Starting phenix.real_space_refine on Mon Jun 23 04:07:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8e_39043/06_2025/8y8e_39043.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8e_39043/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y8e_39043/06_2025/8y8e_39043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8e_39043/06_2025/8y8e_39043.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8e_39043/06_2025/8y8e_39043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8e_39043/06_2025/8y8e_39043.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 16, 'GLU:plan': 9, 'ARG: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: {'GLN:plan1': 8, 'ASP:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 8, 'HIS:plan': 3, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 11} 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: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 10, 'GLU:plan': 1, 'ARG:plan': 8} 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: 16.87, per 1000 atoms: 0.63 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: 6.82 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 3.47 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: 11.41 Time building geometry restraints manager: 8.15 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 1221 or resid 1301 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 1221 or resid 1301 through 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 122 \ 1 or resid 1301 through 1304)) } 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: 273.410 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: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 63.610 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.130 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 343.100 ------------------------------------------------------------------------------- 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 : 6.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP C 344 HIS 0.001 0.000 HIS C 799 PHE 0.006 0.001 PHE A 681 TYR 0.009 0.001 TYR A1148 ARG 0.002 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 16) link_NAG-ASN : angle 0.92915 ( 48) hydrogen bonds : bond 0.23133 ( 646) hydrogen bonds : angle 8.14034 ( 1794) SS BOND : bond 0.00093 ( 66) SS BOND : angle 0.47318 ( 132) covalent geometry : bond 0.00190 (27247) covalent geometry : angle 0.43307 (37209) *********************** 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 : 3.174 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: 0.6288 (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: 0.6553 (tp30) REVERT: C 979 PHE cc_start: 0.5001 (OUTLIER) cc_final: 0.2024 (t80) REVERT: C 1026 LEU cc_start: 0.6547 (tp) cc_final: 0.6292 (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: 0.5881 (t0) REVERT: B 850 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7451 (mt) REVERT: B 949 ILE cc_start: 0.7982 (pt) cc_final: 0.7561 (mm) REVERT: B 1028 LYS cc_start: 0.7406 (ttmt) cc_final: 0.7182 (ttmt) REVERT: B 1091 GLN cc_start: 0.6930 (mm-40) cc_final: 0.6625 (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: 0.5791 (p90) REVERT: A 553 GLU cc_start: 0.4485 (OUTLIER) cc_final: 0.4045 (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: 0.7757 (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: 0.7076 (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: 0.7890 (tt) REVERT: A 920 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6914 (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: 0.7021 (mm-40) REVERT: A 1038 GLN cc_start: 0.7350 (pp30) cc_final: 0.7107 (pp30) REVERT: A 1060 GLU cc_start: 0.7140 (tt0) cc_final: 0.5651 (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: 0.7543 (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: 0.4328 time to fit residues: 419.4092 Evaluate side-chains 471 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 435 time to evaluate : 2.715 ------------------------------------------------------------------------------- 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 298 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 148 optimal weight: 0.0770 chunk 91 optimal weight: 0.4980 chunk 180 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 276 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 overall best weight: 1.0342 ------------------------------------------------------------------------------- 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 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 413 ASN B 591 ASN B 709 GLN B 847 ASN B 870 ASN B 874 ASN B1009 ASN B1030 GLN B1117 GLN ** B1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1181 ASN B1201 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 343 ASN A 694 ASN A 826 HIS A 847 ASN A 854 GLN A 923 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN A1079 ASN A1180 GLN A1211 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.210183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.172587 restraints weight = 58661.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.177869 restraints weight = 34709.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.179625 restraints weight = 20662.127| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27329 Z= 0.153 Angle : 0.573 10.602 37389 Z= 0.301 Chirality : 0.044 0.230 4322 Planarity : 0.004 0.060 4821 Dihedral : 5.854 58.368 4160 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.36 % Allowed : 11.21 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.13), residues: 3506 helix: -0.40 (0.20), residues: 663 sheet: -1.59 (0.21), residues: 569 loop : -2.56 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 971 HIS 0.010 0.001 HIS A 142 PHE 0.033 0.002 PHE A 379 TYR 0.029 0.001 TYR C1148 ARG 0.006 0.001 ARG B 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 16) link_NAG-ASN : angle 1.42844 ( 48) hydrogen bonds : bond 0.04121 ( 646) hydrogen bonds : angle 6.01842 ( 1794) SS BOND : bond 0.00436 ( 66) SS BOND : angle 1.31074 ( 132) covalent geometry : bond 0.00325 (27247) covalent geometry : angle 0.56685 (37209) *********************** 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 557 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 461 time to evaluate : 2.880 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: 0.8312 (p0) cc_final: 0.7942 (p0) REVERT: C 641 TYR cc_start: 0.7378 (m-80) cc_final: 0.6587 (m-80) REVERT: C 674 SER cc_start: 0.8243 (m) cc_final: 0.7789 (p) REVERT: C 845 GLU cc_start: 0.6685 (tm-30) cc_final: 0.6413 (tm-30) REVERT: C 870 ASN cc_start: 0.6958 (m-40) cc_final: 0.6745 (m110) REVERT: C 879 VAL cc_start: 0.5891 (OUTLIER) cc_final: 0.5656 (t) REVERT: C 936 CYS cc_start: 0.7633 (t) cc_final: 0.7289 (t) REVERT: C 952 GLU cc_start: 0.7153 (tp30) cc_final: 0.6784 (tp30) REVERT: C 979 PHE cc_start: 0.5067 (OUTLIER) cc_final: 0.1769 (t80) REVERT: C 1135 GLN cc_start: 0.7507 (tp40) cc_final: 0.6762 (mm-40) REVERT: B 155 MET cc_start: 0.6161 (mmm) cc_final: 0.5938 (mmm) REVERT: B 187 LYS cc_start: 0.6433 (ptpp) cc_final: 0.5348 (mtmt) REVERT: B 206 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7178 (mtt90) REVERT: B 289 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6810 (mm-30) REVERT: B 676 ARG cc_start: 0.7096 (ttm170) cc_final: 0.6192 (ttm170) REVERT: B 691 LEU cc_start: 0.7531 (tp) cc_final: 0.7142 (pp) REVERT: B 740 SER cc_start: 0.8338 (t) cc_final: 0.8055 (t) REVERT: B 838 ASN cc_start: 0.7694 (t0) cc_final: 