues: 570 loop : -2.13 (0.13), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 264 TYR 0.037 0.001 TYR C1148 PHE 0.038 0.001 PHE A 224 TRP 0.029 0.001 TRP A 344 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00227 (27247) covalent geometry : angle 0.57231 (37209) SS BOND : bond 0.00259 ( 66) SS BOND : angle 1.06609 ( 132) hydrogen bonds : bond 0.03259 ( 646) hydrogen bonds : angle 5.09550 ( 1794) link_NAG-ASN : bond 0.00295 ( 16) link_NAG-ASN : angle 1.71463 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 435 time to evaluate : 0.740 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 54 ARG cc_start: 0.6770 (ptp90) cc_final: 0.6383 (ptp-110) REVERT: C 323 ASN cc_start: 0.8222 (p0) cc_final: 0.7888 (p0) REVERT: C 476 CYS cc_start: 0.3843 (OUTLIER) cc_final: 0.2060 (m) REVERT: C 622 TYR cc_start: 0.7474 (p90) cc_final: 0.7128 (p90) REVERT: C 674 SER cc_start: 0.7891 (m) cc_final: 0.7583 (p) REVERT: C 720 VAL cc_start: 0.7042 (OUTLIER) cc_final: 0.6758 (p) REVERT: C 813 ASP cc_start: 0.6744 (m-30) cc_final: 0.6377 (m-30) REVERT: C 952 GLU cc_start: 0.7214 (tp30) cc_final: 0.6782 (tp30) REVERT: C 979 PHE cc_start: 0.4766 (OUTLIER) cc_final: 0.2145 (t80) REVERT: C 998 ASN cc_start: 0.7764 (m110) cc_final: 0.7459 (m-40) REVERT: C 1054 ILE cc_start: 0.8044 (pt) cc_final: 0.7069 (mm) REVERT: C 1075 ASP cc_start: 0.7093 (t0) cc_final: 0.6885 (t0) REVERT: C 1096 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7964 (mm) REVERT: C 1135 GLN cc_start: 0.7577 (tp40) cc_final: 0.6953 (mm-40) REVERT: B 90 TYR cc_start: 0.7274 (m-80) cc_final: 0.7007 (m-10) REVERT: B 187 LYS cc_start: 0.6550 (ptpp) cc_final: 0.5981 (mttt) REVERT: B 289 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6829 (mm-30) REVERT: B 768 GLU cc_start: 0.5915 (tm-30) cc_final: 0.5655 (tm-30) REVERT: B 827 ASP cc_start: 0.6976 (m-30) cc_final: 0.6660 (m-30) REVERT: B 840 ASN cc_start: 0.7983 (m-40) cc_final: 0.7727 (m-40) REVERT: B 850 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7420 (mt) REVERT: B 1093 LEU cc_start: 0.8313 (mt) cc_final: 0.7906 (mp) REVERT: B 1185 MET cc_start: 0.2014 (OUTLIER) cc_final: 0.1551 (tmm) REVERT: A 28 TYR cc_start: 0.7405 (t80) cc_final: 0.7099 (t80) REVERT: A 140 GLN cc_start: 0.7059 (tm-30) cc_final: 0.6858 (tp-100) REVERT: A 201 HIS cc_start: 0.5671 (m-70) cc_final: 0.5401 (m-70) REVERT: A 289 GLU cc_start: 0.6446 (pp20) cc_final: 0.6072 (pp20) REVERT: A 427 TYR cc_start: 0.6047 (p90) cc_final: 0.5803 (p90) REVERT: A 582 SER cc_start: 0.8047 (m) cc_final: 0.7693 (p) REVERT: A 794 PHE cc_start: 0.5035 (p90) cc_final: 0.3933 (p90) REVERT: A 822 TYR cc_start: 0.6235 (m-80) cc_final: 0.5835 (m-80) REVERT: A 879 VAL cc_start: 0.7765 (m) cc_final: 0.7285 (t) REVERT: A 884 PHE cc_start: 0.5933 (OUTLIER) cc_final: 0.5686 (t80) REVERT: A 904 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6229 (mt-10) REVERT: A 906 LEU cc_start: 0.8366 (mp) cc_final: 0.7707 (tt) REVERT: A 915 ASP cc_start: 0.6809 (p0) cc_final: 0.6331 (p0) REVERT: A 920 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 933 ASP cc_start: 0.6975 (t0) cc_final: 0.6724 (t0) REVERT: A 952 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6146 (mp0) REVERT: A 967 MET cc_start: 0.5703 (mtm) cc_final: 0.5428 (mtm) REVERT: A 1012 LEU cc_start: 0.8017 (pt) cc_final: 0.7674 (pp) REVERT: A 1017 ASN cc_start: 0.7265 (m-40) cc_final: 0.6971 (m-40) REVERT: A 1059 GLN cc_start: 0.8020 (mm110) cc_final: 0.7711 (mm110) REVERT: A 1060 GLU cc_start: 0.7346 (tt0) cc_final: 0.6979 (tt0) REVERT: A 1105 ARG cc_start: 0.6962 (tpm-80) cc_final: 0.6637 (tpm-80) REVERT: A 1135 GLN cc_start: 0.7405 (mm-40) cc_final: 0.6984 (tm-30) outliers start: 94 outliers final: 69 residues processed: 498 average time/residue: 0.1675 time to fit residues: 134.0962 Evaluate side-chains 503 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 426 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 476 CYS Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 979 PHE Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain C residue 1197 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 876 HIS Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 940 PHE Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1176 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 5 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 319 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 237 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS A 923 ASN ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.204118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.166235 restraints weight = 57487.