0.7353 (m-40) REVERT: B 850 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7346 (mt) REVERT: B 949 ILE cc_start: 0.8128 (pt) cc_final: 0.7678 (mm) REVERT: B 1091 GLN cc_start: 0.7097 (mm-40) cc_final: 0.6818 (mm-40) REVERT: A 28 TYR cc_start: 0.7540 (t80) cc_final: 0.7164 (t80) REVERT: A 201 HIS cc_start: 0.5828 (m-70) cc_final: 0.5508 (m-70) REVERT: A 224 PHE cc_start: 0.7189 (p90) cc_final: 0.6893 (p90) REVERT: A 289 GLU cc_start: 0.5978 (pp20) cc_final: 0.5726 (pp20) REVERT: A 700 VAL cc_start: 0.8446 (m) cc_final: 0.8058 (p) REVERT: A 884 PHE cc_start: 0.5920 (OUTLIER) cc_final: 0.5609 (t80) REVERT: A 906 LEU cc_start: 0.8545 (mp) cc_final: 0.7737 (tt) REVERT: A 920 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7128 (mm-30) REVERT: A 952 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: A 1008 PHE cc_start: 0.6981 (m-80) cc_final: 0.6453 (m-80) REVERT: A 1012 LEU cc_start: 0.8136 (pt) cc_final: 0.7663 (pp) REVERT: A 1060 GLU cc_start: 0.7228 (tt0) cc_final: 0.6866 (tt0) REVERT: A 1076 ARG cc_start: 0.6889 (tpp80) cc_final: 0.6647 (tpp80) REVERT: A 1085 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8332 (tp) REVERT: A 1100 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7614 (tppt) outliers start: 96 outliers final: 59 residues processed: 534 average time/residue: 0.3873 time to fit residues: 333.4803 Evaluate side-chains 490 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 425 time to evaluate : 2.461 ------------------------------------------------------------------------------- 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 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 935 LEU 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 782 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 830 SER 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 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 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 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 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 1003 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 274 optimal weight: 0.0030 chunk 131 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 309 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 304 optimal weight: 3.9990 chunk 176 optimal weight: 0.0030 chunk 134 optimal weight: 3.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN B 291 GLN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 HIS B1126 ASN B1201 ASN A 483 ASN A 923 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.209292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.171304 restraints weight = 58232.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.177802 restraints weight = 31625.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.178680 restraints weight = 17230.615| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27329 Z= 0.138 Angle : 0.555 10.761 37389 Z= 0.288 Chirality : 0.044 0.208 4322 Planarity : 0.004 0.080 4821 Dihedral : 5.586 58.090 4144 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.71 % Allowed : 12.82 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.14), residues: 3506 helix: -0.09 (0.21), residues: 657 sheet: -1.60 (0.20), residues: 606 loop : -2.45 (0.12), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 332 HIS 0.007 0.001 HIS A 201 PHE 0.023 0.001 PHE C1212 TYR 0.029 0.001 TYR C1148 ARG 0.005 0.000 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 16) link_NAG-ASN : angle 1.46436 ( 48) hydrogen bonds : bond 0.03811 ( 646) hydrogen bonds : angle 5.63697 ( 1794) SS BOND : bond 0.00325 ( 66) SS BOND : angle 1.05143 ( 132) covalent geometry : bond 0.00293 (27247) covalent geometry : angle 0.55060 (37209) *********************** 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 539 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 433 time to evaluate : 3.567 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: 0.8363 (p0) cc_final: 0.7988 (p0) REVERT: C 622 TYR cc_start: 0.7184 (p90) cc_final: 0.6897 (p90) REVERT: C 641 TYR cc_start: 0.7352 (m-80) cc_final: 0.6855 (m-10) REVERT: C 674 SER cc_start: 0.8292 (m) cc_final: 0.7895 (p) REVERT: C 813 ASP cc_start: 0.6786 (m-30) cc_final: 0.6521 (t0) REVERT: C 818 VAL cc_start: 0.7250 (OUTLIER) cc_final: 0.6070 (p) REVERT: C 845 GLU cc_start: 0.6680 (tm-30) cc_final: 0.6457 (tm-30) REVERT: C 870 ASN cc_start: 0.6939 (m-40) cc_final: 0.6674 (m110) REVERT: C 936 CYS cc_start: 0.7634 (t) cc_final: 0.7318 (t) REVERT: C 952 GLU cc_start: 0.7175 (tp30) cc_final: 0.6847 (tp30) REVERT: C 979 PHE cc_start: 0.5025 (OUTLIER) cc_final: 0.2016 (t80) REVERT: C 1076 ARG cc_start: 0.7591 (mtm-85) cc_final: 0.7376 (mtm110) REVERT: C 1096 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8042 (mm) REVERT: C 1131 LEU cc_start: 0.7278 (pt) cc_final: 0.6919 (pt) REVERT: C 1135 GLN cc_start: 0.7601 (tp40) cc_final: 0.7044 (mm-40) REVERT: B 187 LYS cc_start: 0.6484 (ptpp) cc_final: 0.5419 (mtmt) REVERT: B 206 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.7224 (mtt-85) REVERT: B 289 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6844 (mm-30) REVERT: B 691 LEU cc_start: 0.7559 (tp) cc_final: 0.7136 (pp) REVERT: B 694 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8317 (p0) REVERT: B 740 SER cc_start: 0.8366 (t) cc_final: 0.8132 (t) REVERT: B 813 ASP cc_start: 0.6145 (t0) cc_final: 0.5883 (m-30) REVERT: B 850 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7339 (mt) REVERT: B 949 ILE cc_start: 0.8118 (pt) cc_final: 0.7707 (mm) REVERT: B 1091 GLN cc_start: 0.7105 (mm-40) cc_final: 0.6868 (mm-40) REVERT: A 28 TYR cc_start: 0.7600 (t80) cc_final: 0.7251 (t80) REVERT: A 201 HIS cc_start: 0.5775 (m-70) cc_final: 0.5423 (m-70) REVERT: A 224 PHE cc_start: 0.7182 (p90) cc_final: 0.6899 (p90) REVERT: A 289 GLU cc_start: 0.6187 (pp20) cc_final: 0.5957 (pp20) REVERT: A 358 THR cc_start: 0.8444 (m) cc_final: 0.8139 (t) REVERT: A 427 TYR cc_start: 0.6161 (p90) cc_final: 0.5944 (p90) REVERT: A 681 PHE cc_start: 0.6452 (t80) cc_final: 0.6183 (t80) REVERT: A 700 VAL cc_start: 0.8447 (m) cc_final: 0.8064 (p) REVERT: A 763 ARG cc_start: 0.6908 (mtm-85) cc_final: 0.6511 (mtt90) REVERT: A 794 PHE cc_start: 0.5172 (p90) cc_final: 0.4797 (p90) REVERT: A 820 SER cc_start: 0.6756 (t) cc_final: 0.6235 (p) REVERT: A 851 ASP cc_start: 0.6631 (m-30) cc_final: 0.6395 (m-30) REVERT: A 884 PHE cc_start: 0.5992 (OUTLIER) cc_final: 0.5642 (t80) REVERT: A 904 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6794 (mt-10) REVERT: A 906 LEU cc_start: 0.8463 (mp) cc_final: 0.7850 (tt) REVERT: A 920 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7163 (mm-30) REVERT: A 952 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: A 1012 LEU cc_start: 0.8127 (pt) cc_final: 0.7886 (pp) REVERT: A 1085 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8379 (tp) REVERT: A 1100 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7602 (tppt) outliers start: 106 outliers final: 68 residues processed: 506 average time/residue: 0.3916 time to fit residues: 320.5688 Evaluate side-chains 502 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 426 time to evaluate : 2.557 ------------------------------------------------------------------------------- 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 724 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 814 CYS Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 867 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 1057 SER Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1104 SER 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 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 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 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 1157 LEU Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1173 LYS 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 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 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 144 optimal weight: 0.6980 chunk 342 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 30.0000 chunk 283 optimal weight: 0.0670 chunk 228 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 ASN A1079 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.208691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.170650 restraints weight = 58485.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.175767 restraints weight = 32990.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.179044 restraints weight = 19857.849| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27329 Z= 0.128 Angle : 0.545 11.153 37389 Z= 0.283 Chirality : 0.044 0.214 4322 Planarity : 0.004 0.055 4821 Dihedral : 5.504 57.343 4142 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.16 % Favored : 90.82 % Rotamer: Outliers : 3.78 % Allowed : 13.42 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.14), residues: 3506 helix: 0.10 (0.21), residues: 649 sheet: -1.61 (0.21), residues: 586 loop : -2.32 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 971 HIS 0.006 0.001 HIS A 201 PHE 0.021 0.001 PHE C 202 TYR 0.024 0.001 TYR A 673 ARG 0.006 0.000 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 16) link_NAG-ASN : angle 1.46322 ( 48) hydrogen bonds : bond 0.03554 ( 646) hydrogen bonds : angle 5.41719 ( 1794) SS BOND : bond 0.00348 ( 66) SS BOND : angle 0.92305 ( 132) covalent geometry : bond 0.00274 (27247) covalent geometry : angle 0.54111 (37209) *********************** 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 541 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 433 time to evaluate : 3.014 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 202 PHE cc_start: 0.6442 (p90) cc_final: 0.6124 (p90) REVERT: C 323 ASN cc_start: 0.8324 (p0) cc_final: 0.7956 (p0) REVERT: C 674 SER cc_start: 0.8148 (m) cc_final: 0.7749 (p) REVERT: C 813 ASP cc_start: 0.6812 (m-30) cc_final: 0.6594 (m-30) REVERT: C 845 GLU cc_start: 0.6653 (tm-30) cc_final: 0.6398 (tm-30) REVERT: C 870 ASN cc_start: 0.6980 (m-40) cc_final: 0.6714 (m110) REVERT: C 882 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6965 (mp) REVERT: C 936 CYS cc_start: 0.7689 (t) cc_final: 0.7415 (t) REVERT: C 952 GLU cc_start: 0.7193 (tp30) cc_final: 0.6780 (tp30) REVERT: C 979 PHE cc_start: 0.4952 (OUTLIER) cc_final: 0.2113 (t80) REVERT: C 1028 LYS cc_start: 0.7780 (mtmt) cc_final: 0.7529 (mtmm) REVERT: C 1096 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8083 (mm) REVERT: C 1131 LEU cc_start: 0.7298 (pt) cc_final: 0.6918 (pt) REVERT: C 1135 GLN cc_start: 0.7591 (tp40) cc_final: 0.7123 (mm-40) REVERT: B 151 CYS cc_start: 0.5175 (m) cc_final: 0.4795 (m) REVERT: B 187 LYS cc_start: 0.6517 (ptpp) cc_final: 0.5616 (mtmt) REVERT: B 206 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.7334 (mtt-85) REVERT: B 289 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6854 (mm-30) REVERT: B 691 LEU cc_start: 0.7526 (tp) cc_final: 0.7091 (pp) REVERT: B 740 SER cc_start: 0.8424 (t) cc_final: 0.8216 (t) REVERT: B 746 TYR cc_start: 0.5436 (t80) cc_final: 0.5223 (t80) REVERT: B 813 ASP cc_start: 0.6101 (t0) cc_final: 0.5865 (m-30) REVERT: B 838 ASN cc_start: 0.7784 (t0) cc_final: 0.7519 (t0) REVERT: B 850 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7470 (mt) REVERT: B 1091 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6917 (mm-40) REVERT: B 1093 LEU cc_start: 0.8410 (mt) cc_final: 0.8038 (mp) REVERT: A 28 TYR cc_start: 0.7570 (t80) cc_final: 0.7232 (t80) REVERT: A 201 HIS cc_start: 0.5737 (m-70) cc_final: 0.5452 (m-70) REVERT: A 289 GLU cc_start: 0.6360 (pp20) cc_final: 0.6006 (pp20) REVERT: A 303 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 427 TYR cc_start: 0.6304 (p90) cc_final: 0.6086 (p90) REVERT: A 681 PHE cc_start: 0.6541 (t80) cc_final: 0.6230 (t80) REVERT: A 700 VAL cc_start: 0.8455 (m) cc_final: 0.8046 (p) REVERT: A 820 SER cc_start: 0.6924 (t) cc_final: 0.6430 (p) REVERT: A 884 PHE cc_start: 0.6079 (OUTLIER) cc_final: 0.5719 (t80) REVERT: A 904 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6680 (mt-10) REVERT: A 906 LEU cc_start: 0.8412 (mp) cc_final: 0.7758 (tt) REVERT: A 920 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7219 (mm-30) REVERT: A 952 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: A 1012 LEU cc_start: 0.8147 (pt) cc_final: 0.7889 (pp) REVERT: A 1030 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7465 (mm-40) REVERT: A 1060 GLU cc_start: 0.7478 (tt0) cc_final: 0.6511 (tt0) REVERT: A 1085 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8409 (tp) REVERT: A 1100 LYS cc_start: 0.7933 (mmmt) cc_final: 0.7599 (tppt) REVERT: A 1191 TYR cc_start: 0.5023 (OUTLIER) cc_final: 0.4816 (t80) REVERT: A 1193 TYR cc_start: 0.5929 (OUTLIER) cc_final: 0.5567 (m-80) outliers start: 108 outliers final: 72 residues processed: 507 average time/residue: 0.3676 time to fit residues: 299.2301 Evaluate side-chains 506 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 424 time to evaluate : 4.076 ------------------------------------------------------------------------------- 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 321 ILE 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 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 1057 SER Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1104 SER 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 614 ILE 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 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 1159 SER Chi-restraints excluded: chain A residue 20 CYS 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 303 VAL 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 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 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 1085 LEU Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1191 TYR Chi-restraints excluded: chain A residue 1193 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 127 optimal weight: 0.8980 chunk 348 optimal weight: 0.3980 chunk 151 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 165 optimal weight: 30.0000 chunk 89 optimal weight: 0.7980 chunk 278 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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** C 874 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 ASN A 923 ASN ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.207047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.168386 restraints weight = 58018.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.173410 restraints weight = 35354.