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.171211 restraints weight = 33815.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.173883 restraints weight = 19495.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.174724 restraints weight = 15194.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.174918 restraints weight = 13834.977| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 27329 Z= 0.238 Angle : 0.701 10.932 37389 Z= 0.367 Chirality : 0.048 0.326 4322 Planarity : 0.005 0.062 4821 Dihedral : 6.066 59.758 4131 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 3.26 % Allowed : 16.11 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.14), residues: 3506 helix: -0.32 (0.20), residues: 652 sheet: -1.49 (0.22), residues: 547 loop : -2.34 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 693 TYR 0.033 0.002 TYR B 958 PHE 0.038 0.002 PHE A 224 TRP 0.034 0.002 TRP A 971 HIS 0.008 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00498 (27247) covalent geometry : angle 0.69213 (37209) SS BOND : bond 0.00435 ( 66) SS BOND : angle 1.50989 ( 132) hydrogen bonds : bond 0.04540 ( 646) hydrogen bonds : angle 5.62350 ( 1794) link_NAG-ASN : bond 0.00577 ( 16) link_NAG-ASN : angle 2.36431 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 442 time to evaluate : 0.941 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: C 202 PHE cc_start: 0.6357 (p90) cc_final: 0.6023 (p90) REVERT: C 215 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6671 (p0) REVERT: C 323 ASN cc_start: 0.8293 (p0) cc_final: 0.7997 (p0) REVERT: C 476 CYS cc_start: 0.3820 (OUTLIER) cc_final: 0.1987 (m) REVERT: C 674 SER cc_start: 0.8107 (m) cc_final: 0.7827 (p) REVERT: C 714 ASP cc_start: 0.6329 (m-30) cc_final: 0.6076 (t0) REVERT: C 952 GLU cc_start: 0.7265 (tp30) cc_final: 0.6851 (tp30) REVERT: C 967 MET cc_start: 0.3570 (pp-130) cc_final: 0.2853 (pp-130) REVERT: C 979 PHE cc_start: 0.5067 (OUTLIER) cc_final: 0.2337 (t80) REVERT: C 998 ASN cc_start: 0.7839 (m110) cc_final: 0.7612 (m-40) REVERT: C 1054 ILE cc_start: 0.8275 (pt) cc_final: 0.7440 (mp) REVERT: C 1096 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8031 (mm) REVERT: C 1135 GLN cc_start: 0.7595 (tp40) cc_final: 0.7039 (mm-40) REVERT: B 157 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6480 (mm-30) REVERT: B 187 LYS cc_start: 0.6833 (ptpp) cc_final: 0.5715 (ptpp) REVERT: B 289 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6875 (mm-30) REVERT: B 465 HIS cc_start: 0.7203 (p90) cc_final: 0.6773 (p90) REVERT: B 768 GLU cc_start: 0.5964 (tm-30) cc_final: 0.5658 (tm-30) REVERT: B 827 ASP cc_start: 0.7110 (m-30) cc_final: 0.6824 (m-30) REVERT: B 850 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7399 (mt) REVERT: B 1028 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6684 (pptt) REVERT: A 28 TYR cc_start: 0.7626 (t80) cc_final: 0.7311 (t80) REVERT: A 201 HIS cc_start: 0.5712 (m-70) cc_final: 0.5495 (m-70) REVERT: A 289 GLU cc_start: 0.6652 (pp20) cc_final: 0.6396 (pp20) REVERT: A 582 SER cc_start: 0.8328 (m) cc_final: 0.7922 (p) REVERT: A 613 GLU cc_start: 0.7552 (tp30) cc_final: 0.7295 (tp30) REVERT: A 625 TYR cc_start: 0.6608 (m-80) cc_final: 0.6005 (m-80) REVERT: A 794 PHE cc_start: 0.5037 (p90) cc_final: 0.3779 (p90) REVERT: A 822 TYR cc_start: 0.6348 (m-80) cc_final: 0.5893 (m-80) REVERT: A 832 TYR cc_start: 0.7034 (m-80) cc_final: 0.6743 (m-80) REVERT: A 884 PHE cc_start: 0.6190 (OUTLIER) cc_final: 0.5944 (t80) REVERT: A 885 LYS cc_start: 0.7907 (tptp) cc_final: 0.7676 (tptp) REVERT: A 904 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6613 (mt-10) REVERT: A 906 LEU cc_start: 0.8397 (mp) cc_final: 0.7687 (tt) REVERT: A 920 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7283 (mm-30) REVERT: A 952 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: A 967 MET cc_start: 0.5701 (mtm) cc_final: 0.5444 (mtm) REVERT: A 1012 LEU cc_start: 0.8082 (pt) cc_final: 0.7828 (pp) REVERT: A 1017 ASN cc_start: 0.7473 (m-40) cc_final: 0.7188 (m-40) REVERT: A 1030 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7545 (mm-40) REVERT: A 1059 GLN cc_start: 0.8238 (mm110) cc_final: 0.7818 (mm110) REVERT: A 1060 GLU cc_start: 0.7569 (tt0) cc_final: 0.7195 (tt0) REVERT: A 1105 ARG cc_start: 0.7013 (tpm-80) cc_final: 0.6677 (tpm-80) outliers start: 93 outliers final: 74 residues processed: 501 average time/residue: 0.1719 time to fit residues: 138.4160 Evaluate side-chains 518 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 436 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 476 CYS Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 910 LYS Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 979 PHE Chi-restraints excluded: chain C residue 1057 SER Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain C residue 1197 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 876 HIS Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 940 PHE Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1176 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 84 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 67 optimal weight: 0.5980 chunk 320 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN A 923 ASN ** A1036 ASN ** 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 = 0.4595 r_free = 0.4595 target = 0.204831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.166737 restraints weight = 57453.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.172277 restraints weight = 33131.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.175800 restraints weight = 18869.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.176172 restraints weight = 13555.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.176436 restraints weight = 12580.461| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27329 Z= 0.150 Angle : 0.641 14.390 37389 Z= 0.327 Chirality : 0.045 0.299 4322 Planarity : 0.005 0.066 4821 Dihedral : 5.788 58.032 4129 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 2.84 % Allowed : 16.85 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.14), residues: 3506 helix: -0.15 (0.20), residues: 661 sheet: -1.54 (0.22), residues: 552 loop : -2.32 (0.12), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 54 TYR 0.031 0.002 TYR C1193 PHE 0.037 0.001 PHE A 224 TRP 0.029 0.002 TRP A 971 HIS 0.005 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00323 (27247) covalent geometry : angle 0.63364 (37209) SS BOND : bond 0.00323 ( 66) SS BOND : angle 1.32411 ( 132) hydrogen bonds : bond 0.03822 ( 646) hydrogen bonds : angle 5.40040 ( 1794) link_NAG-ASN : bond 0.00325 ( 16) link_NAG-ASN : angle 2.03034 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 433 time to evaluate : 0.791 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 323 ASN cc_start: 0.8269 (p0) cc_final: 0.7955 (p0) REVERT: C 476 CYS cc_start: 0.3843 (OUTLIER) cc_final: 0.2026 (m) REVERT: C 674 SER cc_start: 0.7939 (m) cc_final: 0.7659 (p) REVERT: C 813 ASP cc_start: 0.6876 (m-30) cc_final: 0.6365 (m-30) REVERT: C 867 LEU cc_start: 0.3260 (OUTLIER) cc_final: 0.2560 (pt) REVERT: C 952 GLU cc_start: 0.7246 (tp30) cc_final: 0.6842 (tp30) REVERT: C 967 MET cc_start: 0.3512 (pp-130) cc_final: 0.2819 (pp-130) REVERT: C 979 PHE cc_start: 0.4999 (OUTLIER) cc_final: 0.2180 (t80) REVERT: C 998 ASN cc_start: 0.7902 (m110) cc_final: 0.7655 (m-40) REVERT: C 1096 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7939 (mm) REVERT: C 1135 GLN cc_start: 0.7515 (tp40) cc_final: 0.6973 (mm-40) REVERT: B 187 LYS cc_start: 0.6735 (ptpp) cc_final: 0.5432 (ptpp) REVERT: B 254 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5791 (pp) REVERT: B 289 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6857 (mm-30) REVERT: B 465 HIS cc_start: 0.7251 (p90) cc_final: 0.6847 (p90) REVERT: B 768 GLU cc_start: 0.5958 (tm-30) cc_final: 0.5703 (tm-30) REVERT: B 827 ASP cc_start: 0.7085 (m-30) cc_final: 0.6801 (m-30) REVERT: B 850 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7448 (mt) REVERT: B 1028 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6603 (pptt) REVERT: B 1093 LEU cc_start: 0.8378 (mt) cc_final: 0.7996 (mp) REVERT: B 1105 ARG cc_start: 0.6896 (tpt90) cc_final: 0.6670 (tpt90) REVERT: A 28 TYR cc_start: 0.7600 (t80) cc_final: 0.7280 (t80) REVERT: A 201 HIS cc_start: 0.5662 (m-70) cc_final: 0.5410 (m-70) REVERT: A 289 GLU cc_start: 0.6502 (pp20) cc_final: 0.6255 (pp20) REVERT: A 582 SER cc_start: 0.8201 (m) cc_final: 0.7831 (p) REVERT: A 613 GLU cc_start: 0.7517 (tp30) cc_final: 0.7198 (tp30) REVERT: A 794 PHE cc_start: 0.4955 (p90) cc_final: 0.3726 (p90) REVERT: A 822 TYR cc_start: 0.6347 (m-80) cc_final: 0.5840 (m-80) REVERT: A 832 TYR cc_start: 0.6994 (m-80) cc_final: 0.6756 (m-80) REVERT: A 884 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5837 (t80) REVERT: A 906 LEU cc_start: 0.8360 (mp) cc_final: 0.7702 (tt) REVERT: A 920 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7235 (mm-30) REVERT: A 933 ASP cc_start: 0.7066 (t0) cc_final: 0.6841 (t0) REVERT: A 952 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: A 967 MET cc_start: 0.5874 (mtm) cc_final: 0.5614 (mtm) REVERT: A 1012 LEU cc_start: 0.8017 (pt) cc_final: 0.7678 (pp) REVERT: A 1017 ASN cc_start: 0.7371 (m-40) cc_final: 0.7046 (m-40) REVERT: A 1059 GLN cc_start: 0.8157 (mm110) cc_final: 0.7772 (mm110) REVERT: A 1060 GLU cc_start: 0.7494 (tt0) cc_final: 0.7118 (tt0) REVERT: A 1105 ARG cc_start: 0.6980 (tpm-80) cc_final: 0.6656 (tpm-80) REVERT: A 1135 GLN cc_start: 0.7307 (mm-40) cc_final: 0.7020 (tm-30) outliers start: 81 outliers final: 66 residues processed: 490 average time/residue: 0.1578 time to fit residues: 124.3063 Evaluate side-chains 501 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 426 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 476 CYS Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 979 PHE Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1197 ILE Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 876 HIS Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 938 GLN Chi-restraints excluded: chain B residue 940 PHE Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1045 GLN Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1176 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 222 optimal weight: 2.9990 chunk 47 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.204891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.166985 restraints weight = 57318.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.172891 restraints weight = 32255.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.174946 restraints weight = 18563.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.175636 restraints weight = 14560.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.175636 restraints weight = 13500.346| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 27329 Z= 0.195 Angle : 0.828 59.157 37389 Z= 0.473 Chirality : 0.056 1.597 4322 Planarity : 0.005 0.101 4821 Dihedral : 5.788 58.096 4129 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 2.77 % Allowed : 16.88 % Favored : 80.35 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.14), residues: 3506 helix: -0.17 (0.20), residues: 661 sheet: -1.54 (0.22), residues: 552 loop : -2.32 (0.12), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 54 TYR 0.028 0.001 TYR C1148 PHE 0.035 0.001 PHE A 224 TRP 0.025 0.002 TRP A 971 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00396 (27247) covalent geometry : angle 0.82305 (37209) SS BOND : bond 0.00343 ( 66) SS BOND : angle 1.37179 ( 132) hydrogen bonds : bond 0.03857 ( 646) hydrogen bonds : angle 5.40738 ( 1794) link_NAG-ASN : bond 0.00339 ( 16) link_NAG-ASN : angle 2.02857 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5189.99 seconds wall clock time: 90 minutes 23.33 seconds (5423.33 seconds total)