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.178256 restraints weight = 20647.691| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27329 Z= 0.164 Angle : 0.582 12.064 37389 Z= 0.301 Chirality : 0.045 0.236 4322 Planarity : 0.004 0.059 4821 Dihedral : 5.597 57.344 4138 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.96 % Allowed : 14.40 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.14), residues: 3506 helix: 0.00 (0.21), residues: 646 sheet: -1.68 (0.22), residues: 550 loop : -2.29 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 971 HIS 0.006 0.001 HIS A 201 PHE 0.023 0.001 PHE B 764 TYR 0.024 0.001 TYR C1148 ARG 0.007 0.001 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 16) link_NAG-ASN : angle 1.74682 ( 48) hydrogen bonds : bond 0.03840 ( 646) hydrogen bonds : angle 5.45714 ( 1794) SS BOND : bond 0.00335 ( 66) SS BOND : angle 0.95625 ( 132) covalent geometry : bond 0.00346 (27247) covalent geometry : angle 0.57706 (37209) *********************** 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 548 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 435 time to evaluate : 3.034 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 202 PHE cc_start: 0.6446 (p90) cc_final: 0.6210 (p90) REVERT: C 323 ASN cc_start: 0.8382 (p0) cc_final: 0.8036 (p0) REVERT: C 674 SER cc_start: 0.8162 (m) cc_final: 0.7801 (p) REVERT: C 845 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6380 (tm-30) REVERT: C 855 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6597 (mt) REVERT: C 870 ASN cc_start: 0.7010 (m-40) cc_final: 0.6736 (m110) REVERT: C 882 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.7000 (mp) REVERT: C 952 GLU cc_start: 0.7178 (tp30) cc_final: 0.6757 (tp30) REVERT: C 979 PHE cc_start: 0.4969 (OUTLIER) cc_final: 0.2155 (t80) REVERT: C 1028 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7660 (mtmm) REVERT: C 1054 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7115 (mm) REVERT: C 1096 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8031 (mm) REVERT: C 1131 LEU cc_start: 0.7293 (pt) cc_final: 0.6923 (pt) REVERT: C 1135 GLN cc_start: 0.7594 (tp40) cc_final: 0.6942 (mm-40) REVERT: B 97 ASP cc_start: 0.5606 (t70) cc_final: 0.5400 (t0) REVERT: B 187 LYS cc_start: 0.6669 (ptpp) cc_final: 0.5429 (ptpp) REVERT: B 206 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.7224 (mtt90) REVERT: B 232 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5977 (mm) REVERT: B 289 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6810 (mm-30) REVERT: B 813 ASP cc_start: 0.6099 (t0) cc_final: 0.5895 (m-30) REVERT: B 838 ASN cc_start: 0.7803 (t0) cc_final: 0.7476 (t0) REVERT: B 850 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7389 (mt) REVERT: B 1093 LEU cc_start: 0.8444 (mt) cc_final: 0.8060 (mp) REVERT: A 28 TYR cc_start: 0.7689 (t80) cc_final: 0.7350 (t80) REVERT: A 201 HIS cc_start: 0.5660 (m-70) cc_final: 0.5410 (m-70) REVERT: A 427 TYR cc_start: 0.6265 (p90) cc_final: 0.5938 (p90) REVERT: A 662 LEU cc_start: 0.8126 (mt) cc_final: 0.7853 (pt) REVERT: A 822 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.6033 (m-80) REVERT: A 884 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.5806 (t80) REVERT: A 904 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6661 (mt-10) REVERT: A 906 LEU cc_start: 0.8390 (mp) cc_final: 0.7795 (tt) REVERT: A 920 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7214 (mm-30) REVERT: A 933 ASP cc_start: 0.7368 (t0) cc_final: 0.7149 (t0) REVERT: A 952 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: A 958 TYR cc_start: 0.8150 (m-10) cc_final: 0.7867 (m-10) REVERT: A 1012 LEU cc_start: 0.8152 (pt) cc_final: 0.7883 (pp) REVERT: A 1030 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7418 (mm-40) REVERT: A 1059 GLN cc_start: 0.8166 (mm110) cc_final: 0.7773 (mm110) REVERT: A 1060 GLU cc_start: 0.7557 (tt0) cc_final: 0.7153 (tt0) REVERT: A 1085 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8408 (tp) REVERT: A 1100 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7620 (tppt) REVERT: A 1120 ARG cc_start: 0.6114 (mtp85) cc_final: 0.5552 (mtp85) REVERT: A 1193 TYR cc_start: 0.5856 (OUTLIER) cc_final: 0.5646 (m-80) outliers start: 113 outliers final: 84 residues processed: 510 average time/residue: 0.4229 time to fit residues: 350.3146 Evaluate side-chains 517 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 421 time to evaluate : 2.741 ------------------------------------------------------------------------------- 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 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 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 697 CYS Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 724 VAL 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 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 1054 ILE 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 1104 SER 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 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 232 LEU 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 651 SER 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 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 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 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 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 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 1045 GLN 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 1085 LEU Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1193 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 165 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 241 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 73 optimal weight: 0.0970 chunk 62 optimal weight: 0.8980 chunk 336 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 333 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 ** C 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 ASN B 26 ASN B 938 GLN A 923 ASN A1036 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.207823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.170117 restraints weight = 58205.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.175012 restraints weight = 33245.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.178454 restraints weight = 19666.648| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27329 Z= 0.116 Angle : 0.558 11.528 37389 Z= 0.286 Chirality : 0.043 0.226 4322 Planarity : 0.004 0.056 4821 Dihedral : 5.377 57.419 4135 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 3.92 % Allowed : 15.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.14), residues: 3506 helix: 0.16 (0.21), residues: 653 sheet: -1.63 (0.22), residues: 559 loop : -2.21 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 332 HIS 0.004 0.001 HIS A 201 PHE 0.019 0.001 PHE B 681 TYR 0.026 0.001 TYR C1148 ARG 0.006 0.000 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 16) link_NAG-ASN : angle 1.58252 ( 48) hydrogen bonds : bond 0.03437 ( 646) hydrogen bonds : angle 5.26048 ( 1794) SS BOND : bond 0.00292 ( 66) SS BOND : angle 0.88641 ( 132) covalent geometry : bond 0.00251 (27247) covalent geometry : angle 0.55425 (37209) *********************** 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 535 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 423 time to evaluate : 2.900 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 323 ASN cc_start: 0.8300 (p0) cc_final: 0.7945 (p0) REVERT: C 476 CYS cc_start: 0.3918 (OUTLIER) cc_final: 0.2062 (m) REVERT: C 674 SER cc_start: 0.8094 (m) cc_final: 0.7736 (p) REVERT: C 813 ASP cc_start: 0.6851 (m-30) cc_final: 0.6403 (m-30) REVERT: C 845 GLU cc_start: 0.6668 (tm-30) cc_final: 0.6312 (tm-30) REVERT: C 855 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6642 (mt) REVERT: C 870 ASN cc_start: 0.6961 (m-40) cc_final: 0.6696 (m110) REVERT: C 882 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.7007 (mp) REVERT: C 952 GLU cc_start: 0.7187 (tp30) cc_final: 0.6787 (tp30) REVERT: C 979 PHE cc_start: 0.4960 (OUTLIER) cc_final: 0.2098 (t80) REVERT: C 998 ASN cc_start: 0.7711 (m110) cc_final: 0.7414 (m-40) REVERT: C 1028 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7603 (mtmm) REVERT: C 1054 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7337 (mt) REVERT: C 1096 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8049 (mm) REVERT: C 1135 GLN cc_start: 0.7606 (tp40) cc_final: 0.6945 (mm-40) REVERT: B 187 LYS cc_start: 0.6552 (ptpp) cc_final: 0.5393 (ptpp) REVERT: B 206 ARG cc_start: 0.7508 (ttm-80) cc_final: 0.7142 (mtt90) REVERT: B 289 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6872 (mm-30) REVERT: B 656 ILE cc_start: 0.5804 (mm) cc_final: 0.5492 (mm) REVERT: B 838 ASN cc_start: 0.7792 (t0) cc_final: 0.7501 (t0) REVERT: B 850 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7415 (mt) REVERT: B 1093 LEU cc_start: 0.8380 (mt) cc_final: 0.7995 (mp) REVERT: B 1185 MET cc_start: 0.2087 (tmm) cc_final: 0.1691 (tmm) REVERT: A 28 TYR cc_start: 0.7596 (t80) cc_final: 0.7252 (t80) REVERT: A 140 GLN cc_start: 0.7212 (tm-30) cc_final: 0.6916 (tp-100) REVERT: A 201 HIS cc_start: 0.5663 (m-70) cc_final: 0.5427 (m-70) REVERT: A 289 GLU cc_start: 0.6429 (pp20) cc_final: 0.6208 (pp20) REVERT: A 427 TYR cc_start: 0.6223 (p90) cc_final: 0.5918 (p90) REVERT: A 822 TYR cc_start: 0.6303 (OUTLIER) cc_final: 0.5969 (m-80) REVERT: A 884 PHE cc_start: 0.5986 (OUTLIER) cc_final: 0.5663 (t80) REVERT: A 906 LEU cc_start: 0.8403 (mp) cc_final: 0.7747 (tt) REVERT: A 920 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7195 (mm-30) REVERT: A 952 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6308 (mp0) REVERT: A 958 TYR cc_start: 0.8085 (m-10) cc_final: 0.7798 (m-10) REVERT: A 967 MET cc_start: 0.5709 (mtm) cc_final: 0.5408 (mtm) REVERT: A 1012 LEU cc_start: 0.8114 (pt) cc_final: 0.7814 (pp) REVERT: A 1017 ASN cc_start: 0.7542 (m-40) cc_final: 0.7221 (m-40) REVERT: A 1030 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7563 (mm-40) REVERT: A 1036 ASN cc_start: 0.7591 (m110) cc_final: 0.7364 (m-40) REVERT: A 1059 GLN cc_start: 0.8091 (mm110) cc_final: 0.7675 (mm110) REVERT: A 1060 GLU cc_start: 0.7530 (tt0) cc_final: 0.7117 (tt0) REVERT: A 1065 LEU cc_start: 0.7292 (mp) cc_final: 0.7075 (tp) REVERT: A 1085 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8414 (tp) REVERT: A 1100 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7678 (tppt) REVERT: A 1135 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7085 (tm-30) outliers start: 112 outliers final: 78 residues processed: 502 average time/residue: 0.3571 time to fit residues: 290.8122 Evaluate side-chains 504 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 414 time to evaluate : 2.701 ------------------------------------------------------------------------------- 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 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 697 CYS 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 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 1054 ILE 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 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 283 SER 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 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 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 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 106 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 287 LEU 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 677 VAL Chi-restraints excluded: chain A residue 682 TYR 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 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 1045 GLN 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 1135 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 49 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 351 ASN C 371 ASN ** C 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN A 372 ASN A 826 HIS A 923 ASN ** A 954 GLN ** 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 = 0.4560 r_free = 0.4560 target = 0.201833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.163132 restraints weight = 57723.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.169251 restraints weight = 33403.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.170384 restraints weight = 18549.984| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 27329 Z= 0.310 Angle : 0.744 11.478 37389 Z= 0.395 Chirality : 0.049 0.278 4322 Planarity : 0.005 0.060 4821 Dihedral : 6.358 59.944 4133 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % Rotamer: Outliers : 4.10 % Allowed : 15.55 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.13), residues: 3506 helix: -0.67 (0.20), residues: 654 sheet: -1.76 (0.21), residues: 573 loop : -2.43 (0.12), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 344 HIS 0.011 0.002 HIS C 234 PHE 0.042 0.002 PHE B 764 TYR 0.038 0.002 TYR B 958 ARG 0.012 0.001 ARG B1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 16) link_NAG-ASN : angle 2.48121 ( 48) hydrogen bonds : bond 0.05129 ( 646) hydrogen bonds : angle 6.02461 ( 1794) SS BOND : bond 0.00488 ( 66) SS BOND : angle 1.41777 ( 132) covalent geometry : bond 0.00640 (27247) covalent geometry : angle 0.73594 (37209) *********************** 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 569 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 452 time to evaluate : 2.550 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: C 319 ARG cc_start: 0.7626 (mmt-90) cc_final: 0.7057 (mmt180) REVERT: C 323 ASN cc_start: 0.8372 (p0) cc_final: 0.8067 (p0) REVERT: C 476 CYS cc_start: 0.4092 (OUTLIER) cc_final: 0.2331 (m) REVERT: C 674 SER cc_start: 0.8255 (m) cc_final: 0.7949 (p) REVERT: C 693 ARG cc_start: 0.7670 (ptp-170) cc_final: 0.7430 (ptp-170) REVERT: C 838 ASN cc_start: 0.6847 (t0) cc_final: 0.6573 (t0) REVERT: C 845 GLU cc_start: 0.6679 (tm-30) cc_final: 0.6401 (tm-30) REVERT: C 855 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6643 (mt) REVERT: C 867 LEU cc_start: 0.3318 (OUTLIER) cc_final: 0.2930 (pp) REVERT: C 882 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7032 (mp) REVERT: C 979 PHE cc_start: 0.5244 (OUTLIER) cc_final: 0.2905 (t80) REVERT: C 998 ASN cc_start: 0.7763 (m110) cc_final: 0.7341 (m-40) REVERT: C 1054 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7670 (mp) REVERT: C 1135 GLN cc_start: 0.7664 (tp40) cc_final: 0.7055 (mm-40) REVERT: B 157 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6601 (mm-30) REVERT: B 187 LYS cc_start: 0.6948 (ptpp) cc_final: 0.5729 (ptpp) REVERT: B 289 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6921 (mm-30) REVERT: B 465 HIS cc_start: 0.7271 (p90) cc_final: 0.6893 (p90) REVERT: B 684 ASN cc_start: 0.7111 (t0) cc_final: 0.6896 (t0) REVERT: B 827 ASP cc_start: 0.7167 (m-30) cc_final: 0.6905 (m-30) REVERT: B 838 ASN cc_start: 0.7844 (t0) cc_final: 0.7621 (t0) REVERT: B 850 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7453 (mt) REVERT: B 1173 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6773 (pttm) REVERT: A 201 HIS cc_start: 0.5707 (m-70) cc_final: 0.5499 (m-70) REVERT: A 289 GLU cc_start: 0.6700 (pp20) cc_final: 0.6443 (pp20) REVERT: A 427 TYR cc_start: 0.6294 (p90) cc_final: 0.5987 (p90) REVERT: A 613 GLU cc_start: 0.7497 (tp30) cc_final: 0.7208 (tp30) REVERT: A 625 TYR cc_start: 0.6644 (m-80) cc_final: 0.6040 (m-80) REVERT: A 662 LEU cc_start: 0.8296 (mt) cc_final: 0.7852 (pt) REVERT: A 884 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.5900 (t80) REVERT: A 904 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6301 (mt-10) REVERT: A 906 LEU cc_start: 0.8427 (mp) cc_final: 0.7742 (tt) REVERT: A 912 LYS cc_start: 0.7800 (ttpp) cc_final: 0.7594 (ttpp) REVERT: A 920 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7214 (mm-30) REVERT: A 952 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: A 967 MET cc_start: 0.5861 (mtm) cc_final: 0.5519 (mtm) REVERT: A 1012 LEU cc_start: 0.8136 (pt) cc_final: 0.7894 (pp) REVERT: A 1017 ASN cc_start: 0.7523 (m-40) cc_final: 0.7246 (m-40) REVERT: A 1059 GLN cc_start: 0.8270 (mm110) cc_final: 0.7969 (mm110) REVERT: A 1060 GLU cc_start: 0.7632 (tt0) cc_final: 0.7245 (tt0) REVERT: A 1065 LEU cc_start: 0.7531 (mp) cc_final: 0.7323 (tp) REVERT: A 1100 LYS cc_start: 0.8132 (mmmt) cc_final: 0.7647 (tppt) REVERT: A 1105 ARG cc_start: 0.6976 (tpm-80) cc_final: 0.6695 (tpm-80) REVERT: A 1135 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: A 1193 TYR cc_start: 0.5929 (m-80) cc_final: 0.5728 (m-80) outliers start: 117 outliers final: 87 residues processed: 529 average time/residue: 0.3624 time to fit residues: 309.2303 Evaluate side-chains 529 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 431 time to evaluate : 2.810 ------------------------------------------------------------------------------- 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 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 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 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 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 935 LEU Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 946 LEU 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 1057 SER Chi-restraints excluded: chain C residue 1074 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 221 THR Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 300 ASN 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 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 790 ILE 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 1061 ILE Chi-restraints excluded: chain B residue 1096 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 1173 LYS 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 142 HIS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 287 LEU 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 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 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 1128 ASN Chi-restraints excluded: chain A residue 1135 GLN 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 251 optimal weight: 10.0000 chunk 305 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 311 optimal weight: 0.7980 chunk 222 optimal weight: 0.5980 chunk 313 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 694 ASN ** C 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.204277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.166206 restraints weight = 57975.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.171439 restraints weight = 32448.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.173632 restraints weight = 19337.654| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27329 Z= 0.131 Angle : 0.618 12.362 37389 Z= 0.317 Chirality : 0.045 0.238 4322 Planarity : 0.005 0.060 4821 Dihedral : 5.738 59.523 4130 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.19 % Allowed : 16.99 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.14), residues: 3506 helix: -0.19 (0.20), residues: 668 sheet: -1.65 (0.22), residues: 572 loop : -2.30 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 344 HIS 0.005 0.001 HIS A 201 PHE 0.025 0.001 PHE A 817 TYR 0.028 0.001 TYR C1148 ARG 0.006 0.000 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 16) link_NAG-ASN : angle 1.93219 ( 48) hydrogen bonds : bond 0.03688 ( 646) hydrogen bonds : angle 5.44793 ( 1794) SS BOND : bond 0.00311 ( 66) SS BOND : angle 0.94330 ( 132) covalent geometry : bond 0.00284 (27247) covalent geometry : angle 0.61305 (37209) *********************** 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 526 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 435 time to evaluate : 2.560 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: 0.8302 (p0) cc_final: 0.7944 (p0) REVERT: C 476 CYS cc_start: 0.3967 (OUTLIER) cc_final: 0.2232 (m) REVERT: C 674 SER cc_start: 0.8062 (m) cc_final: 0.7764 (p) REVERT: C 693 ARG cc_start: 0.7421 (ptp-170) cc_final: 0.7052 (ptp-170) REVERT: C 721 LEU cc_start: 0.8020 (mp) cc_final: 0.7801 (mt) REVERT: C 838 ASN cc_start: 0.6783 (t0) cc_final: 0.6525 (t0) REVERT: C 845 GLU cc_start: 0.6608 (tm-30) cc_final: 0.6339 (tm-30) REVERT: C 855 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6650 (mt) REVERT: C 867 LEU cc_start: 0.3257 (OUTLIER) cc_final: 0.2911 (pp) REVERT: C 979 PHE cc_start: 0.5036 (OUTLIER) cc_final: 0.2212 (t80) REVERT: C 1050 LYS cc_start: 0.7989 (mmmm) cc_final: 0.7718 (mmmm) REVERT: C 1054 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7618 (mt) REVERT: C 1075 ASP cc_start: 0.7240 (t0) cc_final: 0.6970 (t0) REVERT: C 1135 GLN cc_start: 0.7517 (tp40) cc_final: 0.6962 (mm-40) REVERT: C 1191 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.5871 (m-10) REVERT: B 187 LYS cc_start: 0.6677 (ptpp) cc_final: 0.5484 (ptpp) REVERT: B 289 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6857 (mm-30) REVERT: B 465 HIS cc_start: 0.7290 (p90) cc_final: 0.6934 (p90) REVERT: B 684 ASN cc_start: 0.6951 (t0) cc_final: 0.6732 (t0) REVERT: B 827 ASP cc_start: 0.7037 (m-30) cc_final: 0.6749 (m-30) REVERT: B 850 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7420 (mt) REVERT: B 1093 LEU cc_start: 0.8355 (mt) cc_final: 0.7979 (mp) REVERT: A 28 TYR cc_start: 0.7693 (t80) cc_final: 0.7371 (t80) REVERT: A 107 LYS cc_start: 0.7153 (tptt) cc_final: 0.6753 (tptt) REVERT: A 140 GLN cc_start: 0.7335 (tm-30) cc_final: 0.7093 (tp-100) REVERT: A 201 HIS cc_start: 0.5665 (m-70) cc_final: 0.5416 (m-70) REVERT: A 289 GLU cc_start: 0.6510 (pp20) cc_final: 0.6241 (pp20) REVERT: A 427 TYR cc_start: 0.6221 (p90) cc_final: 0.5835 (p90) REVERT: A 613 GLU cc_start: 0.7451 (tp30) cc_final: 0.7186 (tp30) REVERT: A 662 LEU cc_start: 0.8220 (mt) cc_final: 0.7859 (pt) REVERT: A 673 TYR cc_start: 0.6942 (t80) cc_final: 0.6638 (t80) REVERT: A 884 PHE cc_start: 0.6040 (OUTLIER) cc_final: 0.5757 (t80) REVERT: A 904 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6170 (mt-10) REVERT: A 906 LEU cc_start: 0.8381 (mp) cc_final: 0.7704 (tt) REVERT: A 920 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7189 (mm-30) REVERT: A 952 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: A 967 MET cc_start: 0.5863 (mtm) cc_final: 0.5562 (mtm) REVERT: A 1012 LEU cc_start: 0.8031 (pt) cc_final: 0.7699 (pp) REVERT: A 1017 ASN cc_start: 0.7467 (m-40) cc_final: 0.7158 (m-40) REVERT: A 1060 GLU cc_start: 0.7538 (tt0) cc_final: 0.7022 (tt0) REVERT: A 1065 LEU cc_start: 0.7441 (mp) cc_final: 0.7218 (tp) REVERT: A 1105 ARG cc_start: 0.6945 (tpm-80) cc_final: 0.6643 (tpm-80) REVERT: A 1135 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: A 1193 TYR cc_start: 0.5940 (m-80) cc_final: 0.5720 (m-80) REVERT: A 1212 PHE cc_start: 0.3473 (OUTLIER) cc_final: 0.2854 (t80) outliers start: 91 outliers final: 70 residues processed: 498 average time/residue: 0.3705 time to fit residues: 296.7843 Evaluate side-chains 506 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 425 time to evaluate : 2.785 ------------------------------------------------------------------------------- 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 216 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 287 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 663 THR Chi-restraints excluded: chain C residue 720 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 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 1057 SER Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1191 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 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 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 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 A residue 20 CYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 LEU 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 379 PHE 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 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 1057 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1135 GLN Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1212 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 275 optimal weight: 9.9990 chunk 139 optimal weight: 0.3980 chunk 279 optimal weight: 5.9990 chunk 116 optimal weight: 0.2980 chunk 285 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 11 optimal weight: 0.2980 chunk 212 optimal weight: 2.9990 chunk 286 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 167 optimal weight: 20.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS B 938 GLN A 923 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.206064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.168559 restraints weight = 58022.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.174034 restraints weight = 32611.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.175742 restraints weight = 19502.868| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27329 Z= 0.116 Angle : 0.615 13.252 37389 Z= 0.312 Chirality : 0.046 0.694 4322 Planarity : 0.004 0.063 4821 Dihedral : 5.536 58.856 4126 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.01 % Allowed : 17.41 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.14), residues: 3506 helix: 0.06 (0.21), residues: 659 sheet: -1.65 (0.22), residues: 546 loop : -2.17 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 332 HIS 0.004 0.001 HIS A 201 PHE 0.025 0.001 PHE B 681 TYR 0.030 0.001 TYR C1148 ARG 0.007 0.000 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 16) link_NAG-ASN : angle 2.54362 ( 48) hydrogen bonds : bond 0.03423 ( 646) hydrogen bonds : angle 5.24589 ( 1794) SS BOND : bond 0.00284 ( 66) SS BOND : angle 1.17409 ( 132) covalent geometry : bond 0.00255 (27247) covalent geometry : angle 0.60606 (37209) *********************** 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 511 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 425 time to evaluate : 2.896 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: C 319 ARG cc_start: 0.7490 (mmt-90) cc_final: 0.6952 (mpt180) REVERT: C 323 ASN cc_start: 0.8239 (p0) cc_final: 0.7879 (p0) REVERT: C 476 CYS cc_start: 0.3896 (OUTLIER) cc_final: 0.2130 (m) REVERT: C 674 SER cc_start: 0.8055 (m) cc_final: 0.7771 (p) REVERT: C 693 ARG cc_start: 0.7448 (ptp-170) cc_final: 0.7183 (ptp-170) REVERT: C 720 VAL cc_start: 0.7102 (OUTLIER) cc_final: 0.6528 (t) REVERT: C 813 ASP cc_start: 0.6869 (m-30) cc_final: 0.6451 (m-30) REVERT: C 845 GLU cc_start: 0.6556 (tm-30) cc_final: 0.6303 (tm-30) REVERT: C 862 MET cc_start: 0.6760 (mmm) cc_final: 0.6479 (mmm) REVERT: C 867 LEU cc_start: 0.3240 (OUTLIER) cc_final: 0.2909 (pp) REVERT: C 979 PHE cc_start: 0.4985 (OUTLIER) cc_final: 0.2232 (t80) REVERT: C 1054 ILE cc_start: 0.8132 (pt) cc_final: 0.7194 (mm) REVERT: C 1096 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7960 (mm) REVERT: C 1135 GLN cc_start: 0.7509 (tp40) cc_final: 0.6924 (mm-40) REVERT: C 1191 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.5907 (m-10) REVERT: B 187 LYS cc_start: 0.6687 (ptpp) cc_final: 0.5558 (ptpp) REVERT: B 289 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6860 (mm-30) REVERT: B 465 HIS cc_start: 0.7228 (p90) cc_final: 0.6869 (p90) REVERT: B 827 ASP cc_start: 0.6997 (m-30) cc_final: 0.6741 (m-30) REVERT: B 850 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7474 (mt) REVERT: B 1075 ASP cc_start: 0.7316 (t0) cc_final: 0.6914 (t0) REVERT: B 1093 LEU cc_start: 0.8368 (mt) cc_final: 0.8001 (mp) REVERT: A 28 TYR cc_start: 0.7596 (t80) cc_final: 0.7276 (t80) REVERT: A 201 HIS cc_start: 0.5675 (m-70) cc_final: 0.5433 (m-70) REVERT: A 289 GLU cc_start: 0.6505 (pp20) cc_final: 0.6139 (pp20) REVERT: A 427 TYR cc_start: 0.6240 (p90) cc_final: 0.5876 (p90) REVERT: A 613 GLU cc_start: 0.7404 (tp30) cc_final: 0.7148 (tp30) REVERT: A 662 LEU cc_start: 0.8211 (mt) cc_final: 0.7849 (pt) REVERT: A 673 TYR cc_start: 0.6939 (t80) cc_final: 0.6664 (t80) REVERT: A 884 PHE cc_start: 0.5883 (OUTLIER) cc_final: 0.5600 (t80) REVERT: A 885 LYS cc_start: 0.7690 (mmtm) cc_final: 0.7272 (mmtm) REVERT: A 904 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6481 (mt-10) REVERT: A 906 LEU cc_start: 0.8336 (mp) cc_final: 0.7697 (tt) REVERT: A 920 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7135 (mm-30) REVERT: A 952 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: A 967 MET cc_start: 0.5797 (mtm) cc_final: 0.5551 (mtm) REVERT: A 1012 LEU cc_start: 0.8014 (pt) cc_final: 0.7680 (pp) REVERT: A 1017 ASN cc_start: 0.7436 (m-40) cc_final: 0.7114 (m-40) REVERT: A 1065 LEU cc_start: 0.7405 (mp) cc_final: 0.7177 (tp) REVERT: A 1105 ARG cc_start: 0.6950 (tpm-80) cc_final: 0.6665 (tpm-80) REVERT: A 1193 TYR cc_start: 0.5914 (m-80) cc_final: 0.5678 (m-80) REVERT: A 1212 PHE cc_start: 0.3383 (OUTLIER) cc_final: 0.2831 (t80) outliers start: 86 outliers final: 70 residues processed: 483 average time/residue: 0.3644 time to fit residues: 282.7868 Evaluate side-chains 497 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 417 time to evaluate : 2.466 ------------------------------------------------------------------------------- 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 216 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 287 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 663 THR Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 738 MET 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 1074 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1191 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 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 697 CYS Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 793 ASN 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 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 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 287 LEU 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 403 LEU Chi-restraints excluded: chain A residue 461 VAL 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 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 1057 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 43 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 272 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 190 optimal weight: 0.4980 chunk 324 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** A 923 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.205528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.166781 restraints weight = 57413.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.172462 restraints weight = 31824.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.174604 restraints weight = 18434.214| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27329 Z= 0.155 Angle : 0.633 12.901 37389 Z= 0.325 Chirality : 0.046 0.788 4322 Planarity : 0.005 0.071 4821 Dihedral : 5.620 56.613 4126 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.87 % Allowed : 17.51 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.14), residues: 3506 helix: 0.02 (0.21), residues: 649 sheet: -1.60 (0.21), residues: 597 loop : -2.20 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 332 HIS 0.005 0.001 HIS A 142 PHE 0.021 0.001 PHE B 681 TYR 0.026 0.001 TYR B 958 ARG 0.009 0.001 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 16) link_NAG-ASN : angle 2.63922 ( 48) hydrogen bonds : bond 0.03719 ( 646) hydrogen bonds : angle 5.31283 ( 1794) SS BOND : bond 0.00327 ( 66) SS BOND : angle 1.18760 ( 132) covalent geometry : bond 0.00334 (27247) covalent geometry : angle 0.62326 (37209) ********************** 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 503 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 421 time to evaluate : 2.621 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 319 ARG cc_start: 0.7525 (mmt-90) cc_final: 0.6919 (mmt180) REVERT: C 323 ASN cc_start: 0.8230 (p0) cc_final: 0.7893 (p0) REVERT: C 476 CYS cc_start: 0.3965 (OUTLIER) cc_final: 0.2338 (m) REVERT: C 674 SER cc_start: 0.8117 (m) cc_final: 0.7820 (p) REVERT: C 693 ARG cc_start: 0.7538 (ptp-170) cc_final: 0.7284 (ptp-110) REVERT: C 721 LEU cc_start: 0.7958 (mp) cc_final: 0.7742 (mt) REVERT: C 813 ASP cc_start: 0.6948 (m-30) cc_final: 0.6460 (m-30) REVERT: C 845 GLU cc_start: 0.6636 (tm-30) cc_final: 0.6376 (tm-30) REVERT: C 867 LEU cc_start: 0.3179 (OUTLIER) cc_final: 0.2803 (pp) REVERT: C 979 PHE cc_start: 0.5082 (OUTLIER) cc_final: 0.2988 (t80) REVERT: C 995 ASP cc_start: 0.5841 (t0) cc_final: 0.4630 (t0) REVERT: C 998 ASN cc_start: 0.7814 (m110) cc_final: 0.7598 (p0) REVERT: C 1050 LYS cc_start: 0.8086 (mmtp) cc_final: 0.7858 (mmmm) REVERT: C 1075 ASP cc_start: 0.7157 (t0) cc_final: 0.6955 (t0) REVERT: C 1076 ARG cc_start: 0.7762 (mtm110) cc_final: 0.7468 (mtp-110) REVERT: C 1096 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7913 (mm) REVERT: C 1135 GLN cc_start: 0.7541 (tp40) cc_final: 0.6957 (mm-40) REVERT: C 1191 TYR cc_start: 0.6198 (OUTLIER) cc_final: 0.5986 (m-10) REVERT: B 187 LYS cc_start: 0.6684 (ptpp) cc_final: 0.5610 (ptpp) REVERT: B 289 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6896 (mm-30) REVERT: B 465 HIS cc_start: 0.7186 (p90) cc_final: 0.6836 (p90) REVERT: B 827 ASP cc_start: 0.7046 (m-30) cc_final: 0.6797 (m-30) REVERT: B 850 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7459 (mt) REVERT: B 1075 ASP cc_start: 0.7326 (t0) cc_final: 0.6923 (t0) REVERT: B 1093 LEU cc_start: 0.8425 (mt) cc_final: 0.8071 (mp) REVERT: A 28 TYR cc_start: 0.7667 (t80) cc_final: 0.7349 (t80) REVERT: A 201 HIS cc_start: 0.5694 (m-70) cc_final: 0.5456 (m-70) REVERT: A 289 GLU cc_start: 0.6559 (pp20) cc_final: 0.6289 (pp20) REVERT: A 427 TYR cc_start: 0.6188 (p90) cc_final: 0.5818 (p90) REVERT: A 613 GLU cc_start: 0.7473 (tp30) cc_final: 0.7212 (tp30) REVERT: A 625 TYR cc_start: 0.6545 (m-80) cc_final: 0.6115 (m-80) REVERT: A 662 LEU cc_start: 0.8240 (mt) cc_final: 0.7871 (pt) REVERT: A 884 PHE cc_start: 0.5994 (OUTLIER) cc_final: 0.5695 (t80) REVERT: A 885 LYS cc_start: 0.7738 (mmtm) cc_final: 0.7145 (mmtm) REVERT: A 904 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6545 (mt-10) REVERT: A 906 LEU cc_start: 0.8383 (mp) cc_final: 0.7744 (tt) REVERT: A 920 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7264 (mm-30) REVERT: A 952 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: A 967 MET cc_start: 0.5808 (mtm) cc_final: 0.5586 (mtm) REVERT: A 1012 LEU cc_start: 0.8049 (pt) cc_final: 0.7720 (pp) REVERT: A 1017 ASN cc_start: 0.7451 (m-40) cc_final: 0.7102 (m-40) REVERT: A 1060 GLU cc_start: 0.7733 (tt0) cc_final: 0.7524 (tp30) REVERT: A 1105 ARG cc_start: 0.7018 (tpm-80) cc_final: 0.6726 (tpm-80) REVERT: A 1193 TYR cc_start: 0.6085 (m-80) cc_final: 0.5652 (m-80) REVERT: A 1212 PHE cc_start: 0.3452 (OUTLIER) cc_final: 0.3013 (t80) outliers start: 82 outliers final: 69 residues processed: 477 average time/residue: 0.3596 time to fit residues: 276.0281 Evaluate side-chains 493 residues out of total 3169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 415 time to evaluate : 2.582 ------------------------------------------------------------------------------- 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 216 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 287 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 621 ASN 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 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 1074 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1191 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 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 651 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 793 ASN 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 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 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 287 LEU 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 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 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 1100 LYS Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 285 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 287 optimal weight: 0.4980 chunk 178 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 310 optimal weight: 0.2980 chunk 15 optimal weight: 40.0000 chunk 129 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 351 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 923 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.205979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.167744 restraints weight = 57434.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.172531 restraints weight = 33508.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.175660 restraints weight = 19857.354| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27329 Z= 0.136 Angle : 0.621 13.368 37389 Z= 0.318 Chirality : 0.046 0.729 4322 Planarity : 0.005 0.067 4821 Dihedral : 5.554 57.845 4126 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.84 % Allowed : 17.55 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.14), residues: 3506 helix: 0.07 (0.21), residues: 656 sheet: -1.56 (0.22), residues: 570 loop : -2.20 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 332 HIS 0.004 0.001 HIS A 201 PHE 0.021 0.001 PHE B 681 TYR 0.027 0.001 TYR A 673 ARG 0.007 0.001 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 16) link_NAG-ASN : angle 2.34568 ( 48) hydrogen bonds : bond 0.03547 ( 646) hydrogen bonds : angle 5.23263 ( 1794) SS BOND : bond 0.00311 ( 66) SS BOND : angle 1.08516 ( 132) covalent geometry : bond 0.00296 (27247) covalent geometry : angle 0.61332 (37209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12268.11 seconds wall clock time: 219 minutes 34.21 seconds (13174.21 seconds total)